2 @string{AcP = "Academic Press"}
3 @string{CoRR = "arXiv Computing Research Repository"}.
4 @string{ACM = "Association for Computing Machinery"}
5 @string{KAstrom = "{\AA}str{\"o}m, K.~J."}
6 @string{ACM:SIGCSE = "ACM Special Interest Group on Computer Science Education Bulletin"}
7 @string{ACM:CSur = "ACM Computing Surveys"}
8 @string{ACS:ChemBiol = "ACS Chem Biol"}
10 @string{APL = "Applied Physics Letters"}
11 @string{DAbramavicius = "Abramavicius, Darius"}
12 @string{JFAbril = "Abril, J. F."}
13 @string{JAbu-Threideh = "Abu-Threideh, J."}
14 @string{KAdachi = "Adachi, Kengo"}
15 @string{MDAdams = "Adams, M. D."}
16 @string{AW = "Addison-Wesley Longman Publishing Co., Inc."}
17 @string{AdvExpMedBiol = "Advances in Experimental Medicine and Biology"}
18 @string{SAinavarapu = "Ainavarapu, Sri Rama Koti"}
19 @string{DAioanei = "Aioanei, Daniel"}
20 @string{TRAlbrecht = "Albreacht, T.~R."}
21 @string{AMB = "Algorithms for molecular biology: AMB"}
22 @string{FAli = "Ali, F."}
23 @string{JFAllemand = "Allemand, Jean-Fran\c{c}ois"}
24 @string{DAllen = "Allen, D."}
25 @string{MAllen = "Allen, Mark D."}
26 @string{RAlon = "Alon, Ronen"}
27 @string{PAmanatides = "Amanatides, P."}
28 @string{NMAmer = "Amer, Nabil M."}
29 @string{AJP = "American Journal of Physics"}
30 @string{APS = "American Physical Society"}
31 @string{AS = "American Scientist"}
32 @string{ASA = "American Statistical Association"}
33 @string{HAn = "An, H."}
34 @string{KNAn = "An, Kai-Nan"}
35 @string{ABioChem = "Analytical biochemistry"}
36 @string{BAndreopoulos = "Andreopoulos, Bill"}
37 @string{IAndricioaei = "Andricioaei, Ioan"}
38 @string{ACIEE = "Angew. Chem. Int. Ed. Engl."}
39 @string{ARBBS = "Annu Rev Biophys Biomol Struct"}
40 @string{ARBC = "Annual Review of Biochemistry"}
41 @string{DAnselmetti = "Anselmetti, Dario"}
42 @string{AAntoniadis = "Antoniadis, Anestis"}
43 @string{AMC = "Applied Mathematics and Computation"}
44 @string{SArcidiacono = "Arcidiacono, S"}
45 @string{CArciola = "Arciola, Carla Renata"}
46 @string{ABArtyukhin = "Artyukhin, Alexander B."}
47 @string{DAruliah = "Aruliah, Dhavide A."}
48 @string{SAsakawa = "Asakawa, S."}
49 @string{AAwe = "Awe, A."}
50 @string{SBedard = "B\'edard, Sabrina"}
51 @string{WBaase = "Baase, Walter A."}
52 @string{YBaba = "Baba, Y."}
53 @string{HBaden = "Baden, H."}
54 @string{CBadilla = "Badilla, Carmen L."}
55 @string{VBafna = "Bafna, V."}
56 @string{BBagchi = "Bagchi, B."}
57 @string{MBalamurali = "Balamurali, M. M."}
58 @string{DBaldwin = "Baldwin, D."}
59 @string{ABaljon = "Baljon, Arlette R. C."}
60 @string{RBallerini = "Ballerini, R."}
61 @string{RMBallew = "Ballew, R. M."}
62 @string{MBalsera = "Balsera, M."}
63 @string{GBaneyx = "Baneyx, Gretchen"}
64 @string{RBar-Ziv = "Bar-Ziv, Roy"}
65 @string{WBBarbazuk = "Barbazuk, W. B."}
66 @string{MBarnstead = "Barnstead, M."}
67 @string{DBarrick = "Barrick, Doug"}
68 @string{IBarrow = "Barrow, I."}
69 @string{FWBartels = "Bartels, Frank Wilco"}
70 @string{BBarz = "Barz, Bogdan"}
71 @string{TBasche = "Basche, Th."}
72 @string{PBaschieri = "Baschieri, Paolo"}
73 @string{ABasu = "Basu, A."}
74 @string{LBaugh = "Baugh, Loren"}
75 @string{BBaumgarth = "Baumgarth, Birgit"}
76 @string{SBaumhueter = "Baumhueter, S."}
77 @string{JBaxendale = "Baxendale, J."}
78 @string{EABayer = "Bayer, Edward A."}
79 @string{EBeasley = "Beasley, E."}
80 @string{JBechhoefer = "Bechhoefer, John"}
81 @string{BBechinger = "Bechinger, Burkhard"}
82 @string{ABecker = "Becker, Anke"}
83 @string{GSBeddard = "Beddard, Godfrey S."}
84 @string{TBeebe = "Beebe, Thomas P."}
85 @string{KBeeson = "Beeson, K."}
86 @string{GIBell = "Bell, G. I."}
87 @string{FBenedetti = "Benedetti, Fabrizio"}
88 @string{VBenes = "Benes, Vladimir"}
89 @string{ABensimon = "Bensimon, A."}
90 @string{DBensimon = "Bensimon, David"}
91 @string{DRBentley = "Bentley, D. R."}
92 @string{HJCBerendsen = "Berendsen, Herman J. C."}
93 @string{KBergSorensen = "Berg-S{\o}rensen, Kirstine"}
94 @string{EBergantino = "Bergantino, Elisabetta"}
95 @string{DBerk = "Berk, D."}
96 @string{FBerkemeier = "Berkemeier, Felix"}
97 @string{BBerne = "Berne, Bruce J."}
98 @string{MBertz = "Bertz, Morten"}
99 @string{RBest = "Best, Robert B."}
100 @string{GBethel = "Bethel, G."}
101 @string{NBhasin = "Bhasin, Nishant"}
102 @string{KBiddick = "Biddick, K."}
103 @string{KBillings = "Billings, Kate S."}
104 @string{GBinnig = "Binnig, Gerd"}
105 @string{BCBPRC = "Biochemical and Biophysical Research Communications"}
106 @string{Biochem = "Biochemistry"}
107 @string{BBABE = "Biochimica et Biophysica Acta (BBA) - Bioenergetics"}
108 @string{BIOINFO = "Bioinformatics (Oxford, England)"}
109 @string{Biomet = "Biometrika"}
110 @string{BPJ = "Biophysical Journal"}
111 %string{BPJ = "Biophys. J."}
112 @string{BIOSENSE = "Biosensors and Bioelectronics"}
113 @string{BIOTECH = "Biotechnology and Bioengineering"}
114 @string{JBirchler = "Birchler, James A."}
115 @string{AWBlake = "Blake, Anthony W."}
116 @string{JBlawzdziewicz = "Blawzdziewicz, Jerzy"}
117 @string{LBlick = "Blick, L."}
118 @string{RBolanos = "Bolanos, R."}
119 @string{VBonazzi = "Bonazzi, V."}
120 @string{Borgia = "Borgia"}
121 @string{MBorkovec = "Borkovec, Michal"}
122 @string{RBrandon = "Brandon, R."}
123 @string{EBranscomb = "Branscomb, E."}
124 @string{EBraverman = "Braverman, Elena"}
125 @string{WBreyer = "Breyer, Wendy A."}
126 @string{FBrochard-Wyart = "Brochard-Wyart, F."}
127 @string{DJBrockwell = "Brockwell, David J."}
128 @string{SBroder = "Broder, S."}
129 @string{SBroedel = "Broedel, Sheldon E."}
130 @string{ABrolo = "Brolo, Alexandre G."}
131 @string{FBrooks = "Brooks, Jr., Frederick P."}
132 @string{BrooksCole = "Brooks/Cole"}
133 @string{BDBrowerToland = "Brower-Toland, Brent D."}
134 @string{CTBrown = "Brown, C. Titus"}
135 @string{MBrucale = "Brucale, Marco"}
136 @string{TBruls = "Bruls, T."}
137 @string{VBrumfeld = "Brumfeld, Vlad"}
138 @string{JDBryngelson = "Bryngelson, J. D."}
139 @string{LBubacco = "Bubacco, Luigi"}
140 @string{JBuckheit = "Buckheit, Jonathan B."}
141 @string{ABuguin = "Buguin, A."}
142 @string{ABulhassan = "Bulhassan, Ahmed"}
143 @string{BBullard = "Bullard, Belinda"}
144 @string{RBunk = "Bunk, Richard"}
145 @string{NABurnham = "Burnham, N.~A."}
146 @string{DBusam = "Busam, D."}
147 @string{GBussi = "Bussi, Giovanni"}
148 @string{CBustamante = "Bustamante, Carlos"}
149 @string{YBustanji = "Bustanji, Yasser"}
150 @string{HJButt = {Butt, Hans-J\"urgen}}
151 @string{CUP = "Cambridge University Press"}
152 @string{MCaminha = "Caminha, M."}
153 @string{ICampbell = "Campbell, Iain D."}
154 @string{MJCampbell = "Campbell, M. J."}
155 @string{DSCannell = "Cannell, D.~S."}
156 @string{YCao = "Cao, Yi"}
157 @string{MCapitanio = "Capitanio, M."}
158 @string{MCargill = "Cargill, M."}
159 @string{PCarl = "Carl, Philippe"}
160 @string{BACarnes = "Carnes, B. A."}
161 @string{JCarnes-Stine = "Carnes-Stine, J."}
162 @string{MCarrionVazquez = "Carrion-Vazquez, Mariano"}
163 @string{CCarter = "Carter, C."}
164 @string{ACarver = "Carver, A."}
165 @string{JJCatanese = "Catanese, J.~J."}
166 @string{PCaulk = "Caulk, P."}
167 @string{CCecconi = "Cecconi, Ciro"}
168 @string{ACenter = "Center, A."}
169 @string{CTChan = "Chan, C.~T."}
170 @string{HSChan = "Chan, H.~S."}
171 @string{AChand = "Chand, Ami"}
172 @string{IChandramouliswaran = "Chandramouliswaran, I."}
173 @string{CHChang = "Chang, Chung-Hung"}
174 @string{EChapman = "Chapman, Edwin R."}
175 @string{RCharlab = "Charlab, R."}
176 @string{KChaturvedi = "Chaturvedi, K."}
177 @string{AChauhan = "Chauhan, A."}
178 @string{VPChauhan = "Chauhan, V.~P."}
179 @string{CChauzy = "Chauzy, C."}
180 @string{SChe = "Che, Shunai"}
181 @string{CEC = "Chemical Engineering Communications"}
182 @string{CHEMREV = "Chemical reviews"}
183 @string{CHEM = "Chemistry (Weinheim an der Bergstrasse, Germany)"}
184 @string{CPC = "Chemphyschem"}
185 @string{HCChen = "Chen, H. C."}
186 @string{LChen = "Chen, L."}
187 @string{XNChen = "Chen, X. N."}
188 @string{XiChen = "Chen, Xinyong"}
189 @string{XuChen = "Chen, Xuming"}
190 @string{JFCheng = "Cheng, J. F."}
191 @string{MLCheng = "Cheng, M. L."}
192 @string{VGCheung = "Cheung, V. G."}
193 @string{YHChiang = "Chiang, Y. H."}
194 @string{AChinwalla = "Chinwalla, A."}
195 @string{FChow = "Chow, Flora"}
196 @string{JChoy = "Choy, Jason"}
197 @string{BChu = "Chu, Benjamin"}
198 @string{XChu = "Chu, Xueying"}
199 @string{TYChung = "Chung, Tse-Yu"}
200 @string{CLChyan = "Chyan, Chia-Lin"}
201 @string{GCiccotti = "Ciccotti, Giovanni"}
202 @string{JClaerbout = "Claerbout, Jon F."}
203 @string{AGClark = "Clark, A. G."}
204 @string{Clarke = "Clarke"}
205 @string{JClarke = "Clarke, Jane"}
206 @string{JClarkson = "Clarkson, John"}
207 @string{HClausen-Schaumann = "Clausen-Schaumann, H."}
208 @string{JMClaverie = "Claverie, J. M."}
209 @string{WWCleland = "Cleland, W.~W."}
210 @string{KClerc-Blankenburg = "Clerc-Blankenburg, K."}
211 @string{NJCobb = "Cobb, Nathan J."}
212 @string{GHCohen = "Cohen, G.~H."}
213 @string{FSCollins = "Collins, Francis S."}
214 @string{CUP = "Columbia University Press"}
215 @string{CPR = "Computer Physics Reports"}
216 @string{CSE = "Computing in Science \& Engineering"}
217 @string{UniProtConsort = "Consortium, The UniProt"}
218 @string{MConti = "Conti, Matteo"}
219 @string{CEP = "Control Engineering Practice"}
220 @string{GACoon = "Coon, G.~A."}
221 @string{PVCornish = "Cornish, Peter V."}
222 @string{MNCourel = "Courel, M. N."}
223 @string{GCowan = "Cowan, Glen"}
224 @string{DRCox = "Cox, D. R."}
225 @string{MCoyne = "Coyne, M."}
226 @string{DCraig = "Craig, David"}
227 @string{ACravchik = "Cravchik, A."}
228 @string{PSCremer = "Cremer, Paul S."}
229 @string{CCroarkin = "Croarkin, Carroll"}
230 @string{VCroquette = "Croquette, Vincent"}
231 @string{LCCruz = "Cruz, Luis Cruz"}
232 @string{YCui = "Cui, Y."}
233 @string{COSB = "Current Opinion in Structural Biology"}
234 @string{COCB = "Current Opinion in Chemical Biology"}
235 @string{LCurry = "Curry, L."}
236 @string{CDahlke = "Dahlke, C."}
237 @string{FDahlquist = "Dahlquist, Frederick W."}
238 @string{PDalhaimer = "Dalhaimer, Paul"}
239 @string{SDanaher = "Danaher, S."}
240 @string{LDavenport = "Davenport, L."}
241 @string{MCDavies = "Davies, M.~C."}
242 @string{MDavis = "Davis, Matt"}
243 @string{SDecatur = "Decatur, Sean M."}
244 @string{WDeGrado = "DeGrado, William F."}
245 @string{PDebrunner = "Debrunner, P."}
246 @string{ADelcher = "Delcher, A."}
247 @string{WDeLorbe = "DeLorbe, William J."}
248 @string{BDelpech = "Delpech, B."}
249 @string{Demography = "Demography"}
250 @string{ZDeng = "Deng, Z."}
251 @string{RDesilets = "Desilets, R."}
252 @string{IDew = "Dew, I."}
253 @string{CDewhurst = "Dewhurst, Charles"}
254 @string{VDiFrancesco = "Di Francesco, V."}
255 @string{KDiemer = "Diemer, K."}
256 @string{GDietler = "Dietler, Giovanni"}
257 @string{HDietz = "Dietz, Hendrik"}
258 @string{SDietz = "Dietz, S."}
259 @string{EDijkstra = "Dijkstra, Edsger Wybe"}
260 @string{KADill = "Dill, K. A."}
261 @string{RDima = "Dima, Ruxandra I."}
262 @string{DDischer = "Discher, Dennis E."}
263 @string{KDixon = "Dixon, K."}
264 @string{KDodson = "Dodson, K."}
265 @string{NDoggett = "Doggett, N."}
266 @string{MDombroski = "Dombroski, M."}
267 @string{MDonnelly = "Donnelly, M."}
268 @string{DDonoho = "Donoho, David L."}
269 @string{CDornmair = "Dornmair, C."}
270 @string{MDors = "Dors, M."}
271 @string{LDougan = "Dougan, Lorna"}
272 @string{LDoup = "Doup, L."}
273 @string{BDrake = "Drake, B."}
274 @string{TDrobek = "Drobek, T."}
275 @string{Drexel = "Drexel University"}
276 @string{OKDudko = "Dudko, Olga K."}
277 @string{YFDufrene = "Dufr{\^e}ne, Yves F."}
278 @string{ADunham = "Dunham, A."}
279 @string{DDunlap = "Dunlap, D."}
280 @string{PDunn = "Dunn, P."}
281 @string{VDupres = "Dupres, Vincent"}
282 @string{HJDyson = "Dyson, H.~Jane"}
283 @string{EMBORep = "EMBO Rep"}
284 @string{EMBO = "EMBO Rep."}
285 @string{REckel = "Eckel, R."}
286 @string{KEilbeck = "Eilbeck, K."}
287 @string{MElbaum = "Elbaum, Michael"}
288 @string{E:NHPL = "Elsevier, North-Holland Personal Library"}
289 @string{DEly = "Ely, D."}
290 @string{SEmerling = "Emerling, S."}
291 @string{TEndo = "Endo, Toshiya"}
292 @string{SWEnglander = "Englander, S. Walter"}
293 @string{HErickson = "Erickson, Harold P."}
294 @string{MEsaki = "Esaki, Masatoshi"}
295 @string{SEsparham = "Esparham, S."}
296 @string{EBJ = "European Biophysics Journal"}
297 @string{EJP = "European Journal of Physics"}
298 @string{EPL = "Europhysics Letters"}
299 @string{CEvangelista = "Evangelista, C."}
300 @string{CAEvans = "Evans, C. A."}
301 @string{EEvans = "Evans, E."}
302 @string{RSEvans = "Evans, R. S."}
303 @string{MEvstigneev = "Evstigneev, M."}
304 @string{DFasulo = "Fasulo, D."}
305 @string{FEBS = "FEBS letters"}
306 @string{XFei = "Fei, Xiaofang"}
307 @string{JFernandez = "Fernandez, Julio M."}
308 @string{SFerriera = "Ferriera, S."}
309 @string{AEFilippov = "Filippov, A. E."}
310 @string{LFinzi = "Finzi, L."}
311 @string{TEFisher = "Fisher, T. E."}
312 @string{MFlanigan = "Flanigan, M."}
313 @string{BFlannery = "Flannery, B."}
314 @string{LFlorea = "Florea, L."}
315 @string{ELFlorin = "Florin, Ernst-Ludwig"}
316 @string{HFlyvbjerg = "Flyvbjerg, Henrik"}
317 @string{FoldDes = "Fold Des"}
318 @string{NRForde = "Forde, Nancy R."}
319 @string{CFosler = "Fosler, C."}
320 @string{SFossey = "Fossey, S. A."}
321 @string{SFowler = "Fowler, Susan B."}
322 @string{GFranzen = "Franzen, Gereon"}
323 @string{SFreitag = "Freitag, S."}
324 @string{LFrench = "French, L."}
325 @string{RWFriddle = "Friddle, Raymond W."}
326 @string{CFriedman = "Friedman, C."}
327 @string{RFriedman = "Friedman, Ran"}
328 @string{MFritz = "Fritz, M."}
329 @string{HFuchs = "Fuchs, Harald"}
330 @string{TFujii = "Fujii, Tadashi"}
331 @string{HFujita = "Fujita, Hideaki"}
332 @string{AFujiyama = "Fujiyama, A."}
333 @string{RFulton = "Fulton, R."}
334 @string{TFunck = "Funck, Theodor"}
335 @string{TFurey = "Furey, T."}
336 @string{SFuruike = "Furuike, Shou"}
337 @string{GLGaborMiklos = "Gabor Miklos, G. L."}
338 @string{AEGabrielian = "Gabrielian, A. E."}
339 @string{WGan = "Gan, W."}
340 @string{DNGanchev = "Ganchev, Dragomir N."}
341 @string{MGao = "Gao, Mu"}
342 @string{DGarcia = "Garcia, D."}
343 @string{TGarcia = "Garcia, Tzintzuni"}
344 @string{NGarg = "Garg, N."}
345 @string{HEGaub = "Gaub, Hermann E."}
346 @string{MGautel = "Gautel, Mathias"}
347 @string{LAGavrilov = "Gavrilov, L. A."}
348 @string{NSGavrilova = "Gavrilova, N. S."}
349 @string{WGe = "Ge, W."}
350 @string{UGeisler = "Geisler, Ulrich"}
351 @string{GENE = "Gene"}
352 @string{CGerber = "Gerber, Christoph"}
353 @string{CGergely = "Gergely, C."}
354 @string{RGibbs = "Gibbs, R."}
355 @string{DGilbert = "Gilbert, D."}
356 @string{HGire = "Gire, H."}
357 @string{MGiuntini = "Giuntini, M."}
358 @string{FGittes = "Gittes, Frederick"}
359 @string{SGlanowski = "Glanowski, S."}
360 @string{JGlaser = "Glaser, Jens"}
361 @string{KGlasser = "Glasser, K."}
362 @string{AGlodek = "Glodek, A."}
363 @string{GGloeckner = "Gloeckner, G."}
364 @string{AGluecksmann = "Gluecksmann, A."}
365 @string{JDGocayne = "Gocayne, J. D."}
366 @string{AGomezCasado = "Gomez-Casado, Alberto"}
367 @string{BGompertz = "Gompertz, Benjamin"}
368 @string{FGong = "Gong, F."}
369 @string{GordonBreach = "Gordon Breach Scientific Publishing Ltd."}
370 @string{MGorokhov = "Gorokhov, M."}
371 @string{JHGorrell = "Gorrell, J. H."}
372 @string{SAGould = "Gould, S.~A."}
373 @string{KGraham = "Graham, K."}
374 @string{HLGranzier = "Granzier, Henk L."}
375 @string{FGrater = "Gr{\"a}ter, Frauke"}
376 @string{EDGreen = "Green, E. D."}
377 @string{SGGregory = "Gregory, S. G."}
378 @string{BGropman = "Gropman, B."}
379 @string{CGrossman = "Grossman, C."}
380 @string{HGrubmuller = {Grubm\"uller, Helmut}}
381 @string{AGrutzner = {Gr\"utzner, Anika}}
382 @string{ZGu = "Gu, Z."}
383 @string{PGuan = "Guan, P."}
384 @string{RGuigo = "Guig\'o, R."}
385 @string{EJGumbel = "Gumbel, Emil Julius"}
386 @string{HJGuntherodt = "Guntherodt, Hans-Joachim"}
387 @string{NGuo = "Guo, N."}
388 @string{YGuo = "Guo, Yi"}
389 @string{MGutman = "Gutman, Menachem"}
390 @string{RTGuy = "Guy, Richard T."}
391 @string{PHanggi = {H\"anggi, Peter}}
392 @string{THa = "Ha, Taekjip"}
393 @string{JHaack = "Haack, Julie A."}
394 @string{SHaddock = "Haddock, Steven H.~D."}
395 @string{GHager = "Hager, Gabriele"}
396 @string{THagglund = "H{\"a}gglund, T."}
397 @string{RHajjar = "Hajjar, Roger J."}
398 @string{AHalpern = "Halpern, A."}
399 @string{KHalvorsen = "Halvorsen, Ken"}
400 @string{FHan = "Han, Fangpu"}
401 @string{CCHang = "Hang, C.~C."}
402 @string{SHannenhalli = "Hannenhalli, S."}
403 @string{HHansma = "Hansma, H. G."}
404 @string{PHansma = "Hansma, Paul K."}
405 @string{DHarbrecht = "Harbrecht, Douglas"}
406 @string{SHarper = "Harper, Sandy"}
407 @string{MHarris = "Harris, M."}
408 @string{BHart = "Hart, B."}
409 @string{DPHart = "Hart, D.P."}
410 @string{JWHatfield = "Hatfield, John William"}
411 @string{THatton = "Hatton, T."}
412 @string{MHattori = "Hattori, M."}
413 @string{DHaussler = "Haussler, D."}
414 @string{THawkins = "Hawkins, T."}
415 @string{CHaynes = "Haynes, C."}
416 @string{JHaynes = "Haynes, J."}
417 @string{WHeckl = "Heckl, W. M."}
418 @string{CVHeer = "Heer, C.~V."}
419 @string{JHeil = "Heil, J."}
420 @string{RHeilig = "Heilig, R."}
421 @string{TJHeiman = "Heiman, T. J."}
422 @string{CHeiner = "Heiner, C."}
423 @string{MHelmes = "Helmes, M."}
424 @string{JHemmerle = "Hemmerle, J."}
425 @string{SHenderson = "Henderson, S."}
426 @string{BHeymann = "Heymann, Berthold"}
427 @string{NHiaro = "Hiaro, N."}
428 @string{MEHiggins = "Higgins, M. E."}
429 @string{THilburn = "Hilburn, Thomas B."}
430 @string{LHillier = "Hillier, L."}
431 @string{HHinssen = "Hinssen, Horst"}
432 @string{PHinterdorfer = "Hinterdorfer, Peter"}
433 @string{HistochemJ = "Histochem J"}
434 @string{SHladun = "Hladun, S."}
435 @string{WKHo = "Ho, W.~K."}
436 @string{RHochstrasser = "Hochstrasser, Robin M."}
437 @string{CSHodges = "Hodges, C.~S."}
438 @string{CHoff = "Hoff, C."}
439 @string{WHoff = "Hoff, Wouter D."}
440 @string{JLHolden = "Holden, J. L."}
441 @string{RAHolt = "Holt, R. A."}
442 @string{GHofmann = "Hofmann, Gerd"}
443 @string{MHonda = "Honda, M."}
444 @string{NPCHong = "Hong, Neil P. Chue"}
445 @string{XHong = "Hong, Xia"}
446 @string{LHood = "Hood, L."}
447 @string{JHoover = "Hoover, J."}
448 @string{JHorber = "Horber, J. K. H."}
449 @string{HHosser = "Hosser, H."}
450 @string{DHostin = "Hostin, D."}
451 @string{JHouck = "Houck, J."}
452 @string{AHoumeida = "Houmeida, Ahmed"}
453 @string{JHoward = "Howard, J."}
454 @string{THowland = "Howland, T."}
455 @string{BHsiao = "Hsiao, Benjamin S."}
456 @string{CKHu = "Hu, Chin-Kun"}
457 @string{DLHu = "Hu, David L."}
458 @string{BHuang = "Huang, Baiqu"}
459 @string{HHuang = "Huang, Hector Han-Li"}
460 @string{MHubain = "Hubain, Maurice"}
461 @string{AJHudspeth = "Hudspeth, A.~J."}
462 @string{KHuff = "Huff, Katy"}
463 @string{JHughes = "Hughes, John"}
464 @string{GHummer = "Hummer, Gerhard"}
465 @string{SJHumphray = "Humphray, S. J."}
466 @string{WLHung = "Hung, Wen-Liang"}
467 @string{MHunkapiller = "Hunkapiller, M."}
468 @string{DHHuson = "Huson, D. H."}
469 @string{JHutter = "Hutter, Jeffrey L."}
470 @string{CHyeon = "Hyeon, Changbong"}
471 @string{IEEE:TIT = "IEEE Transactions on Information Theory"}
472 @string{IEEE:SPM = "IEEE Signal Processing Magazine"}
473 @string{CIbegwam = "Ibegwam, C."}
474 @string{JRIdol = "Idol, J. R."}
475 @string{SImprota = "Improta, S."}
476 @string{TInoue = "Inoue, Tadashi"}
477 @string{IJBMM = "International Journal of Biological Macromolecules"}
478 @string{IJCIS = "International Journal of Computer \& Information Sciences"}
479 @string{AItkin = "Itkin, Anna"}
480 @string{HItoh = "Itoh, Hiroyasu"}
481 @string{AIrback = "Irback, Anders"}
482 @string{AMIsaacs = "Isaacs, Adrian M."}
483 @string{BIsralewitz = "Isralewitz, B."}
484 @string{SIstrail = "Istrail, S."}
485 @string{MIvemeyer = "Ivemeyer, M."}
486 @string{DIzhaky = "Izhaky, David"}
487 @string{SIzrailev = "Izrailev, S."}
488 @string{TJahnke = "J{\"a}hnke, Torsten"}
489 @string{WJang = "Jang, W."}
490 @string{HJanovjak = "Janovjak, Harald"}
491 @string{LJanosi = "Janosi, Lorant"}
492 @string{AJanshoff = "Janshoff, Andreas"}
493 @string{JJAP = "Japanese Journal of Applied Physics"}
494 @string{MJaschke = "Jaschke, Manfred"}
495 @string{DJennings = "Jennings, D."}
496 @string{HFJi = "Ji, Hai-Feng"}
497 @string{RRJi = "Ji, R. R."}
498 @string{YJia = "Jia, Yiwei"}
499 @string{SJiang = "Jiang, Shaoyi"}
500 @string{XJiang = "Jiang, Xingqun"}
501 @string{DJohannsmann = "Johannsmann, Diethelm"}
502 @string{CJohnson = "Johnson, Colin P."}
503 @string{JJohnson = "Johnson, J."}
504 @string{AJollymore = "Jollymore, Ashlee"}
505 @string{REJones = "Jones, R.E."}
506 @string{SJones = "Jones, S."}
507 @string{CJordan = "Jordan, C."}
508 @string{JJordan = "Jordan, J."}
509 %string{JACS = "J Am Chem Soc"}
510 @string{JACS = "Journal of the American Chemical Society"}
511 @string{JASA = "Journal of the American Statistical Association"}
512 @string{JAP = "Journal of Applied Physics"}
513 @string{JBM = "J Biomech"}
514 @string{JBT = "J Biotechnol"}
515 @string{JCPPCB = "Journal de Chimie Physique et de Physico-Chimie Biologique"}
516 @string{JCS = "Journal of Cell Science"}
517 @string{JCompP = "Journal of Computational Physics"}
518 @string{JEChem = "Journal of Electroanalytical Chemistry"}
519 @string{JMathBiol = "J Math Biol"}
520 @string{JMicro = "Journal of Microscopy"}
521 @string{JPhysio = "Journal of Physiology"}
522 @string{JStructBiol = "Journal of Structural Biology"}
523 @string{JTB = "J Theor Biol"}
524 @string{JMB = "Journal of Molecular Biology"}
525 @string{JP:CM = "Journal of Physics: Condensed Matter"}
526 @string{JP:CON = "Journal of Physics: Conference Series"}
527 @string{JRNBS:C = "Journal of Research of the National Bureau of Standards. Section C: Engineering and Instrumentation"}
528 @string{WSJuang = "Juang, F.~S."}
529 @string{DAJuckett = "Juckett, D. A."}
530 @string{SRJun = "Jun, Se-Ran"}
531 @string{DKaftan = "Kaftan, David"}
532 @string{LKagan = "Kagan, L."}
533 @string{FKalush = "Kalush, F."}
534 @string{ELKaplan = "Kaplan, E. L."}
535 @string{RKapon = "Kapon, Ruti"}
536 @string{AKardinal = "Kardinal, Angelika"}
537 @string{BKarlak = "Karlak, B."}
538 @string{MKarplus = "Karplus, Martin"}
539 @string{MKarrenbach = "Karrenbach, Martin"}
540 @string{JKasha = "Kasha, J."}
541 @string{KKawasaki = "Kawasaki, K."}
542 @string{ZKe = "Ke, Z."}
543 @string{AKejariwal = "Kejariwal, A."}
544 @string{MSKellermayer = "Kellermayer, Mikl\'os S. Z."}
545 @string{TKempe = "Kempe, Thomas"}
546 @string{SKennedy = "Kennedy, S."}
547 @string{SBHKent = "Kent, Stephen B. H."}
548 @string{WJKent = "Kent, W. J."}
549 @string{KAKetchum = "Ketchum, K. A."}
550 @string{FKienberger = "Kienberger, Ferry"}
551 @string{SHKim = "Kim, Sung-Hou"}
552 @string{WKing = "King, William Trevor"}
553 @string{KKinosita = "{Kinosita Jr.}, Kazuhiko"}
554 @string{IRKirsch = "Kirsch, I. R."}
555 @string{JKlafter = "Klafter, J."}
556 @string{AKleiner = "Kleiner, Ariel"}
557 @string{DKlimov = "Klimov, Dmitri K."}
558 @string{LKline = "Kline, L."}
559 @string{LKlumb = "Klumb, L."}
560 @string{KAPPP = "Kluwer Academic Publishers--Plenum Publishers"}
561 @string{CDKodira = "Kodira, C. D."}
562 @string{SKoduru = "Koduru, S."}
563 @string{PKoehl = "Koehl, Patrice"}
564 @string{BKolmerer = "Kolmerer, B."}
565 @string{JKorenberg = "Korenberg, J."}
566 @string{IKosztin = "Kosztin, Ioan"}
567 @string{JKovacevic = "Kovacevic, Jelena"}
568 @string{CKraft = "Kraft, C."}
569 @string{HAKramers = "Kramers, H. A."}
570 @string{AKrammer = "Krammer, Andre"}
571 @string{SKravitz = "Kravitz, S."}
572 @string{HJKreuzer = {Kreuzer, Hans J\"urgen}}
573 @string{MMGKrishna = "Krishna, Mallela M. G."}
574 @string{KKroy = "Kroy, Klaus"}
575 @string{HHKu = "Ku, H.~H."}
576 @string{TAKucaba = "Kucaba, T. A."}
577 @string{Kucherlapati = "Kucherlapati"}
578 @string{JKudoh = "Kudoh, J."}
579 @string{MKuhn = "Kuhn, Michael"}
580 @string{MKulke = "Kulke, Michael"}
581 @string{CKwok = "Kwok, Carol H."}
582 @string{RLevy = "L\'evy, R"}
583 @string{DLabeit = "Labeit, Dietmar"}
584 @string{SLabeit = "Labeit, Siegfried"}
585 @string{DLabudde = "Labudde, Dirk"}
586 @string{SLahmers = "Lahmers, Sunshine"}
587 @string{ZLai = "Lai, Z."}
588 @string{CLam = "Lam, Canaan"}
589 @string{JLamb = "Lamb, Jonathan C."}
590 @string{LANG = "Langmuir"}
591 % "Langmuir : the ACS journal of surfaces and colloids",
592 @string{WLau = "Lau, Wai Leung"}
593 @string{RLaw = "Law, Richard"}
594 @string{BLazareva = "Lazareva, B."}
595 @string{MLeake = "Leake, Mark C."}
596 @string{ELee = "Lee, E."}
597 @string{HLee = "Lee, Haeshin"}
598 @string{SLee = "Lee, Sunyoung"}
599 @string{HLehmann = "Lehmann, H."}
600 @string{HLehrach = "Lehrach, H."}
601 @string{YLei = "Lei, Y."}
602 @string{PLelkes = "Lelkes, Peter I."}
603 @string{OLequin = "Lequin, Olivier"}
604 @string{CLethias = "Lethias, Claire"}
605 @string{SLeuba = "Leuba, Sanford H."}
606 @string{ALeung = "Leung, A."}
607 @string{MLeuschner = "Leuschner, Mirko"}
608 @string{AJLevine = "Levine, A. J."}
609 @string{CLevinthal = "Levinthal, Cyrus"}
610 @string{ALevitsky = "Levitsky, A."}
611 @string{SLevy = "Levy, S."}
612 @string{MLewis = "Lewis, M."}
613 @string{JLItalien = "L'Italien, James J."}
614 @string{BLi = "Li, Bing"}
615 @string{CYLi = "Li, Christopher Y."}
616 @string{HLi = "Li, Hongbin"}
617 @string{JLi = "Li, J."}
618 @string{LeLi = "Li, Lewyn"}
619 @string{LiLi = "Li, Lingyu"}
620 @string{MSLi = "Li, Mai Suan"}
621 @string{PWLi = "Li, P. W."}
622 @string{YLi = "Li, Yajun"}
623 @string{ZLi = "Li, Z."}
624 @string{YLiang = "Liang, Y."}
625 @string{GLiao = "Liao, George"}
626 @string{FCLin = "Lin, Fan-Chi"}
627 @string{JLin = "Lin, Jianhua"}
628 @string{SHLin = "Lin, Sheng-Hsien"}
629 @string{XLin = "Lin, X."}
630 @string{JLindahl = "Lindahl, Joakim"}
631 @string{SLindsay = "Lindsay, Stuart M."}
632 @string{WALinke = "Linke, Wolfgang A."}
633 @string{RLippert = "Lippert, R."}
634 @string{JLis = "Lis, John T."}
635 @string{RLiu = "Liu, Runcong"}
636 @string{WLiu = "Liu, W."}
637 @string{XLiu = "Liu, X."}
638 @string{YLiu = "Liu, Yichun"}
639 @string{LLivadaru = "Livadaru, L."}
640 @string{YSLo = "Lo, Yu-Shiu"}
641 @string{GLois = "Lois, Gregg"}
642 @string{JLopez = "Lopez, J."}
643 @string{LANL = "Los Alamos National Laboratory"}
644 @string{LAS = "Los Alamos Science"}
645 @string{ALove = "Love, A."}
646 @string{FLu = "Lu, F."}
647 @string{HLu = "Lu, Hui"}
648 @string{QLu = "Lu, Qinghua"}
649 @string{MLudwig = "Ludwig, Markus"}
650 @string{ZPLuo = "Luo, Zong-Ping"}
651 @string{ZLuthey-Schulten = "Luthey-Schulten, Z."}
652 @string{EMunck = {M\"unck, E.}}
653 @string{DMa = "Ma, D."}
654 @string{LMa = "Ma, Liang"}
655 @string{MMaaloum = "Maaloum, Mounir"}
656 @string{Macromol = "Macromolecules"}
657 @string{AMadan = "Madan, A."}
658 @string{VVMaduro = "Maduro, V. V."}
659 @string{CMaingonnat = "Maingonnat, C."}
660 @string{SMajid = "Majid, Sophia"}
661 @string{WMajoros = "Majoros, W."}
662 @string{DEMakarov = "Makarov, Dmitrii E."}
663 @string{RMamdani = "Mamdani, Reneeta"}
664 @string{SMammi = "Mammi, Stefano"}
665 @string{EMandello = "Mandello, Enrico"}
666 @string{GManderson = "Manderson, Gavin"}
667 @string{FMann = "Mann, F."}
668 @string{AMansson = "M{\aa}nsson, Alf"}
669 @string{ERMardis = "Mardis, E. R."}
670 @string{JMarion = "Marion, J."}
671 @string{JFMarko = "Marko, John F."}
672 @string{MMarra = "Marra, M."}
673 @string{PMarszalek = "Marszalek, Piotr E."}
674 @string{MMartin = "Martin, M. J."}
675 @string{YMartin = "Martin, Y."}
676 @string{HMassa = "Massa, H."}
677 @string{MIT = "Massachusetts Institute of Technology"}
678 @string{GAMatei = "Matei, G.~A."}
679 @string{DMaterassi = "Materassi, Donatello"}
680 @string{JMathe = "Math\'e, J\'er\^ome"}
681 @string{AMatouschek = "Matouschek, Andreas"}
682 @string{BMatthews = "Matthews, Brian W."}
683 @string{DMay = "May, D."}
684 @string{RMayer = "Mayer, Richard"}
685 @string{LMayne = "Mayne, Leland"}
686 @string{AMays = "Mays, A."}
687 @string{OTMcCann = "McCann, O. T."}
688 @string{SMcCawley = "McCawley, S."}
689 @string{JMcDaniel = "McDaniel, J."}
690 @string{JMcEntyre = "McEntyre, J."}
691 @string{McGraw-Hill = "McGraw-Hill"}
692 @string{TMcIntosh = "McIntosh, T."}
693 @string{VAMcKusick = "McKusick, V. A."}
694 @string{IMcMullen = "McMullen, I."}
695 @string{JDMcPherson = "McPherson, J. D."}
696 @string{TMeasey = "Measey, Thomas J."}
697 @string{MAD = "Mech Ageing Dev"}
698 @string{PMeier = "Meier, Paul"}
699 @string{AMeller = "Meller, Amit"}
700 @string{CCMello = "Mello, Cecilia C."}
701 @string{RMerkel = "Merkel, R."}
702 @string{GVMerkulov = "Merkulov, G. V."}
703 @string{FMerzel = "Merzel, Franci"}
704 @string{HMetiu = "Metiu, Horia"}
705 @string{NMetropolis = "Metropolis, Nicholas"}
706 @string{GMeyer = "Meyer, Gerhard"}
707 @string{HMi = "Mi, H."}
708 @string{LMiao = "Miao, Linlin"}
709 @string{CMicheletti = "Micheletti, Cristian"}
710 @string{MMickler = "Mickler, Moritz"}
711 @string{AMiller = "Miller, A."}
712 @string{NMilshina = "Milshina, N."}
713 @string{SMinoshima = "Minoshima, S."}
714 @string{IMitchell = "Mitchell, Ian"}
715 @string{SMitternacht = "Mitternacht, Simon"}
716 @string{NJMlot = "Mlot, Nathan J."}
717 @string{CMobarry = "Mobarry, C."}
718 @string{NMohandas = "Mohandas, N."}
719 @string{SMohanty = "Mohanty, Sandipan"}
720 @string{UMohideen = "Mohideen, U."}
721 @string{PJMohr = "Mohr, Peter J."}
722 @string{VMontana = "Montana, Vedrana"}
723 @string{LMontanaro = "Montanaro, Lucio"}
724 @string{LMontelius = "Montelius, Lars"}
725 @string{CMontemagno = "Montemagno, Carlo D."}
726 @string{KTMontgomery = "Montgomery, K. T."}
727 @string{HMMoore = "Moore, H. M."}
728 @string{MMorgan = "Morgan, Michael"}
729 @string{LMoy = "Moy, L."}
730 @string{MMoy = "Moy, M."}
731 @string{VMoy = "Moy, Vincent T."}
732 @string{SMukamel = "Mukamel, Shaul"}
733 @string{DJMuller = "M{\"u}ller, Daniel J."}
734 @string{PMundel = "Mundeol, P."}
735 @string{EMuneyuki = "Muneyuki, Eiro"}
736 @string{RJMural = "Mural, R. J."}
737 @string{BMurphy = "Murphy, B."}
738 @string{SMurphy = "Murphy, S."}
739 @string{AMuruganujan = "Muruganujan, A."}
740 @string{FMusiani = "Musiani, Francesco"}
741 @string{EWMyers = "Myers, E. W."}
742 @string{RMMyers = "Myers, R. M."}
743 @string{AMylonakis = "Mylonakis, Andreas"}
744 @string{ENachliel = "Nachliel, Esther"}
745 @string{JNadeau = "Nadeau, J."}
746 @string{AKNaik = "Naik, A. K."}
747 @string{NANO = "Nano letters"}
748 @string{NT = "Nanotechnology"}
749 @string{VANarayan = "Narayan, V. A."}
750 @string{ANarechania = "Narechania, A."}
751 @string{PNassoy = "Nassoy, P."}
752 @string{NBS = "National Bureau of Standards"}
753 @string{NAT = "Nature"}
754 @string{NSB = "Nature Structural Biology"}
755 @string{NSMB = "Nature Structural Molecular Biology"}
756 @string{NRMCB = "Nature Reviews Molecular Cell Biology"}
757 @string{SNaylor = "Naylor, S."}
758 @string{CNeagoe = "Neagoe, Ciprian"}
759 @string{BNeelam = "Neelam, B."}
760 @string{MNeitzert = "Neitzert, Marcus"}
761 @string{CNelson = "Nelson, C."}
762 @string{KNelson = "Nelson, K."}
763 @string{RRNetz = "Netz, R.~R."}
764 @string{NR = "Neurochemical research"}
765 @string{NEURON = "Neuron"}
766 @string{RNevo = "Nevo, Reinat"}
767 @string{NJP = "New Journal of Physics"}
768 @string{DBNewell = "Newell, David B."}
769 @string{MNewman = "Newman, M."}
770 @string{INewton = "Newton, Isaac"}
771 @string{SNg = "Ng, Sean P."}
772 @string{NNguyen = "Nguyen, N."}
773 @string{TNguyen = "Nguyen, T."}
774 @string{MNguyen-Duong = "Nguyen-Duong, M."}
775 @string{INicholls = "Nicholls, Ian A."}
776 @string{NNichols = "Nichols, N.~B."}
777 @string{SNie = "Nie, S."}
778 @string{MNodell = "Nodell, M."}
779 @string{AANoegel = "Noegel, Angelika A."}
780 @string{HNoji = "Noji, Hiroyuki"}
781 @string{RNome = "Nome, Rene A."}
782 @string{NNowak = "Nowak, N."}
783 @string{ANoy = "Noy, Aleksandr"}
784 @string{NAR = "Nucleic Acids Research"}
785 @string{JNummela = "Nummela, Jeremiah"}
786 @string{JNunes = "Nunes, Joao"}
787 @string{DNusskern = "Nusskern, D."}
788 @string{GNyakatura = "Nyakatura, G."}
789 @string{CSOHern = "O'Hern, Corey S."}
790 @string{YOberdorfer = {Oberd\"orfer, York}}
791 @string{AOberhauser = "Oberhauser, Andres F."}
792 @string{FOesterhelt = "Oesterhelt, Filipp"}
793 @string{TOhashi = "Ohashi, Tomoo"}
794 @string{BOhler = "Ohler, Benjamin"}
795 @string{PDOlmsted = "Olmsted, Peter D."}
796 @string{AOlsen = "Olsen, A."}
797 @string{SJOlshansky = "Olshansky, S. J."}
798 @string{POmling = {Omlink, P{\"a}r}}
799 @string{JNOnuchic = "Onuchic, J. N."}
800 @string{YOono = "Oono, Y."}
801 @string{GOppenheim = "Oppenheim, Georges"}
802 @string{COpitz = "Optiz, Christiane A."}
803 @string{KOroszlan = "Oroszlan, Krisztina"}
804 @string{EOroudjev = "Oroudjev, E."}
805 @string{KOsoegawa = "Osoegawa, K."}
806 @string{OUP = "Oxford University Press"}
807 @string{EPaci = "Paci, Emanuele"}
808 @string{SPan = "Pan, S."}
809 @string{HSPark = "Park, H. S."}
810 @string{VParpura = "Parpura, Vladimir"}
811 @string{APastore = "Pastore, A."}
812 @string{APatrinos = "Patrinos, Aristides"}
813 @string{FPavone = "Pavone, F. S."}
814 @string{SHPayne = "Payne, Stephen H."}
815 @string{JPeck = "Peck, J."}
816 @string{HPeng = "Peng, Haibo"}
817 @string{QPeng = "Peng, Qing"}
818 @string{RNPerham = "Perham, Richard N."}
819 @string{OPerisic = "Perisic, Ognjen"}
820 @string{CPeterson = "Peterson, Craig L."}
821 @string{MPeterson = "Peterson, M."}
822 @string{SMPeterson = "Peterson, Susan M."}
823 @string{CPfannkoch = "Pfannkoch, C."}
824 @string{PA = "Pfl{\"u}gers Archiv: European journal of physiology"}
825 @string{PTRSL = "Philosophical Transactions of the Royal Society of London"}
826 @string{PR:E = "Phys Rev E Stat Nonlin Soft Matter Phys"}
827 @string{PRL = "Physical Review Letters"}
828 %string{PRL = "Phys Rev Lett"}
829 @string{Physica = "Physica"}
830 @string{GPing = "Ping, Guanghui"}
831 @string{NPinotsis = "Pinotsis, Nikos"}
832 @string{MPlumbley = "Plumbley, Mark"}
833 @string{PLOS:ONE = "PLOS ONE"}
834 %string{PLOS:ONE = "Public Library of Science ONE"}
835 @string{PLOS:BIO = "PLOS Biology"}
836 @string{DPlunkett = "Plunkett, David"}
837 @string{PPodsiadlo = "Podsiadlo, Paul"}
838 @string{ASPolitou = "Politou, A. S."}
839 @string{APoustka = "Poustka, A."}
840 @string{CBPrater = "Prater, C.~B."}
841 @string{GPratesi = "Pratesi, G."}
842 @string{EPratts = "Pratts, E."}
843 @string{WPress = "Press, W."}
844 @string{PNAS = "Proceedings of the National Academy of Sciences of the
845 United States of America"}
846 @string{PBPMB = "Progress in Biophysics and Molecular Biology"}
847 @string{PS = "Protein Science"}
848 @string{PROT = "Proteins"}
849 @string{RSUP = "Published for the Royal Society at the University Press"}
850 @string{EPuchner = "Puchner, Elias M."}
851 @string{VPuri = "Puri, V."}
852 @string{WPyckhout-Hintzen = "Pyckhout-Hintzen, Wim"}
853 @string{HQin = "Qin, Haina"}
854 @string{SQin = "Qin, S."}
855 @string{SRQuake = "Quake, Stephen R."}
856 @string{CQuate = "Quate, Calvin F."}
857 @string{HQureshi = "Qureshi, H."}
858 @string{SERadford = "Radford, Sheena E."}
859 @string{MRadmacher = "Radmacher, M."}
860 @string{MRaible = "Raible, M."}
861 @string{LRamirez = "Ramirez, L."}
862 @string{JRamser = "Ramser, J."}
863 @string{LRandles = "Randles, Lucy G."}
864 @string{VRaussens = "Raussens, Vincent"}
865 @string{IRay = "Ray, I."}
866 @string{MReardon = "Reardon, M."}
867 @string{ALCReddin = "Reddin, Andrew L. C."}
868 @string{SRedick = "Redick, Sambra D."}
869 @string{ZReich = "Reich, Ziv"}
870 @string{TReid = "Reid, T."}
871 @string{PReimann = "Reimann, P."}
872 @string{KReinert = "Reinert, K."}
873 @string{RReinhardt = "Reinhardt, R."}
874 @string{KRemington = "Remington, K."}
875 @string{RMP = "Rev. Mod. Phys."}
876 @string{RSI = "Review of Scientific Instruments"}
877 @string{FRief = "Rief, Frederick"}
878 @string{MRief = "Rief, Matthias"}
879 @string{KRitchie = "Ritchie, K."}
880 @string{MRobbins = "Robbins, Mark O."}
881 @string{CJRoberts = "Roberts, C.~J."}
882 @string{RJRoberts = "Roberts, R. J."}
883 @string{RRobertson = "Robertson, Ragan B."}
884 @string{HRoder = "Roder, Heinrich"}
885 @string{RRodriguez = "Rodriguez, R."}
886 @string{YHRogers = "Rogers, Y. H."}
887 @string{SRogic = "Rogic, S."}
888 @string{MRoman = "Roman, Marisa B."}
889 @string{GRomano = "Romano, G."}
890 @string{DRomblad = "Romblad, D."}
891 @string{RRos = "Ros, Robert"}
892 @string{BRosenberg = "Rosenberg, B."}
893 @string{JRosengren = "Rosengren, Jenny P."}
894 @string{ARosenthal = "Rosenthal, A."}
895 @string{ARoters = "Roters, Andreas"}
896 @string{WRowe = "Rowe, W."}
897 @string{LRowen = "Rowen, L."}
898 @string{BRuhfel = "Ruhfel, B."}
899 @string{DBRusch = "Rusch, D. B."}
900 @string{JMRuysschaert = "Ruysschaert, Jean-Marie"}
901 @string{JPRyckaert = "Ryckaert, Jean-Paul"}
902 @string{NSakaki = "Sakaki, Naoyoshi"}
903 @string{YSakaki = "Sakaki, Y."}
904 @string{SSalzberg = "Salzberg, S."}
905 @string{BSamori = "Samor{\`i}, Bruno"}
906 @string{MSandal = "Sandal, Massimo"}
907 @string{RSanders = "Sanders, R."}
908 @string{ASarkar = "Sarkar, Atom"}
909 @string{TSasaki = "Sasaki, T."}
910 @string{SSato = "Sato, S."}
911 @string{TSato = "Sato, Takehiro"}
912 @string{PSchaaf = "Schaaf, P."}
913 @string{RSchafer = "Schafer, Rolf"}
914 @string{TESchafer = "Sch{\"a}fer, Tilman E."}
915 @string{NScherer = "Scherer, Norbert F."}
916 @string{SScherer = "Scherer, S."}
917 @string{MSchilhabel = "Schilhabel, M."}
918 @string{HSchillers = "Schillers, Hermann"}
919 @string{BSchlegelberger = "Schlegelberger, B."}
920 @string{MSchleicher = "Schleicher, Michael"}
921 @string{MSchlierf = "Schlierf, Michael"}
922 @string{CFSchmidt = "Schmidt, Christoph F."}
923 @string{JSchmidt = "Schmidt, Jacob J."}
924 @string{LSchmitt = "Schmitt, Lutz"}
925 @string{JSchmutz = "Schmutz, J."}
926 @string{GSchuler = "Schuler, G."}
927 @string{GDSchuler = "Schuler, G. D."}
928 @string{KSchulten = "Schulten, Klaus"}
929 @string{ZSchulten = "Schulten, Zan"}
930 @string{MSchwab = "Schwab, M."}
931 @string{ISchwaiger = "Schwaiger, Ingo"}
932 @string{RSchwartz = "Schwartz, R."}
933 @string{RSchweitzerStenner = "Scheitzer-Stenner, Reinhard"}
934 @string{SCI = "Science"}
935 @string{CEScott = "Scott, C. E."}
936 @string{JScott = "Scott, J."}
937 @string{RScott = "Scott, R."}
938 @string{USeifert = "Seifert, Udo"}
939 @string{SKSekatskii = "Sekatskii, Sergey K."}
940 @string{MSekhon = "Sekhon, M."}
941 @string{TSekiguchi = "Sekiguchi, T."}
942 @string{BSenger = "Senger, B."}
943 @string{DBSenn = "Senn, David B."}
944 @string{PSeranski = "Seranski, P."}
945 @string{RSesboue = {Sesbo\"u\'e, R.}}
946 @string{EShakhnovich = "Shakhnovich, Eugene"}
947 @string{GShan = "Shan, Guiye"}
948 @string{JShang = "Shang, J."}
949 @string{WShao = "Shao, W."}
950 @string{DSharma = "Sharma, Deepak"}
951 @string{YJSheng = "Sheng, Yu-Jane"}
952 @string{KShibuya = "Shibuya, K."}
953 @string{JShillcock = "Shillcock, Julian"}
954 @string{AShimizu = "Shimizu, A."}
955 @string{NShimizu = "Shimizu, N."}
956 @string{RShimoKon = "Shimo-Kon, Rieko"}
957 @string{JPShine = "Shine, James P."}
958 @string{AShintani = "Shintani, A."}
959 @string{BShneiderman = "Shneiderman, Ben"}
960 @string{BShue = "Shue, B."}
961 @string{RSiebert = "Siebert, R."}
962 @string{EDSiggia = "Siggia, Eric D."}
963 @string{MSimon = "Simon, M."}
964 @string{MSimpson = "Simpson, M."}
965 @string{GESims = "Sims, Gregory E."}
966 @string{CSitter = "Sitter, C."}
967 @string{KVSjolander = "Sjolander, K. V."}
968 @string{MSkupski = "Skupski, M."}
969 @string{CSlayman = "Slayman, C."}
970 @string{MSmallwood = "Smallwood, M."}
971 @string{CSmith = "Smith, Corey L."}
972 @string{DASmith = "Smith, D. Alastair"}
973 @string{HOSmith = "Smith, H. O."}
974 @string{KBSmith = "Smith, Kathryn B."}
975 @string{MDSmith = "Smith, Micholas Dean"}
976 @string{SSmith = "Smith, S."}
977 @string{SBSmith = "Smith, S. B."}
978 @string{TSmith = "Smith, T."}
979 @string{JSoares = "Soares, J."}
980 @string{NDSocci = "Socci, N. D."}
981 @string{SEG = "Society of Exploration Geophysicists"}
982 @string{ESodergren = "Sodergren, E."}
983 @string{CSoderlund = "Soderlund, C."}
984 @string{JSong = "Song, Jianxing"}
985 @string{JSpanier = "Spanier, Jonathan E."}
986 @string{DSpeicher = "Speicher, David W."}
987 @string{GSpier = "Spier, G."}
988 @string{ASprague = "Sprague, A."}
989 @string{SPRINGER = "Springer Science + Business Media, LLC"}
990 @string{SPRINGER:V = "Springer-Verlag"}
991 @string{DBStaple = "Staple, Douglas B."}
992 @string{RStark = "Stark, R. W."}
993 @string{PSStayton = "Stayton, P. S."}
994 @string{REStenkamp = "Stenkamp, R. E."}
995 @string{SStepaniants = "Stepaniants, S."}
996 @string{EStewart = "Stewart, E."}
997 @string{MRStockmeier = "Stockmeier, M. R."}
998 @string{TStockwell = "Stockwell, T."}
999 @string{NEStone = "Stone, N. E."}
1000 @string{AStout = "Stout, A."}
1001 @string{TRStrick = "Strick, T. R."}
1002 @string{CStroh = "Stroh, Cordula"}
1003 @string{RStrong = "Strong, R."}
1004 @string{JStruckmeier = "Struckmeier, Jens"}
1005 @string{STR = "Structure"}
1006 @string{TStrunz = "Strunz, Torsten"}
1007 @string{MSu = "Su, Meihong"}
1008 @string{GSubramanian = "Subramanian, G."}
1009 @string{ESuh = "Suh, E."}
1010 @string{JSun = "Sun, J."}
1011 @string{YLSun = "Sun, Yu-Long"}
1012 @string{MSundberg = "Sundberg, Mark"}
1013 @string{WSundquist = "Sundquist, Wesley I."}
1014 @string{KSurewicz = "Surewicz, Krystyna"}
1015 @string{WKSurewicz = "Surewicz, Witold K."}
1016 @string{GGSutton = "Sutton, G. G."}
1017 @string{ASzabo = "Szabo, Attila"}
1018 @string{STagerud = "T{\aa}gerud, Sven"}
1019 @string{PTabor = "Tabor, P."}
1020 @string{ATakahashi = "Takahashi, Akiri"}
1021 @string{DTalaga = "Talaga, David S."}
1022 @string{PTalkner = "Talkner, Peter"}
1023 @string{RTampe = "Tamp{\'e}, Robert"}
1024 @string{JTang = "Tang, Jianyong"}
1025 @string{PTavan = "Tavan, P."}
1026 @string{BNTaylor = "Taylor, Barry N."}
1027 @string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
1028 Onderafdeling der Wiskunde"}
1029 @string{SJBTendler = "Tendler, S.~J.~B."}
1030 @string{ITessari = "Tessari, Isabella"}
1031 @string{STeukolsky = "Teukolsky, S."}
1032 @string{CJ = "The Computer Journal"}
1033 @string{JBC = "The Journal of Biological Chemistry"}
1034 @string{JCP = "The Journal of Chemical Physics"}
1035 @string{JPC:B = "The Journal of Physical Chemistry B"}
1036 @string{JPC:C = "The Journal of Physical Chemistry C"}
1037 @string{RS = "The Royal Society"}
1038 @string{DThirumalai = "Thirumalai, Devarajan"}
1039 @string{PDThomas = "Thomas, P. D."}
1040 @string{RThomas = "Thomas, R."}
1041 @string{JThompson = "Thompson, J. B."}
1042 @string{EJThoreson = "Thoreson, E.~J."}
1043 @string{SThornton = "Thornton, S."}
1044 @string{RWTillmann = "Tillmann, R.~W."}
1045 @string{NNTint = "Tint, N. N."}
1046 @string{BTiribilli = "Tiribilli, Bruno"}
1047 @string{TTlusty = "Tlusty, Tsvi"}
1048 @string{PTobias = "Tobias, Paul"}
1049 @string{JTocaHerrera = "Toca-Herrera, Jose L."}
1050 @string{CATovey = "Tovey, Craig A."}
1051 @string{AToyoda = "Toyoda, A."}
1052 @string{TASME = "Transactions of the American Society of Mechanical Engineers"}
1053 @string{BTrask = "Trask, B."}
1054 @string{TBI = "Tribology International"}
1055 @string{JTrinick = "Trinick, John"}
1056 @string{KTrombitas = "Trombit\'as, K."}
1057 @string{ILTrong = "Trong, I. Le"}
1058 @string{CHTsai = "Tsai, Chih-Hui"}
1059 @string{HKTsao = "Tsao, Heng-Kwong"}
1060 @string{STse = "Tse, S."}
1061 @string{ZTshiprut = "Tshiprut, Z."}
1062 @string{JCMTsibris = "Tsibris, J.C.M."}
1063 @string{LTskhovrebova = "Tskhovrebova, Larissa"}
1064 @string{HWTurnbull = "Turnbull, Herbert Westren"}
1065 @string{RTurner = "Turner, R."}
1066 @string{AUlman = "Ulman, Abraham"}
1067 @string{UltraMic = "Ultramicroscopy"}
1068 @string{UIP:Urbana = "University of Illinois Press, Urbana"}
1069 @string{UTMB = "University of Texas Medical Branch"}
1070 @string{MUrbakh = "Urbakh, M."}
1071 @string{FValle = "Valle, Francesco"}
1072 @string{KJVanVliet = "Van Vliet, Krystyn J."}
1073 @string{PVandewalle = "Vandewalle, Patrick"}
1074 @string{CVech = "Vech, C."}
1075 @string{OVelasquez = "Velasquez, O."}
1076 @string{EVenter = "Venter, E."}
1077 @string{JCVenter = "Venter, J. C."}
1078 @string{PHVerdier = "Verdier, Peter H."}
1079 @string{IVetter = "Vetter, Ingrid R."}
1080 @string{MVetterli = "Vetterli, Martin"}
1081 @string{WVetterling = "Vetterling, W."}
1082 @string{MViani = "Viani, Mario B."}
1083 @string{JCVoegel = "Voegel, J.-C."}
1084 @string{VVogel = "Vogel, Viola"}
1085 @string{CWagner-McPherson = "Wagner-McPherson, C."}
1086 @string{RWahl = "Wahl, Reiner"}
1087 @string{TAWaigh = "Waigh, Thomas A."}
1088 @string{BWalenz = "Walenz, B."}
1089 @string{JWallis = "Wallis, J."}
1090 @string{KWalther = "Walther, Kirstin A."}
1091 @string{AJWalton = "Walton, Alan J"}
1092 @string{EBWalton = "Walton, Emily B."}
1093 @string{AWang = "Wang, A."}
1094 @string{FSWang = "Wang, F.~S."}
1095 @string{GWang = "Wang, G."}
1096 @string{JWang = "Wang, J."}
1097 @string{MWang = "Wang, M."}
1098 @string{MDWang = "Wang, Michelle D."}
1099 @string{SWang = "Wang, Shuang"}
1100 @string{XWang = "Wang, X."}
1101 @string{ZWang = "Wang, Z."}
1102 @string{HWatanabe = "Watanabe, Hiroshi"}
1103 @string{KWatanabe = "Watanabe, Kaori"}
1104 @string{RHWaterston = "Waterston, R. H."}
1105 @string{BWaugh = "Waugh, Ben"}
1106 @string{JWegiel = "Wegiel, J."}
1107 @string{MWei = "Wei, M."}
1108 @string{YWei = "Wei, Yen"}
1109 @string{ALWeisenhorn = "Weisenhorn, A.~L."}
1110 @string{JWeissenbach = "Weissenbach, J."}
1111 @string{BLWelch = "Welch, Bernard Lewis"}
1112 @string{GWen = "Wen, G."}
1113 @string{MWen = "Wen, M."}
1114 @string{JWetter = "Wetter, J."}
1115 @string{EPWhite = "White, Ethan P."}
1116 @string{ANWhitehead = "Whitehead, Alfred North"}
1117 @string{AWhittaker = "Whittaker, A."}
1118 @string{HKWickramasinghe = "Wickramasinghe, H. K."}
1119 @string{RWides = "Wides, R."}
1120 @string{AWiita = "Wiita, Arun P."}
1121 @string{MWilchek = "Wilchek, Meir"}
1122 @string{AWilcox = "Wilcox, Alexander J."}
1123 @string{Williams = "Williams"}
1124 @string{CCWilliams = "Williams, C. C."}
1125 @string{MWilliams = "Williams, M."}
1126 @string{SWilliams = "Williams, S."}
1127 @string{WN = "Williams \& Norgate"}
1128 @string{MWilmanns = "Wilmanns, Matthias"}
1129 @string{GWilson = "Wilson, Greg"}
1130 @string{PWilson = "Wilson, Paul"}
1131 @string{RKWilson = "Wilson, R. K."}
1132 @string{SWilson = "Wilson, Scott"}
1133 @string{SWindsor = "Windsor, S."}
1134 @string{EWinn-Deen = "Winn-Deen, E."}
1135 @string{NWirth = "Wirth, Niklaus"}
1136 @string{HMWisniewski = "Wisniewski, H.~M."}
1137 @string{CWitt = "Witt, Christian"}
1138 @string{KWolfe = "Wolfe, K."}
1139 @string{TGWolfsberg = "Wolfsberg, T. G."}
1140 @string{PGWolynes = "Wolynes, P. G."}
1141 @string{WPWong = "Wong, Wesley P."}
1142 @string{TWoodage = "Woodage, T."}
1143 @string{GRWoodcock = "Woodcock, Glenna R."}
1144 @string{JRWortman = "Wortman, J. R."}
1145 @string{PEWright = "Wright, Peter E."}
1146 @string{DWu = "Wu, D."}
1147 @string{GAWu = "Wu, Guohong A."}
1148 @string{JWWu = "Wu, Jong-Wuu"}
1149 @string{MWu = "Wu, M."}
1150 @string{YWu = "Wu, Yiming"}
1151 @string{GJLWuite = "Wuite, Gijs J. L."}
1152 @string{KWylie = "Wylie, K."}
1153 @string{JXi = "Xi, Jun"}
1154 @string{AXia = "Xia, A."}
1155 @string{CXiao = "Xiao, C."}
1156 @string{SXiao = "Xiao, Senbo"}
1157 @string{TYada = "Yada, T."}
1158 @string{CYan = "Yan, C."}
1159 @string{MYandell = "Yandell, M."}
1160 @string{GYang = "Yang, Guoliang"}
1161 @string{YYang = "Yang, Yao"}
1162 @string{BAYankner = "Yankner, Bruce A."}
1163 @string{AYao = "Yao, A."}
1164 @string{RYasuda = "Yaduso, Ryohei"}
1165 @string{JYe = "Ye, J."}
1166 @string{RYeh = "Yeh, Richard C."}
1167 @string{RYonescu = "Yonescu, R."}
1168 @string{SYooseph = "Yooseph, S."}
1169 @string{MYoshida = "Yoshida, Masasuke"}
1170 @string{WYu = "Yu, Weichang"}
1171 @string{JMYuan = "Yuan, Jian-Min"}
1172 @string{MYuan = "Yuan, Menglan"}
1173 @string{AZandieh = "Zandieh, A."}
1174 @string{JZaveri = "Zaveri, J."}
1175 @string{KZaveri = "Zaveri, K."}
1176 @string{MZhan = "Zhan, M."}
1177 @string{HZhang = "Zhang, H."}
1178 @string{JZhang = "Zhang, J."}
1179 @string{QZhang = "Zhang, Q."}
1180 @string{WZhang = "Zhang, W."}
1181 @string{YZhang = "Zhang, Yanjie"}
1182 @string{ZZhang = "Zhang, Zongtao"}
1183 @string{JZhao = "Zhao, Jason Ming"}
1184 @string{LZhao = "Zhao, Liming"}
1185 @string{QZhao = "Zhao, Q."}
1186 @string{SZhao = "Zhao, S."}
1187 @string{LZheng = "Zheng, L."}
1188 @string{XHZheng = "Zheng, X. H."}
1189 @string{FZhong = "Zhong, F."}
1190 @string{MZhong = "Zhong, Mingya"}
1191 @string{WZhong = "Zhong, W."}
1192 @string{HXZhou = "Zhou, Huan-Xiang"}
1193 @string{SZhu = "Zhu, S."}
1194 @string{XZhu = "Zhu, X."}
1195 @string{YJZhu = "Zhu, Ying-Jie"}
1196 @string{WZhuang = "Zhuang, Wei"}
1197 @string{JZidar = "Zidar, Jernej"}
1198 @string{JZiegler = "Ziegler, J.G."}
1199 @string{NZinder = "Zinder, N."}
1200 @string{RCZinober = "Zinober, Rebecca C."}
1201 @string{JZlatanova = "Zlatanova, Jordanka"}
1202 @string{PZou = "Zou, Peng"}
1203 @string{GZuccheri = "Zuccheri, Giampaolo"}
1204 @string{RZwanzig = "Zwanzig, R."}
1205 @string{arXiv = "arXiv"}
1206 @string{PGdeGennes = "de Gennes, P. G."}
1207 @string{PJdeJong = "de Jong, P. J."}
1208 @string{NGvanKampen = "van Kampen, N.G."}
1209 @string{NIST:SEMATECH = "{NIST/SEMATECH}"}
1210 @string{EDCola = "{\uppercase{d}}i Cola, Emanuela"}
1212 @inbook{ NIST:chi-square,
1213 crossref = {NIST:ESH},
1214 chapter = {1.3.5.15: Chi-Square Goodness-of-Fit Test},
1218 url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda35f.htm},
1221 @inbook{ NIST:gumbel,
1222 crossref = {NIST:ESH},
1223 chapter = {1.3.6.6.16: Extreme Value Type {I} Distribution},
1227 url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda366g.htm},
1231 editor = CCroarkin #" and "# PTobias,
1232 author = NIST:SEMATECH,
1233 title = {e-{H}andbook of Statistical Methods},
1236 publisher = NIST:SEMATECH,
1237 address = {Boulder, Colorado},
1238 url = {http://www.itl.nist.gov/div898/handbook/},
1239 note = {This manual was developed from seed material produced by
1243 @misc{ wikipedia:gumbel,
1244 author = "Wikipedia",
1245 title = "Gumbel distribution --- {W}ikipedia{,} The Free Encyclopedia",
1247 url = "http://en.wikipedia.org/wiki/Gumbel_distribution",
1252 title = "Statistics of Extremes",
1255 address = "New York",
1256 wtk_note = "Find and read",
1259 @misc{ wikipedia:GEV,
1260 author = "Wikipedia",
1261 title = "Generalized extreme value distribution --- {W}ikipedia{,}
1262 The Free Encyclopedia",
1264 url = "http://en.wikipedia.org/wiki/Generalized_extreme_value_distribution",
1267 @misc{ wikipedia:gompertz,
1268 author = "Wikipedia",
1269 title = "Gompertz distribution --- {W}ikipedia{,} The Free Encyclopedia",
1271 url = "http://en.wikipedia.org/wiki/Gompertz_distribution",
1274 @misc{ wikipedia:gumbel-t1,
1275 author = "Wikipedia",
1276 title = "Type-1 Gumbel distribution --- {W}ikipedia{,} The Free
1279 url = "http://en.wikipedia.org/wiki/Type-1_Gumbel_distribution",
1282 @misc{ wikipedia:gumbel-t2,
1283 author = "Wikipedia",
1284 title = "Type-2 Gumbel distribution --- {W}ikipedia{,} The Free
1287 url = "http://en.wikipedia.org/wiki/Type-2_Gumbel_distribution",
1290 @article { allemand03,
1291 author = JFAllemand #" and "# DBensimon #" and "# VCroquette,
1292 title = "Stretching {DNA} and {RNA} to probe their interactions with
1301 keywords = "DNA;DNA-Binding
1302 Proteins;Isomerases;Micromanipulation;Microscopy, Atomic Force;Nucleic
1303 Acid Conformation;Nucleotidyltransferases",
1304 abstract = "When interacting with a single stretched DNA, many proteins
1305 modify its end-to-end distance. This distance can be monitored in real
1306 time using various micromanipulation techniques that were initially
1307 used to determine the elastic properties of bare nucleic acids and
1308 their mechanically induced structural transitions. These methods are
1309 currently being applied to the study of DNA enzymes such as DNA and RNA
1310 polymerases, topoisomerases and structural proteins such as RecA. They
1311 permit the measurement of the probability distributions of the rate,
1312 processivity, on-time, affinity and efficiency for a large variety of
1313 DNA-based molecular motors."
1317 author = RAlon #" and "# EABayer #" and "# MWilchek,
1318 title = "Streptavidin contains an {RYD} sequence which mimics the {RGD}
1319 receptor domain of fibronectin",
1326 pages = "1236--1241",
1328 doi = "10.1016/0006-291X(90)90526-S",
1329 url = "http://dx.doi.org/10.1016/0006-291X(90)90526-S",
1330 keywords = "Amino Acid Sequence;Animals;Bacterial Proteins;Binding
1331 Sites;Cell Line;Cell Membrane;Cricetinae;Fibronectins;Molecular
1332 Sequence Data;Streptavidin",
1333 abstract = "Streptavidin binds at low levels and high affinity to cell
1334 surfaces, the cause of which can be traced to the occurrence of a
1335 sequence containing RYD (Arg-Tyr-Asp) in the protein molecule. This
1336 binding is enhanced in the presence of biotin. Cell-bound streptavidin
1337 can be displaced by fibronectin, as well as by RGD- and RYD-containing
1338 peptides. In addition, streptavidin can displace fibronectin from cell
1339 surfaces. The RYD sequence of streptavidin thus mimics RGD (Arg-Gly-
1340 Asp), the universal recognition domain present in fibronectin and other
1341 adhesion-related molecules. The observed adhesion to cells has no
1342 relevance to biotin-binding since the RYD sequence is not part of the
1343 biotin-binding site of streptavidin. Since the use of streptavidin in
1344 avidin-biotin technology is based on its biotin-binding properties,
1345 researchers are hereby warned against its indiscriminate use in
1346 histochemical and cytochemical studies.",
1347 note = "Biological role of streptavidin."
1350 @article { balsera97,
1351 author = MBalsera #" and "# SStepaniants #" and "# SIzrailev #" and "#
1352 YOono #" and "# KSchulten,
1353 title = "Reconstructing potential energy functions from simulated force-
1354 induced unbinding processes",
1360 pages = "1281--1287",
1362 eprint = "http://www.biophysj.org/cgi/reprint/73/3/1281.pdf",
1363 url = "http://www.biophysj.org/cgi/content/abstract/73/3/1281",
1364 keywords = "Binding Sites;Biopolymers;Kinetics;Ligands;Microscopy, Atomic
1365 Force;Models, Chemical;Molecular Conformation;Protein
1366 Conformation;Proteins;Reproducibility of Results;Stochastic
1367 Processes;Thermodynamics",
1368 abstract = "One-dimensional stochastic models demonstrate that molecular
1369 dynamics simulations of a few nanoseconds can be used to reconstruct
1370 the essential features of the binding potential of macromolecules. This
1371 can be accomplished by inducing the unbinding with the help of external
1372 forces applied to the molecules, and discounting the irreversible work
1373 performed on the system by these forces. The fluctuation-dissipation
1374 theorem sets a fundamental limit on the precision with which the
1375 binding potential can be reconstructed by this method. The uncertainty
1376 in the resulting potential is linearly proportional to the irreversible
1377 component of work performed on the system during the simulation. These
1378 results provide an a priori estimate of the energy barriers observable
1379 in molecular dynamics simulations."
1382 @article { baneyx02,
1383 author = GBaneyx #" and "# LBaugh #" and "# VVogel,
1384 title = "Supramolecular Chemistry And Self-assembly Special Feature:
1385 Fibronectin extension and unfolding within cell matrix fibrils
1386 controlled by cytoskeletal tension",
1391 pages = "5139--5143",
1392 doi = "10.1073/pnas.072650799",
1393 eprint = "http://www.pnas.org/cgi/reprint/99/8/5139.pdf",
1394 url = "http://www.pnas.org/cgi/content/abstract/99/8/5139",
1395 abstract = "Evidence is emerging that mechanical stretching can alter the
1396 functional states of proteins. Fibronectin (Fn) is a large,
1397 extracellular matrix protein that is assembled by cells into elastic
1398 fibrils and subjected to contractile forces. Assembly into fibrils
1399 coincides with expression of biological recognition sites that are
1400 buried in Fn's soluble state. To investigate how supramolecular
1401 assembly of Fn into fibrillar matrix enables cells to mechanically
1402 regulate its structure, we used fluorescence resonance energy transfer
1403 (FRET) as an indicator of Fn conformation in the fibrillar matrix of
1404 NIH 3T3 fibroblasts. Fn was randomly labeled on amine residues with
1405 donor fluorophores and site-specifically labeled on cysteine residues
1406 in modules FnIII7 and FnIII15 with acceptor fluorophores.
1407 Intramolecular FRET was correlated with known structural changes of Fn
1408 in denaturing solution, then applied in cell culture as an indicator of
1409 Fn conformation within the matrix fibrils of NIH 3T3 fibroblasts. Based
1410 on the level of FRET, Fn in many fibrils was stretched by cells so that
1411 its dimer arms were extended and at least one FnIII module unfolded.
1412 When cytoskeletal tension was disrupted using cytochalasin D, FRET
1413 increased, indicating refolding of Fn within fibrils. These results
1414 suggest that cell-generated force is required to maintain Fn in
1415 partially unfolded conformations. The results support a model of Fn
1416 fibril elasticity based on unraveling and refolding of FnIII modules.
1417 We also observed variation of FRET between and along single fibrils,
1418 indicating variation in the degree of unfolding of Fn in fibrils.
1419 Molecular mechanisms by which mechanical force can alter the structure
1420 of Fn, converting tensile forces into biochemical cues, are discussed."
1423 @article { basche01,
1424 author = TBasche #" and "# SNie #" and "# JFernandez,
1425 title = "Single molecules",
1430 pages = "10527--10528",
1431 doi = "10.1073/pnas.191365898",
1432 eprint = "http://www.pnas.org/cgi/reprint/98/19/10527.pdf",
1433 url = "http://www.pnas.org/cgi/content/abstract/98/19/10527",
1434 note = "Mini summary of single-molecule techniques and look to future.
1435 Focuses on AFM, but mentions others."
1438 @article { bechhoefer02,
1439 author = JBechhoefer #" and "# SWilson,
1440 title = "Faster, cheaper, safer optical tweezers for the undergraduate
1449 doi = "10.1119/1.1445403",
1450 url = "http://link.aip.org/link/?AJP/70/393/1",
1451 keywords = "student experiments; safety; radiation pressure; laser beam
1453 note = {Good discussion of the effect of correlation time on
1454 calibration. References work on deconvolving thermal noise from
1455 other noise\citep{cowan98}. Excellent detail on power spectrum
1456 derivation and thermal noise for extremely overdamped
1457 oscillators in Appendix A (references \citet{rief65}), except
1458 that their equation A12 is missing a factor of $1/\pi$. I
1459 pointed this out to John Bechhoefer and he confirmed the
1461 project = "Cantilever Calibration"
1464 @article{ berg-sorensen04,
1465 author = KBergSorensen #" and "# HFlyvbjerg,
1466 title = {Power spectrum analysis for optical tweezers},
1473 url = {http://rsi.aip.org/resource/1/rsinak/v75/i3/p594_s1},
1474 doi = {10.1063/1.1645654},
1476 keywords = {radiation pressure, Brownian motion, spectral analysis,
1477 dielectric bodies, measurement by laser beam, flow measurement},
1478 abstract = {The force exerted by an optical trap on a dielectric
1479 bead in a fluid is often found by fitting a Lorentzian to the
1480 power spectrum of Brownian motion of the bead in the trap. We
1481 present explicit functions of the experimental power spectrum that
1482 give the values of the parameters fitted, including error bars and
1483 correlations, for the best such $\chi^2$ fit in a given frequency
1484 range. We use these functions to determine the information
1485 content of various parts of the power spectrum, and find, at odds
1486 with lore, much information at relatively high frequencies.
1487 Applying the method to real data, we obtain perfect fits and
1488 calibrate tweezers with less than 1\% error when the trapping
1489 force is not too strong. Relatively strong traps have power
1490 spectra that cannot be fitted properly with any Lorentzian, we
1491 find. This underscores the need for better understanding of the
1492 power spectrum than the Lorentzian provides. This is achieved
1493 using old and new theory for Brownian motion in an incompressible
1494 fluid, and new results for a popular photodetection system. The
1495 trap and photodetection system are then calibrated simultaneously
1496 in a manner that makes optical tweezers a tool of precision for
1497 force spectroscopy, local viscometry, and probably other
1501 @article{ berg-sorensen05,
1502 author = KBergSorensen #" and "# HFlyvbjerg,
1503 title = {The colour of thermal noise in classical Brownian motion: a
1504 feasibility study of direct experimental observation},
1512 doi = {10.1088/1367-2630/7/1/038},
1513 url = {http://stacks.iop.org/1367-2630/7/i=1/a=038},
1514 eprint = {http://iopscience.iop.org/1367-2630/7/1/038/pdf/1367-2630_7_1_038.pdf},
1515 abstract = {One hundred years after Einstein modelled Brownian
1516 motion, a central aspect of this motion in incompressible fluids
1517 has not been verified experimentally: the thermal noise that
1518 drives the Brownian particle, is not white, as in Einstein's
1519 simple theory. It is slightly coloured, due to hydrodynamics and
1520 the fluctuation--dissipation theorem. This theoretical result from
1521 the 1970s was prompted by computer simulation results in apparent
1522 violation of Einstein's theory. We discuss how a direct
1523 experimental observation of this colour might be carried out by
1524 using optical tweezers to separate the thermal noise from the
1525 particle's dynamic response to it. Since the thermal noise is
1526 almost white, very good statistics is necessary to resolve its
1527 colour. That requires stable equipment and long recording times,
1528 possibly making this experiment one for the future only. We give
1529 results for experimental requirements and for stochastic errors as
1530 functions of experimental window and measurement time, and discuss
1531 some potential sources of systematic errors.},
1534 @article { bedard08,
1535 author = SBedard #" and "# MMGKrishna #" and "# LMayne #" and "#
1537 title = "Protein folding: Independent unrelated pathways or predetermined
1538 pathway with optional errors.",
1545 pages = "7182--7187",
1547 doi = "10.1073/pnas.0801864105",
1548 eprint = "http://www.pnas.org/content/105/20/7182.full.pdf",
1549 url = "http://www.pnas.org/content/105/20/7182.full",
1550 keywords = "Biochemistry;Guanidine;Kinetics;Micrococcal Nuclease;Models,
1551 Biological;Models, Chemical;Models, Theoretical;Protein
1552 Conformation;Protein Denaturation;Protein Folding;Protein Structure,
1553 Secondary;Proteins;Proteomics;Reproducibility of
1554 Results;Thermodynamics",
1555 abstract = "The observation of heterogeneous protein folding kinetics has
1556 been widely interpreted in terms of multiple independent unrelated
1557 pathways (IUP model), both experimentally and in theoretical
1558 calculations. However, direct structural information on folding
1559 intermediates and their properties now indicates that all of a protein
1560 population folds through essentially the same stepwise pathway,
1561 determined by cooperative native-like foldon units and the way that the
1562 foldons fit together in the native protein. It is essential to decide
1563 between these fundamentally different folding mechanisms. This article
1564 shows, contrary to previous supposition, that the heterogeneous folding
1565 kinetics observed for the staphylococcal nuclease protein (SNase) does
1566 not require alternative parallel pathways. SNase folding kinetics can
1567 be fit equally well by a single predetermined pathway that allows for
1568 optional misfolding errors, which are known to occur ubiquitously in
1569 protein folding. Structural, kinetic, and thermodynamic information for
1570 the folding intermediates and pathways of many proteins is consistent
1571 with the predetermined pathway-optional error (PPOE) model but contrary
1572 to the properties implied in IUP models."
1577 title = "Models for the specific adhesion of cells to cells",
1586 url = "http://www.jstor.org/stable/1746930",
1587 keywords = "Antigen-Antibody Reactions; Cell Adhesion; Cell Membrane;
1588 Chemistry, Physical; Electrophysiology; Enzymes; Glycoproteins;
1589 Kinetics; Ligands; Membrane Proteins; Models, Biological; Receptors,
1591 abstract = "A theoretical framework is proposed for the analysis of
1592 adhesion between cells or of cells to surfaces when the adhesion is
1593 mediated by reversible bonds between specific molecules such as antigen
1594 and antibody, lectin and carbohydrate, or enzyme and substrate. From a
1595 knowledge of the reaction rates for reactants in solution and of their
1596 diffusion constants both in solution and on membranes, it is possible
1597 to estimate reaction rates for membrane-bound reactants. Two models are
1598 developed for predicting the rate of bond formation between cells and
1599 are compared with experiments. The force required to separate two cells
1600 is shown to be greater than the expected electrical forces between
1601 cells, and of the same order of magnitude as the forces required to
1602 pull gangliosides and perhaps some integral membrane proteins out of
1603 the cell membrane.",
1604 note = "The Bell model and a fair bit of cell bonding background.",
1605 project = "sawtooth simulation"
1609 author = DBerk #" and "# EEvans,
1610 title = "Detachment of agglutinin-bonded red blood cells. {III}. Mechanical
1611 analysis for large contact areas",
1619 keywords = "Cell Adhesion;Erythrocyte Membrane;Erythrocytes;Hemagglutinatio
1620 n;Hemagglutinins;Humans;Kinetics;Mathematics;Models,
1621 Biological;Pressure",
1622 abstract = "An experimental method and analysis are introduced which
1623 provide direct quantitation of the strength of adhesive contact for
1624 large agglutinin-bonded regions between macroscopically smooth membrane
1625 capsules (e.g., red blood cells). The approach yields intrinsic
1626 properties for separation of adherent regions independent of mechanical
1627 deformation of the membrane capsules during detachment. Conceptually,
1628 the micromechanical method involves one rigid test-capsule surface (in
1629 the form of a perfect sphere) held fixed by a micropipette and a second
1630 deformable capsule maneuvered with another micropipette to force
1631 contact with the test capsule. Only the test capsule is bound with
1632 agglutinin so that the maximum number of cross-bridges can be formed
1633 without steric interference. Following formation of a large adhesion
1634 region by mechanical impingement, the deformable capsule is detached
1635 from the rigid capsule surface by progressive aspiration into the
1636 micropipette. For the particular case modeled here, the deformable
1637 capsule is assumed to be a red blood cell which is preswollen by slight
1638 osmotic hydration before the test. The caliber of the detachment
1639 pipette is chosen so that the capsule will form a smooth cylindrical
1640 ``piston'' inside the pipette as it is aspirated. Because of the high
1641 flexibility of the membrane, the capsule naturally seals against the
1642 tube wall by pressurization even though it does not adhere to the
1643 glass. This arrangement maintains perfect axial symmetry and prevents
1644 the membrane from folding or buckling. Hence, it is possible to
1645 rigorously analyze the mechanics of deformation of the cell body to
1646 obtain the crucial ``transducer'' relation between pipette suction
1647 force and the membrane tension applied directly at the perimeter of the
1648 adhesive contact. Further, the geometry of the cell throughout the
1649 detachment process is predicted which provides accurate specification
1650 of the contact angle theta c between surfaces at the perimeter of the
1651 contact. A full analysis of red cell capsules during detachment has
1652 been carried out; however, it is shown that the shear rigidity of the
1653 red cell membrane can often be neglected so that the red cell can be
1654 treated as if it were an underfilled lipid bilayer vesicle. From the
1655 analysis, the mechanical leverage factor (1-cos theta c) and the
1656 membrane tension at the contact perimeter are determined to provide a
1657 complete description of the local mechanics of membrane separation as
1658 functions of large-scale experimental variables (e.g., suction force,
1659 contact diameter, overall cell length).(ABSTRACT TRUNCATED AT 400
1664 author = RBest #" and "# SFowler #" and "# JTocaHerrera #" and "# JClarke,
1665 title = "A simple method for probing the mechanical unfolding pathway of
1666 proteins in detail",
1671 pages = "12143--12148",
1672 doi = "10.1073/pnas.192351899",
1673 eprint = "http://www.pnas.org/cgi/reprint/99/19/12143.pdf",
1674 url = "http://www.pnas.org/cgi/content/abstract/99/19/12143",
1675 abstract = "Atomic force microscopy is an exciting new single-molecule
1676 technique to add to the toolbox of protein (un)folding methods.
1677 However, detailed analysis of the unfolding of proteins on application
1678 of force has, to date, relied on protein molecular dynamics simulations
1679 or a qualitative interpretation of mutant data. Here we describe how
1680 protein engineering {Phi} value analysis can be adapted to characterize
1681 the transition states for mechanical unfolding of proteins. Single-
1682 molecule studies also have an advantage over bulk experiments, in that
1683 partial {Phi} values arising from partial structure in the transition
1684 state can be clearly distinguished from those averaged over alternate
1685 pathways. We show that unfolding rate constants derived in the standard
1686 way by using Monte Carlo simulations are not reliable because of the
1687 errors involved. However, it is possible to circumvent these problems,
1688 providing the unfolding mechanism is not changed by mutation, either by
1689 a modification of the Monte Carlo procedure or by comparing mutant and
1690 wild-type data directly. The applicability of the method is tested on
1691 simulated data sets and experimental data for mutants of titin I27.",
1692 note = "Points out order-of-magnitude errors in $k_{u0}$ estimation from
1693 fitting Monte Carlo simulations."
1697 author = RBest #" and "# GHummer,
1698 title = "Protein folding kinetics under force from molecular simulation.",
1705 pages = "3706--3707",
1707 doi = "10.1021/ja0762691",
1708 keywords = "Computer Simulation;Kinetics;Models, Chemical;Protein
1709 Folding;Stress, Mechanical;Ubiquitin",
1710 abstract = "Despite a large number of studies on the mechanical unfolding
1711 of proteins, there are still relatively few successful attempts to
1712 refold proteins in the presence of a stretching force. We explore
1713 refolding kinetics under force using simulations of a coarse-grained
1714 model of ubiquitin. The effects of force on the folding kinetics can be
1715 fitted by a one-dimensional Kramers theory of diffusive barrier
1716 crossing, resulting in physically meaningful parameters for the height
1717 and location of the folding activation barrier. By comparing parameters
1718 obtained from pulling in different directions, we find that the
1719 unfolded state plays a dominant role in the refolding kinetics. Our
1720 findings explain why refolding becomes very slow at even moderate
1721 pulling forces and suggest how it could be practically observed in
1722 experiments at higher forces."
1726 author = RBest #" and "# EPaci #" and "# GHummer #" and "# OKDudko,
1727 title = "Pulling direction as a reaction coordinate for the mechanical
1728 unfolding of single molecules.",
1735 pages = "5968--5976",
1737 doi = "10.1021/jp075955j",
1738 keywords = "Computer Simulation;Kinetics;Models, Molecular;Protein
1739 Folding;Protein Structure, Tertiary;Time Factors;Ubiquitin",
1740 abstract = "The folding and unfolding kinetics of single molecules, such as
1741 proteins or nucleic acids, can be explored by mechanical pulling
1742 experiments. Determining intrinsic kinetic information, at zero
1743 stretching force, usually requires an extrapolation by fitting a
1744 theoretical model. Here, we apply a recent theoretical approach
1745 describing molecular rupture in the presence of force to unfolding
1746 kinetic data obtained from coarse-grained simulations of ubiquitin.
1747 Unfolding rates calculated from simulations over a broad range of
1748 stretching forces, for different pulling directions, reveal a
1749 remarkable ``turnover'' from a force-independent process at low force
1750 to a force-dependent process at high force, akin to the ``roll-over''
1751 in unfolding rates sometimes seen in studies using chemical denaturant.
1752 While such a turnover in rates is unexpected in one dimension, we
1753 demonstrate that it can occur for dynamics in just two dimensions. We
1754 relate the turnover to the quality of the pulling direction as a
1755 reaction coordinate for the intrinsic folding mechanism. A novel
1756 pulling direction, designed to be the most relevant to the intrinsic
1757 folding pathway, results in the smallest turnover. Our results are in
1758 accord with protein engineering experiments and simulations which
1759 indicate that the unfolding mechanism at high force can differ from the
1760 intrinsic mechanism. The apparent similarity between extrapolated and
1761 intrinsic rates in experiments, unexpected for different unfolding
1762 barriers, can be explained if the turnover occurs at low forces."
1765 @article { borgia08,
1766 author = Borgia #" and "# Williams #" and "# Clarke,
1767 title = "Single-Molecule Studies of Protein Folding",
1775 doi = "10.1146/annurev.biochem.77.060706.093102",
1776 eprint = "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioch
1777 em.77.060706.093102",
1778 url = "http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.
1780 abstract = "Although protein-folding studies began several decades ago, it
1781 is only recently that the tools to analyze protein folding at the
1782 single-molecule level have been developed. Advances in single-molecule
1783 fluorescence and force spectroscopy techniques allow investigation of
1784 the folding and dynamics of single protein molecules, both at
1785 equilibrium and as they fold and unfold. The experiments are far from
1786 simple, however, both in execution and in interpretation of the
1787 results. In this review, we discuss some of the highlights of the work
1788 so far and concentrate on cases where comparisons with the classical
1789 experiments can be made. We conclude that, although there have been
1790 relatively few startling insights from single-molecule studies, the
1791 rapid progress that has been made suggests that these experiments have
1792 significant potential to advance our understanding of protein folding.
1793 In particular, new techniques offer the possibility to explore regions
1794 of the energy landscape that are inaccessible to classical ensemble
1795 measurements and, perhaps, to observe rare events undetectable by other
1799 @article { braverman08,
1800 author = EBraverman #" and "# RMamdani,
1801 title = "Continuous versus pulse harvesting for population models in
1802 constant and variable environment",
1806 journal = JMathBiol,
1811 doi = "10.1007/s00285-008-0169-z",
1813 "http://www.springerlink.com/content/a1m23v50201m2401/fulltext.pdf",
1814 url = "http://www.springerlink.com/content/a1m23v50201m2401/",
1815 abstract = "We consider both autonomous and nonautonomous population models
1816 subject to either impulsive or continuous harvesting. It is
1817 demonstrated in the paper that the impulsive strategy can be as good as
1818 the continuous one, but cannot outperform it. We introduce a model,
1819 where certain harm to the population is incorporated in each harvesting
1820 event, and study it for the logistic and the Gompertz laws of growth.
1821 In this case, impulsive harvesting is not only the optimal strategy but
1822 is the only possible one.",
1823 note = "An example of non-exponential Gomperz law."
1826 @article { brochard-wyart99,
1827 author = FBrochard-Wyart #" and "# ABuguin #" and "# PGdeGennes,
1828 title = "Dynamics of taut {DNA} chains",
1835 "http://www.iop.org/EJ/article/0295-5075/47/2/171/epl_47_2_171.pdf",
1836 url = "http://stacks.iop.org/0295-5075/47/171",
1837 abstract = {We discuss the dynamics of stretched DNA chains, subjected to a
1838 tension force f, in a "taut" regime where ph = flp0/kBT $>$ 1 (lp0
1839 being the unperturbed persistence length). We deal with two variables:
1840 the local transverse displacements u, and the longitudinal position of
1841 a monomer u[?]. The variables u and u[?] follow two distinct Rouse
1842 equations, with diffusion coefficients D[?] = f/e (where e is the
1843 solvent viscosity) and D[?] = 4ph1/2D[?]. We apply these ideas to a
1844 discussion of various transient regimes.},
1845 note = "Theory for weakly bending relaxation modes in WLCs and FJCs."
1848 @article { brockwell02,
1849 author = DJBrockwell #" and "# GSBeddard #" and "# JClarkson #" and "#
1850 RCZinober #" and "# AWBlake #" and "# JTrinick #" and "# PDOlmsted #"
1851 and "# DASmith #" and "# SERadford,
1852 title = "The effect of core destabilization on the mechanical resistance of
1861 doi = "10.1016/S0006-3495(02)75182-5",
1862 eprint = "http://www.biophysj.org/cgi/reprint/83/1/458.pdf",
1863 url = "http://www.biophysj.org/cgi/content/abstract/83/1/458",
1864 keywords = "Amino Acid Sequence; Dose-Response Relationship, Drug;
1865 Kinetics; Magnetic Resonance Spectroscopy; Models, Molecular; Molecular
1866 Sequence Data; Monte Carlo Method; Muscle Proteins; Mutation; Peptide
1867 Fragments; Protein Denaturation; Protein Folding; Protein Kinases;
1868 Protein Structure, Secondary; Protein Structure, Tertiary; Proteins;
1870 abstract = "It is still unclear whether mechanical unfolding probes the
1871 same pathways as chemical denaturation. To address this point, we have
1872 constructed a concatamer of five mutant I27 domains (denoted (I27)(5)*)
1873 and used it for mechanical unfolding studies. This protein consists of
1874 four copies of the mutant C47S, C63S I27 and a single copy of C63S I27.
1875 These mutations severely destabilize I27 (DeltaDeltaG(UN) = 8.7 and
1876 17.9 kJ mol(-1) for C63S I27 and C47S, C63S I27, respectively). Both
1877 mutations maintain the hydrogen bond network between the A' and G
1878 strands postulated to be the major region of mechanical resistance for
1879 I27. Measuring the speed dependence of the force required to unfold
1880 (I27)(5)* in triplicate using the atomic force microscope allowed a
1881 reliable assessment of the intrinsic unfolding rate constant of the
1882 protein to be obtained (2.0 x 10(-3) s(-1)). The rate constant of
1883 unfolding measured by chemical denaturation is over fivefold faster
1884 (1.1 x 10(-2) s(-1)), suggesting that these techniques probe different
1885 unfolding pathways. Also, by comparing the parameters obtained from the
1886 mechanical unfolding of a wild-type I27 concatamer with that of
1887 (I27)(5)*, we show that although the observed forces are considerably
1888 lower, core destabilization has little effect on determining the
1889 mechanical sensitivity of this domain."
1892 @article { brockwell03,
1893 author = DJBrockwell #" and "# EPaci #" and "# RCZinober #" and "#
1894 GSBeddard #" and "# PDOlmsted #" and "# DASmith #" and "# RNPerham #"
1896 title = "Pulling geometry defines the mechanical resistance of a beta-sheet
1906 doi = "10.1038/nsb968",
1907 eprint = "http://www.nature.com/nsmb/journal/v10/n9/pdf/nsb968.pdf",
1908 url = "http://www.nature.com/nsmb/journal/v10/n9/abs/nsb968.html",
1909 keywords = "Anisotropy;Escherichia coli;Kinetics;Models, Molecular;Monte
1910 Carlo Method;Protein Folding;Protein Structure, Secondary;Protein
1911 Structure, Tertiary;Proteins;Software;Temperature;Thermodynamics",
1912 abstract = "Proteins show diverse responses when placed under mechanical
1913 stress. The molecular origins of their differing mechanical resistance
1914 are still unclear, although the orientation of secondary structural
1915 elements relative to the applied force vector is thought to have an
1916 important function. Here, by using a method of protein immobilization
1917 that allows force to be applied to the same all-beta protein, E2lip3,
1918 in two different directions, we show that the energy landscape for
1919 mechanical unfolding is markedly anisotropic. These results, in
1920 combination with molecular dynamics (MD) simulations, reveal that the
1921 unfolding pathway depends on the pulling geometry and is associated
1922 with unfolding forces that differ by an order of magnitude. Thus, the
1923 mechanical resistance of a protein is not dictated solely by amino acid
1924 sequence, topology or unfolding rate constant, but depends critically
1925 on the direction of the applied extension.",
1926 note = "Another scaffold effect paper.",
1929 @article { brower-toland02,
1930 author = BDBrowerToland #" and "# CSmith #" and "# RYeh #" and "# JLis #"
1931 and "# CPeterson #" and "# MDWang,
1932 title = "From the Cover: Mechanical disruption of individual nucleosomes
1933 reveals a reversible multistage release of {DNA}",
1938 pages = "1960--1965",
1939 doi = "10.1073/pnas.022638399",
1940 eprint = "http://www.pnas.org/cgi/reprint/99/4/1960.pdf",
1941 url = "http://www.pnas.org/cgi/content/abstract/99/4/1960",
1942 abstract = "The dynamic structure of individual nucleosomes was examined by
1943 stretching nucleosomal arrays with a feedback-enhanced optical trap.
1944 Forced disassembly of each nucleosome occurred in three stages.
1945 Analysis of the data using a simple worm-like chain model yields 76 bp
1946 of DNA released from the histone core at low stretching force.
1947 Subsequently, 80 bp are released at higher forces in two stages: full
1948 extension of DNA with histones bound, followed by detachment of
1949 histones. When arrays were relaxed before the dissociated state was
1950 reached, nucleosomes were able to reassemble and to repeat the
1951 disassembly process. The kinetic parameters for nucleosome disassembly
1952 also have been determined."
1955 @article { bryngelson87,
1956 author = JDBryngelson #" and "# PGWolynes,
1957 title = "Spin glasses and the statistical mechanics of protein folding",
1963 pages = "7524--7528",
1965 keywords = "Kinetics; Mathematics; Models, Theoretical; Protein
1966 Conformation; Proteins; Stochastic Processes",
1967 abstract = "The theory of spin glasses was used to study a simple model of
1968 protein folding. The phase diagram of the model was calculated, and the
1969 results of dynamics calculations are briefly reported. The relation of
1970 these results to folding experiments, the relation of these hypotheses
1971 to previous protein folding theories, and the implication of these
1972 hypotheses for protein folding prediction schemes are discussed.",
1973 note = "Seminal protein folding via energy landscape paper."
1976 @article { bryngelson95,
1977 author = JDBryngelson #" and "# JNOnuchic #" and "# NDSocci #" and "#
1979 title = "Funnels, pathways, and the energy landscape of protein folding: a
1988 doi = "10.1002/prot.340210302",
1989 keywords = "Amino Acid Sequence; Chemistry, Physical; Computer Simulation;
1990 Data Interpretation, Statistical; Kinetics; Models, Chemical; Molecular
1991 Sequence Data; Protein Biosynthesis; Protein Conformation; Protein
1992 Folding; Proteins; Thermodynamics",
1993 abstract = "The understanding, and even the description of protein folding
1994 is impeded by the complexity of the process. Much of this complexity
1995 can be described and understood by taking a statistical approach to the
1996 energetics of protein conformation, that is, to the energy landscape.
1997 The statistical energy landscape approach explains when and why unique
1998 behaviors, such as specific folding pathways, occur in some proteins
1999 and more generally explains the distinction between folding processes
2000 common to all sequences and those peculiar to individual sequences.
2001 This approach also gives new, quantitative insights into the
2002 interpretation of experiments and simulations of protein folding
2003 thermodynamics and kinetics. Specifically, the picture provides simple
2004 explanations for folding as a two-state first-order phase transition,
2005 for the origin of metastable collapsed unfolded states and for the
2006 curved Arrhenius plots observed in both laboratory experiments and
2007 discrete lattice simulations. The relation of these quantitative ideas
2008 to folding pathways, to uniexponential vs. multiexponential behavior in
2009 protein folding experiments and to the effect of mutations on folding
2010 is also discussed. The success of energy landscape ideas in protein
2011 structure prediction is also described. The use of the energy landscape
2012 approach for analyzing data is illustrated with a quantitative analysis
2013 of some recent simulations, and a qualitative analysis of experiments
2014 on the folding of three proteins. The work unifies several previously
2015 proposed ideas concerning the mechanism protein folding and delimits
2016 the regions of validity of these ideas under different thermodynamic
2020 @article { bullard06,
2021 author = BBullard #" and "# TGarcia #" and "# VBenes #" and "# MLeake #"
2022 and "# WALinke #" and "# AOberhauser,
2023 title = "The molecular elasticity of the insect flight muscle proteins
2024 projectin and kettin",
2029 pages = "4451--4456",
2030 doi = "10.1073/pnas.0509016103",
2031 eprint = "http://www.pnas.org/cgi/reprint/103/12/4451.pdf",
2032 url = "http://www.pnas.org/cgi/content/abstract/103/12/4451",
2033 abstract = "Projectin and kettin are titin-like proteins mainly responsible
2034 for the high passive stiffness of insect indirect flight muscles, which
2035 is needed to generate oscillatory work during flight. Here we report
2036 the mechanical properties of kettin and projectin by single-molecule
2037 force spectroscopy. Force-extension and force-clamp curves obtained
2038 from Lethocerus projectin and Drosophila recombinant projectin or
2039 kettin fragments revealed that fibronectin type III domains in
2040 projectin are mechanically weaker (unfolding force, Fu {approx} 50-150
2041 pN) than Ig-domains (Fu {approx} 150-250 pN). Among Ig domains in
2042 Sls/kettin, the domains near the N terminus are less stable than those
2043 near the C terminus. Projectin domains refolded very fast [85% at 15
2044 s-1 (25{degrees}C)] and even under high forces (15-30 pN). Temperature
2045 affected the unfolding forces with a Q10 of 1.3, whereas the refolding
2046 speed had a Q10 of 2-3, probably reflecting the cooperative nature of
2047 the folding mechanism. High bending rigidities of projectin and kettin
2048 indicated that straightening the proteins requires low forces. Our
2049 results suggest that titin-like proteins in indirect flight muscles
2050 could function according to a folding-based-spring mechanism."
2053 @article { bustamante08,
2054 author = CBustamante,
2055 title = "In singulo Biochemistry: When Less Is More",
2061 doi = "10.1146/annurev.biochem.012108.120952",
2062 eprint = "http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.bioch
2064 url = "http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.biochem.
2066 abstract = "It has been over one-and-a-half decades since methods of
2067 single-molecule detection and manipulation were first introduced in
2068 biochemical research. Since then, the application of these methods to
2069 an expanding variety of problems has grown at a vertiginous pace. While
2070 initially many of these experiments led more to confirmatory results
2071 than to new discoveries, today single-molecule methods are often the
2072 methods of choice to establish new mechanism-based results in
2073 biochemical research. Throughout this process, improvements in the
2074 sensitivity, versatility, and both spatial and temporal resolution of
2075 these techniques has occurred hand in hand with their applications. We
2076 discuss here some of the advantages of single-molecule methods over
2077 their bulk counterparts and argue that these advantages should help
2078 establish them as essential tools in the technical arsenal of the
2082 @article { bustamante94,
2083 author = CBustamante #" and "# JFMarko #" and "# EDSiggia #" and "# SSmith,
2084 title = "Entropic elasticity of lambda-phage {DNA}",
2091 pages = "1599--1600",
2093 doi = "10.1126/science.8079175",
2094 eprint = "http://www.sciencemag.org/cgi/reprint/265/5178/1599.pdf",
2095 url = "http://www.sciencemag.org/cgi/content/abstract/265/5178/1599",
2096 keywords = "Bacteriophage lambda; DNA, Viral; Least-Squares Analysis;
2098 note = "WLC interpolation formula."
2101 @article { bustanji03,
2102 author = YBustanji #" and "# CArciola #" and "# MConti #" and "# EMandello
2103 #" and "# LMontanaro #" and "# BSamori,
2104 title = "Dynamics of the interaction between a fibronectin molecule and a
2105 living bacterium under mechanical force",
2110 pages = "13292--13297",
2111 doi = "10.1073/pnas.1735343100",
2112 eprint = "http://www.pnas.org/cgi/reprint/100/23/13292.pdf",
2113 url = "http://www.pnas.org/cgi/content/abstract/100/23/13292",
2114 abstract = "Fibronectin (Fn) is an important mediator of bacterial
2115 invasions and of persistent infections like that of Staphylococcus
2116 epidermis. Similar to many other types of cell-protein adhesion, the
2117 binding between Fn and S. epidermidis takes place under physiological
2118 shear rates. We investigated the dynamics of the interaction between
2119 individual living S. epidermidis cells and single Fn molecules under
2120 mechanical force by using the scanning force microscope. The mechanical
2121 strength of this interaction and the binding site in the Fn molecule
2122 were determined. The energy landscape of the binding/unbinding process
2123 was mapped, and the force spectrum and the association and dissociation
2124 rate constants of the binding pair were measured. The interaction
2125 between S. epidermidis cells and Fn molecules is compared with those of
2126 two other protein/ligand pairs known to mediate different dynamic
2127 states of adhesion of cells under a hydrodynamic flow: the firm
2128 adhesion mediated by biotin/avidin interactions, and the rolling
2129 adhesion, mediated by L-selectin/P-selectin glycoprotein ligand-1
2130 interactions. The inner barrier in the energy landscape of the Fn case
2131 characterizes a high-energy binding mode that can sustain larger
2132 deformations and for significantly longer times than the correspondent
2133 high-strength L-selectin/P-selectin glycoprotein ligand-1 binding mode.
2134 The association kinetics of the former interaction is much slower to
2135 settle than the latter. On this basis, the observations made at the
2136 macroscopic scale by other authors of a strong lability of the
2137 bacterial adhesions mediated by Fn under high turbulent flow are
2138 rationalized at the molecular level."
2142 author = YMartin #" and "# CCWilliams #" and "# HKWickramasinghe,
2143 title = {Atomic force microscope---force mapping and profiling on a
2151 pages = {4723--4729},
2153 issn_online = "1089-7550",
2154 doi = {10.1063/1.338807},
2155 url = {http://jap.aip.org/resource/1/japiau/v61/i10/p4723_s1},
2157 abstract = {A modified version of the atomic force microscope is
2158 introduced that enables a precise measurement of the force between
2159 a tip and a sample over a tip-sample distance range of 30--150
2160 \AA. As an application, the force signal is used to maintain the
2161 tip-sample spacing constant, so that profiling can be achieved
2162 with a spatial resolution of 50 \AA. A second scheme allows the
2163 simultaneous measurement of force and surface profile; this scheme
2164 has been used to obtain material-dependent information from
2165 surfaces of electronic materials.},
2169 author = HJButt #" and "# MJaschke,
2170 title = "Calculation of thermal noise in atomic force microscopy",
2176 doi = "10.1088/0957-4484/6/1/001",
2177 url = "http://stacks.iop.org/0957-4484/6/1",
2178 abstract = "Thermal fluctuations of the cantilever are a fundamental source
2179 of noise in atomic force microscopy. We calculated thermal noise using
2180 the equipartition theorem and considering all possible vibration modes
2181 of the cantilever. The measurable amplitude of thermal noise depends on
2182 the temperature, the spring constant K of the cantilever and on the
2183 method by which the cantilever defletion is detected. If the deflection
2184 is measured directly, e.g. with an interferometer or a scanning
2185 tunneling microscope, the thermal noise of a cantilever with a free end
2186 can be calculated from square root kT/K. If the end of the cantilever
2187 is supported by a hard surface no thermal fluctuations of the
2188 deflection are possible. If the optical lever technique is applied to
2189 measure the deflection, the thermal noise of a cantilever with a free
2190 end is square root 4kT/3K. When the cantilever is supported thermal
2191 noise decreases to square root kT/3K, but it does not vanish.",
2192 note = "Corrections to basic $kx^2 = kB T$ due to higher order modes in
2193 rectangular cantilevers.",
2194 project = "Cantilever Calibration"
2197 @article{ jaschke95,
2198 author = MJaschke #" and "# HJButt,
2199 title = {Height calibration of optical lever atomic force
2200 microscopes by simple laser interferometry},
2205 pages = {1258--1259},
2207 url = {http://rsi.aip.org/resource/1/rsinak/v66/i2/p1258_s1},
2208 doi = {10.1063/1.1146018},
2210 keywords = {atomic force microscopy;calibration;interferometry;laser
2211 beam applications;mirrors;spatial resolution},
2212 abstract = {A new and simple interferometric method for height
2213 calibration of AFM piezo scanners is presented. Except for a small
2214 mirror no additional equipment is required since the fixed
2215 wavelength of the laser diode is used as a calibration
2216 standard. The calibration is appliable in the range between
2217 several ten nm and several $\mu$m. Besides vertical calibration
2218 many problems of piezo elements like hysteresis, nonlinearity,
2219 creep, derating, etc. and their dependence on scan parameters or
2220 temperature can be investigated.},
2224 author = YCao #" and "# MBalamurali #" and "# DSharma #" and "# HLi,
2225 title = "A functional single-molecule binding assay via force spectroscopy",
2230 pages = "15677--15681",
2231 doi = "10.1073/pnas.0705367104",
2232 eprint = "http://www.pnas.org/cgi/reprint/104/40/15677.pdf",
2233 url = "http://www.pnas.org/cgi/content/abstract/104/40/15677",
2234 abstract = "Protein-ligand interactions, including protein-protein
2235 interactions, are ubiquitously essential in biological processes and
2236 also have important applications in biotechnology. A wide range of
2237 methodologies have been developed for quantitative analysis of protein-
2238 ligand interactions. However, most of them do not report direct
2239 functional/structural consequence of ligand binding. Instead they only
2240 detect the change of physical properties, such as fluorescence and
2241 refractive index, because of the colocalization of protein and ligand,
2242 and are susceptible to false positives. Thus, important information
2243 about the functional state of proteinligand complexes cannot be
2244 obtained directly. Here we report a functional single-molecule binding
2245 assay that uses force spectroscopy to directly probe the functional
2246 consequence of ligand binding and report the functional state of
2247 protein-ligand complexes. As a proof of principle, we used protein G
2248 and the Fc fragment of IgG as a model system in this study. Binding of
2249 Fc to protein G does not induce major structural changes in protein G
2250 but results in significant enhancement of its mechanical stability.
2251 Using mechanical stability of protein G as an intrinsic functional
2252 reporter, we directly distinguished and quantified Fc-bound and Fc-free
2253 forms of protein G on a single-molecule basis and accurately determined
2254 their dissociation constant. This single-molecule functional binding
2255 assay is label-free, nearly background-free, and can detect functional
2256 heterogeneity, if any, among proteinligand interactions. This
2257 methodology opens up avenues for studying protein-ligand interactions
2258 in a functional context, and we anticipate that it will find broad
2259 application in diverse protein-ligand systems."
2263 author = PCarl #" and "# CKwok #" and "# GManderson #" and "# DSpeicher #"
2265 title = "Forced unfolding modulated by disulfide bonds in the Ig domains of
2266 a cell adhesion molecule",
2271 pages = "1565--1570",
2272 doi = "10.1073/pnas.031409698",
2273 eprint = "http://www.pnas.org/cgi/reprint/98/4/1565.pdf",
2274 url = "http://www.pnas.org/cgi/content/abstract/98/4/1565",
2278 @article { carrion-vazquez00,
2279 author = MCarrionVazquez #" and "# AOberhauser #" and "# TEFisher #" and "#
2280 PMarszalek #" and "# HLi #" and "# JFernandez,
2281 title = "Mechanical design of proteins studied by single-molecule force
2282 spectroscopy and protein engineering",
2288 doi = "10.1016/S0079-6107(00)00017-1",
2290 eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302160&blo
2292 url = "http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1302160",
2293 keywords = "Elasticity;Hydrogen Bonding;Microscopy, Atomic Force;Protein
2294 Denaturation;Protein Engineering;Protein Folding;Recombinant
2295 Proteins;Signal Processing, Computer-Assisted",
2296 abstract = "Mechanical unfolding and refolding may regulate the molecular
2297 elasticity of modular proteins with mechanical functions. The
2298 development of the atomic force microscopy (AFM) has recently enabled
2299 the dynamic measurement of these processes at the single-molecule
2300 level. Protein engineering techniques allow the construction of
2301 homomeric polyproteins for the precise analysis of the mechanical
2302 unfolding of single domains. alpha-Helical domains are mechanically
2303 compliant, whereas beta-sandwich domains, particularly those that
2304 resist unfolding with backbone hydrogen bonds between strands
2305 perpendicular to the applied force, are more stable and appear
2306 frequently in proteins subject to mechanical forces. The mechanical
2307 stability of a domain seems to be determined by its hydrogen bonding
2308 pattern and is correlated with its kinetic stability rather than its
2309 thermodynamic stability. Force spectroscopy using AFM promises to
2310 elucidate the dynamic mechanical properties of a wide variety of
2311 proteins at the single molecule level and provide an important
2312 complement to other structural and dynamic techniques (e.g., X-ray
2313 crystallography, NMR spectroscopy, patch-clamp).",
2314 note = {Surface contact \fref{figure}{2} is a modified version of
2315 \xref{baljon96}{figure}{1}. They are both good pictures for
2316 explaining that the tip's radius of curvature ($\sim 20\U{nm}$) is
2317 larger than the I27 domains\citet{improta96} ($\sim 2\U{nm}$).},
2320 @article { carrion-vazquez03,
2321 author = MCarrionVazquez #" and "# HLi #" and "# HLu #" and "# PMarszalek
2322 #" and "# AOberhauser #" and "# JFernandez,
2323 title = "The mechanical stability of ubiquitin is linkage dependent",
2332 doi = "10.1038/nsb965",
2333 eprint = "http://www.nature.com/nsmb/journal/v10/n9/pdf/nsb965.pdf",
2334 url = "http://www.nature.com/nsmb/journal/v10/n9/abs/nsb965.html",
2335 keywords = "Humans;Hydrogen Bonding;Kinetics;Lysine;Microscopy, Atomic
2336 Force;Models, Molecular;Polyubiquitin;Protein Binding;Protein
2337 Folding;Protein Structure, Tertiary;Ubiquitin",
2338 abstract = "Ubiquitin chains are formed through the action of a set of
2339 enzymes that covalently link ubiquitin either through peptide bonds or
2340 through isopeptide bonds between their C terminus and any of four
2341 lysine residues. These naturally occurring polyproteins allow one to
2342 study the mechanical stability of a protein, when force is applied
2343 through different linkages. Here we used single-molecule force
2344 spectroscopy techniques to examine the mechanical stability of
2345 N-C-linked and Lys48-C-linked ubiquitin chains. We combined these
2346 experiments with steered molecular dynamics (SMD) simulations and found
2347 that the mechanical stability and unfolding pathway of ubiquitin
2348 strongly depend on the linkage through which the mechanical force is
2349 applied to the protein. Hence, a protein that is otherwise very stable
2350 may be easily unfolded by a relatively weak mechanical force applied
2351 through the right linkage. This may be a widespread mechanism in
2352 biological systems."
2355 @article { carrion-vazquez99a,
2356 author = MCarrionVazquez #" and "# PMarszalek #" and "# AOberhauser #" and
2358 title = "Atomic force microscopy captures length phenotypes in single
2364 pages = "11288--11292",
2365 doi = "10.1073/pnas.96.20.11288",
2366 eprint = "http://www.pnas.org/cgi/reprint/96/20/11288.pdf",
2367 url = "http://www.pnas.org/cgi/content/abstract/96/20/11288",
2371 @article { carrion-vazquez99b,
2372 author = MCarrionVazquez #" and "# AOberhauser #" and "# SFowler #" and "#
2373 PMarszalek #" and "# SBroedel #" and "# JClarke #" and "# JFernandez,
2374 title = "Mechanical and chemical unfolding of a single protein: A
2380 pages = "3694--3699",
2381 doi = "10.1073/pnas.96.7.3694",
2382 eprint = "http://www.pnas.org/cgi/reprint/96/7/3694.pdf",
2383 url = "http://www.pnas.org/cgi/content/abstract/96/7/3694"
2387 author = CLChyan #" and "# FCLin #" and "# HPeng #" and "# JMYuan #" and "#
2388 CHChang #" and "# SHLin #" and "# GYang,
2389 title = "Reversible mechanical unfolding of single ubiquitin molecules",
2393 address = "Department of Chemistry, National Dong Hwa University,
2398 pages = "3995--4006",
2400 doi = "10.1529/biophysj.104.042754",
2401 eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349504738643.pdf",
2402 url = "http://www.cell.com/biophysj/abstract/S0006-3495(04)73864-3",
2404 keywords = "Computer
2405 Simulation;Elasticity;Mechanics;Micromanipulation;Microscopy, Atomic
2406 Force;Models, Chemical;Models, Molecular;Protein Conformation;Protein
2407 Denaturation;Protein Folding;Stress, Mechanical;Structure-Activity
2408 Relationship;Ubiquitin",
2409 abstract = "Single-molecule manipulation techniques have enabled the
2410 characterization of the unfolding and refolding process of individual
2411 protein molecules, using mechanical forces to initiate the unfolding
2412 transition. Experimental and computational results following this
2413 approach have shed new light on the mechanisms of the mechanical
2414 functions of proteins involved in several cellular processes, as well
2415 as revealed new information on the protein folding/unfolding free-
2416 energy landscapes. To investigate how protein molecules of different
2417 folds respond to a stretching force, and to elucidate the effects of
2418 solution conditions on the mechanical stability of a protein, we
2419 synthesized polymers of the protein ubiquitin and characterized the
2420 force-induced unfolding and refolding of individual ubiquitin molecules
2421 using an atomic-force-microscope-based single-molecule manipulation
2422 technique. The ubiquitin molecule was highly resistant to a stretching
2423 force, and the mechanical unfolding process was reversible. A model
2424 calculation based on the hydrogen-bonding pattern in the native
2425 structure was performed to explain the origin of this high mechanical
2426 stability. Furthermore, pH effects were studied and it was found that
2427 the forces required to unfold the protein remained constant within a pH
2428 range around the neutral value, and forces decreased as the solution pH
2429 was lowered to more acidic values.",
2430 note = "includes pH effects",
2433 @article { ciccotti86,
2434 author = GCiccotti #" and "# JPRyckaert,
2435 title = "Molecular dynamics simulation of rigid molecules",
2442 doi = "10.1016/0167-7977(86)90022-5",
2443 url = "http://dx.doi.org/10.1016/0167-7977(86)90022-5",
2444 note = "I haven't read this, but it looks like a nice review of MD with
2448 @article { claverie01,
2449 author = JMClaverie,
2450 title = "Gene number. What if there are only 30,000 human genes?",
2457 pages = "1255--1257",
2459 url = "http://www.sciencemag.org/cgi/content/full/291/5507/1255",
2460 keywords = "Animals;Computational Biology;Drug Industry;Expressed Sequence
2461 Tags;Gene Expression;Gene Expression Regulation;Genes;Genetic
2462 Techniques;Genome, Human;Genomics;Human Genome Project;Humans;Models,
2463 Genetic;Polymorphism, Single Nucleotide;Proteins;RNA, Messenger"
2466 @misc { codata-boltzmann,
2467 key = "codata-boltzmann",
2468 crossref = "codata06",
2469 url = "http://physics.nist.gov/cgi-bin/cuu/Value?k"
2472 @article { codata06,
2473 author = PJMohr #" and "# BNTaylor #" and "# DBNewell,
2475 title = "{CODATA} recommended values of the fundamental physical constants:
2485 doi = "10.1103/RevModPhys.80.633"
2488 @article { collins03,
2489 author = FSCollins #" and "# MMorgan #" and "# APatrinos,
2490 title = "The Human Genome Project: Lessons from large-scale biology.",
2499 doi = "10.1126/science.1084564",
2500 eprint = "http://www.sciencemag.org/cgi/reprint/300/5617/286.pdf",
2501 url = "http://www.sciencemag.org/cgi/content/summary/300/5617/277",
2502 keywords = "Access to Information;Computational Biology;Databases, Nucleic
2503 Acid;Genome, Human;Genomics;Government Agencies;History, 20th
2504 Century;Human Genome Project;Humans;International Cooperation;National
2505 Institutes of Health (U.S.);Private Sector;Public Policy;Public
2506 Sector;Publishing;Quality Control;Sequence Analysis, DNA;United States",
2507 note = "See also: \href{http://www.ornl.gov/sci/techresources/Human_Genome/
2508 project/journals/journals.shtml}{Landmark HPG Papers}"
2511 @article { cornish07,
2512 author = PVCornish #" and "# THa,
2513 title = "A survey of single-molecule techniques in chemical biology",
2517 journal = ACS:ChemBiol,
2522 doi = "10.1021/cb600342a",
2523 keywords = "Animals;Data Collection;Humans;Microscopy, Atomic
2524 Force;Microscopy, Fluorescence;Molecular Biology",
2525 abstract = "Single-molecule methods have revolutionized scientific research
2526 by rendering the investigation of once-inaccessible biological
2527 processes amenable to scientific inquiry. Several of the more
2528 established techniques will be emphasized in this Review, including
2529 single-molecule fluorescence microscopy, optical tweezers, and atomic
2530 force microscopy, which have been applied to many diverse biological
2531 processes. Serving as a taste of all the exciting research currently
2532 underway, recent examples will be discussed of translocation of RNA
2533 polymerase, myosin VI walking, protein folding, and enzyme activity. We
2534 will end by providing an assessment of what the future holds, including
2535 techniques that are currently in development."
2540 title = "Statistical Data Analysis",
2543 address = "New York",
2544 note = "Noise deconvolution in Chapter 11",
2545 project = "Cantilever Calibration"
2549 author = DCraig #" and "# AKrammer #" and "# KSchulten #" and "# VVogel,
2550 title = "Comparison of the early stages of forced unfolding for fibronectin
2551 type {III} modules",
2556 pages = "5590--5595",
2557 doi = "10.1073/pnas.101582198",
2558 eprint = "http://www.pnas.org/cgi/reprint/98/10/5590.pdf",
2559 url = "http://www.pnas.org/cgi/content/abstract/98/10/5590",
2563 @article { delpech01,
2564 author = BDelpech #" and "# MNCourel #" and "# CMaingonnat #" and "#
2565 CChauzy #" and "# RSesboue #" and "# GPratesi,
2566 title = "Hyaluronan digestion and synthesis in an experimental model of
2569 month = "September/October",
2570 journal = HistochemJ,
2575 keywords = "Animals;Culture Media;Humans;Hyaluronic
2576 Acid;Hyaluronoglucosaminidase;Mice;Mice, Nude;Neoplasm
2577 Metastasis;Neoplasm Transplantation;Neoplasms, Experimental;Tumor
2579 abstract = "To approach the question of hyaluronan catabolism in tumours,
2580 we have selected the cancer cell line H460M, a highly metastatic cell
2581 line in the nude mouse. H460M cells release hyaluronidase in culture
2582 media at a high rate of 57 pU/cell/h, without producing hyaluronan.
2583 Hyaluronidase was measured in the H460M cell culture medium at the
2584 optimum pH 3.8, and was not found above pH 4.5, with the enzyme-linked
2585 sorbent assay technique and zymography. Tritiated hyaluronan was
2586 digested at pH 3.8 by cells or cell membranes as shown by gel
2587 permeation chromatography, but no activity was recorded at pH 7 with
2588 this technique. Hyaluronan was digested in culture medium by tumour
2589 slices, prepared from tumours developed in nude mice grafted with H460M
2590 cells, showing that hyaluronan could be digested in complex tissue at
2591 physiological pH. Culture of tumour slices with tritiated acetate
2592 resulted in the accumulation within 2 days of radioactive
2593 macromolecules in the culture medium. The radioactive macromolecular
2594 material was mostly digested by Streptomyces hyaluronidase, showing
2595 that hyaluronan was its main component and that hyaluronan synthesis
2596 occurred together with its digestion. These results demonstrate that
2597 the membrane-associated hyaluronidase of H460M cells can act in vivo,
2598 and that hyaluronan, which is synthesised by the tumour stroma, can be
2599 made soluble and reduced to a smaller size by tumour cells before being
2600 internalised and further digested."
2603 @article { diCola05,
2604 author = EDCola #" and "# TAWaigh #" and "# JTrinick #" and "#
2605 LTskhovrebova #" and "# AHoumeida #" and "# WPyckhout-Hintzen #" and "#
2608 title = "Persistence length of titin from rabbit skeletal muscles measured
2609 with scattering and microrheology techniques",
2616 pages = "4095--4106",
2618 doi = "10.1529/biophysj.104.054908",
2619 eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349505734603.pdf",
2620 url = "http://www.cell.com/biophysj/retrieve/pii/S0006349505734603",
2621 keywords = "Animals;Biophysics;Elasticity;Light;Muscle Proteins;Muscle,
2622 Skeletal;Neutrons;Protein Conformation;Protein
2623 Kinases;Rabbits;Rheology;Scattering, Radiation;Temperature",
2624 abstract = "The persistence length of titin from rabbit skeletal muscles
2625 was measured using a combination of static and dynamic light
2626 scattering, and neutron small angle scattering. Values of persistence
2627 length in the range 9-16 nm were found for titin-II, which corresponds
2628 to mainly physiologically inelastic A-band part of the protein, and for
2629 a proteolytic fragment with 100-nm contour length from the
2630 physiologically elastic I-band part. The ratio of the hydrodynamic
2631 radius to the static radius of gyration indicates that the proteins
2632 obey Gaussian statistics typical of a flexible polymer in a -solvent.
2633 Furthermore, measurements of the flexibility as a function of
2634 temperature demonstrate that titin-II and the I-band titin fragment
2635 experience a similar denaturation process; unfolding begins at 318 K
2636 and proceeds in two stages: an initial gradual 50\% change in
2637 persistence length is followed by a sharp unwinding transition at 338
2638 K. Complementary microrheology (video particle tracking) measurements
2639 indicate that the viscoelasticity in dilute solution behaves according
2640 to the Flory/Fox model, providing a value of the radius of gyration for
2641 titin-II (63 +/- 1 nm) in agreement with static light scattering and
2642 small angle neutron scattering results."
2646 author = HDietz #" and "# MRief,
2647 title = "Exploring the energy landscape of {GFP} by single-molecule
2648 mechanical experiments",
2653 pages = "16192--16197",
2654 doi = "10.1073/pnas.0404549101",
2655 eprint = "http://www.pnas.org/cgi/reprint/101/46/16192.pdf",
2656 url = "http://www.pnas.org/cgi/content/abstract/101/46/16192",
2657 abstract = "We use single-molecule force spectroscopy to drive
2658 single GFP molecules from the native state through their
2659 complex energy landscape into the completely unfolded
2660 state. Unlike many smaller proteins, mechanical GFP unfolding
2661 proceeds by means of two subsequent intermediate states. The
2662 transition from the native state to the first intermediate
2663 state occurs near thermal equilibrium at $\approx35\U{pN}$ and
2664 is characterized by detachment of a seven-residue N-terminal
2665 $\alpha$-helix from the beta barrel. We measure the
2666 equilibrium free energy cost associated with this transition
2667 as 22 kBT. Detachment of this small $\alpha$-helix completely
2668 destabilizes GFP thermodynamically even though the
2669 $\beta$-barrel is still intact and can bear load. Mechanical
2670 stability of the protein on the millisecond timescale,
2671 however, is determined by the activation barrier of unfolding
2672 the $\beta$-barrel out of this thermodynamically unstable
2673 intermediate state. High bandwidth, time-resolved measurements
2674 of the cantilever relaxation phase upon unfolding of the
2675 $\beta$-barrel revealed a second metastable mechanical
2676 intermediate with one complete $\beta$-strand detached from
2677 the barrel. Quantitative analysis of force distributions and
2678 lifetimes lead to a detailed picture of the complex mechanical
2679 unfolding pathway through a rough energy landscape.",
2680 note = "Towards use of Green Flourescent Protein (GFP) as an
2681 embedded force probe. Nice energy-landscape-to-one-dimension
2682 compression graphic.",
2683 project = "Energy landscape roughness"
2686 @article { dietz06a,
2687 author = HDietz #" and "# MRief,
2688 title = "Protein structure by mechanical triangulation",
2695 pages = "1244--1247",
2696 doi = "10.1073/pnas.0509217103",
2697 eprint = "http://www.pnas.org/cgi/reprint/103/5/1244.pdf",
2698 url = "http://www.pnas.org/cgi/content/abstract/103/5/1244",
2699 abstract = "Knowledge of protein structure is essential to understand
2700 protein function. High-resolution protein structure has so far been the
2701 domain of ensemble methods. Here, we develop a simple single-molecule
2702 technique to measure spatial position of selected residues within a
2703 folded and functional protein structure in solution. Construction and
2704 mechanical unfolding of cysteine-engineered polyproteins with
2705 controlled linkage topology allows measuring intramolecular distance
2706 with angstrom precision. We demonstrate the potential of this technique
2707 by determining the position of three residues in the structure of green
2708 fluorescent protein (GFP). Our results perfectly agree with the GFP
2709 crystal structure. Mechanical triangulation can find many applications
2710 where current bulk structural methods fail."
2713 @article { dietz06b,
2714 author = HDietz #" and "# FBerkemeier #" and "# MBertz #" and "# MRief,
2715 title = "Anisotropic deformation response of single protein molecules",
2722 pages = "12724--12728",
2723 doi = "10.1073/pnas.0602995103",
2724 eprint = "http://www.pnas.org/cgi/reprint/103/34/12724.pdf",
2725 url = "http://www.pnas.org/cgi/content/abstract/103/34/12724",
2726 abstract = "Single-molecule methods have given experimental access to the
2727 mechanical properties of single protein molecules. So far, access has
2728 been limited to mostly one spatial direction of force application.
2729 Here, we report single-molecule experiments that explore the mechanical
2730 properties of a folded protein structure in precisely controlled
2731 directions by applying force to selected amino acid pairs. We
2732 investigated the deformation response of GFP in five selected
2733 directions. We found fracture forces widely varying from 100 pN up to
2734 600 pN. We show that straining the GFP structure in one of the five
2735 directions induces partial fracture of the protein into a half-folded
2736 intermediate structure. From potential widths we estimated directional
2737 spring constants of the GFP structure and found values ranging from 1
2738 N/m up to 17 N/m. Our results show that classical continuum mechanics
2739 and simple mechanistic models fail to describe the complex mechanics of
2740 the GFP protein structure and offer insights into the mechanical design
2741 of protein materials."
2745 author = HDietz #" and "# MRief,
2746 title = "Detecting Molecular Fingerprints in Single Molecule Force
2747 Spectroscopy Using Pattern Recognition",
2752 pages = "5540--5542",
2754 doi = "10.1143/JJAP.46.5540",
2755 url = "http://jjap.ipap.jp/link?JJAP/46/5540/",
2756 keywords = "single molecule, protein mechanics, force spectroscopy, AFM,
2757 pattern recognition, GFP",
2758 abstract = "Single molecule force spectroscopy has given experimental
2759 access to the mechanical properties of protein molecules. Typically,
2760 less than 1% of the experimental recordings reflect true single
2761 molecule events due to abundant surface and multiple-molecule
2762 interactions. A key issue in single molecule force spectroscopy is thus
2763 to identify the characteristic mechanical `fingerprint' of a specific
2764 protein in noisy data sets. Here, we present an objective pattern
2765 recognition algorithm that is able to identify fingerprints in such
2767 note = "Automatic force curve selection. Seems a bit shoddy. Details
2771 @article{ berkemeier11,
2772 author = FBerkemeier #" and "# MBertz #" and "# SXiao #" and "#
2773 NPinotsis #" and "# MWilmanns #" and "# FGrater #" and "# MRief,
2774 title = "Fast-folding $\alpha$-helices as reversible strain absorbers
2775 in the muscle protein myomesin.",
2780 address = "Physik Department E22, Technische Universit{\"a}t
2781 M{\"u}nchen, James-Franck-Stra{\ss}e, 85748 Garching, Germany.",
2784 pages = "14139--14144",
2785 keywords = "Biomechanics",
2786 keywords = "Kinetics",
2787 keywords = "Microscopy, Atomic Force",
2788 keywords = "Molecular Dynamics Simulation",
2789 keywords = "Muscle Proteins",
2790 keywords = "Protein Folding",
2791 keywords = "Protein Multimerization",
2792 keywords = "Protein Stability",
2793 keywords = "Protein Structure, Secondary",
2794 keywords = "Protein Structure, Tertiary",
2795 keywords = "Protein Unfolding",
2796 abstract = "The highly oriented filamentous protein network of
2797 muscle constantly experiences significant mechanical load during
2798 muscle operation. The dimeric protein myomesin has been identified
2799 as an important M-band component supporting the mechanical
2800 integrity of the entire sarcomere. Recent structural studies have
2801 revealed a long $\alpha$-helical linker between the C-terminal
2802 immunoglobulin (Ig) domains My12 and My13 of myomesin. In this
2803 paper, we have used single-molecule force spectroscopy in
2804 combination with molecular dynamics simulations to characterize
2805 the mechanics of the myomesin dimer comprising immunoglobulin
2806 domains My12-My13. We find that at forces of approximately 30?pN
2807 the $\alpha$-helical linker reversibly elongates allowing the
2808 molecule to extend by more than the folded extension of a full
2809 domain. High-resolution measurements directly reveal the
2810 equilibrium folding/unfolding kinetics of the individual helix. We
2811 show that $\alpha$-helix unfolding mechanically protects the
2812 molecule homodimerization from dissociation at physiologically
2813 relevant forces. As fast and reversible molecular springs the
2814 myomesin $\alpha$-helical linkers are an essential component for
2815 the structural integrity of the M band.",
2817 doi = "10.1073/pnas.1105734108",
2818 URL = "http://www.ncbi.nlm.nih.gov/pubmed/21825161",
2823 author = KADill #" and "# HSChan,
2824 title = "From Levinthal to pathways to funnels.",
2832 doi = "10.1038/nsb0197-10",
2833 eprint = "http://www.nature.com/nsmb/journal/v4/n1/pdf/nsb0197-10.pdf",
2834 url = "http://www.nature.com/nsmb/journal/v4/n1/abs/nsb0197-10.html",
2835 keywords = "Kinetics;Models, Chemical;Protein Folding",
2836 abstract = "While the classical view of protein folding kinetics relies on
2837 phenomenological models, and regards folding intermediates in a
2838 structural way, the new view emphasizes the ensemble nature of protein
2839 conformations. Although folding has sometimes been regarded as a linear
2840 sequence of events, the new view sees folding as parallel microscopic
2841 multi-pathway diffusion-like processes. While the classical view
2842 invoked pathways to solve the problem of searching for the needle in
2843 the haystack, the pathway idea was then seen as conflicting with
2844 Anfinsen's experiments showing that folding is pathway-independent
2845 (Levinthal's paradox). In contrast, the new view sees no inherent
2846 paradox because it eliminates the pathway idea: folding can funnel to a
2847 single stable state by multiple routes in conformational space. The
2848 general energy landscape picture provides a conceptual framework for
2849 understanding both two-state and multi-state folding kinetics. Better
2850 tests of these ideas will come when new experiments become available
2851 for measuring not just averages of structural observables, but also
2852 correlations among their fluctuations. At that point we hope to learn
2853 much more about the real shapes of protein folding landscapes.",
2854 note = "Pretty folding funnel figures."
2857 @article { discher06,
2858 author = DDischer #" and "# NBhasin #" and "# CJohnson,
2859 title = "Covalent chemistry on distended proteins",
2864 pages = "7533--7534",
2865 doi = "10.1073/pnas.0602388103",
2866 eprint = "http://www.pnas.org/cgi/reprint/103/20/7533.pdf",
2867 url = "http://www.pnas.org/cgi/content/abstract/103/20/7533.pdf"
2871 author = OKDudko #" and "# AEFilippov #" and "# JKlafter #" and "# MUrbakh,
2872 title = "Beyond the conventional description of dynamic force spectroscopy
2880 pages = "11378--11381",
2882 doi = "10.1073/pnas.1534554100",
2883 eprint = "http://www.pnas.org/content/100/20/11378.full.pdf",
2884 url = "http://www.pnas.org/content/100/20/11378.abstract",
2885 keywords = "Spectrum Analysis;Temperature",
2886 abstract = "Dynamic force spectroscopy of single molecules is described by
2887 a model that predicts a distribution of rupture forces, the
2888 corresponding mean rupture force, and variance, which are all amenable
2889 to experimental tests. The distribution has a pronounced asymmetry,
2890 which has recently been observed experimentally. The mean rupture force
2891 follows a (lnV)2/3 dependence on the pulling velocity, V, and differs
2892 from earlier predictions. Interestingly, at low pulling velocities, a
2893 rebinding process is obtained whose signature is an intermittent
2894 behavior of the spring force, which delays the rupture. An extension to
2895 include conformational changes of the adhesion complex is proposed,
2896 which leads to the possibility of bimodal distributions of rupture
2901 author = OKDudko #" and "# GHummer #" and "# ASzabo,
2902 title = "Intrinsic rates and activation free energies from single-molecule
2903 pulling experiments",
2912 doi = "10.1103/PhysRevLett.96.108101",
2913 keywords = "Biophysics;Computer Simulation;Data Interpretation,
2914 Statistical;Kinetics;Micromanipulation;Models, Chemical;Models,
2915 Molecular;Molecular Conformation;Muscle Proteins;Nucleic Acid
2916 Conformation;Protein Binding;Protein Denaturation;Protein
2917 Folding;Protein Kinases;RNA;Stress, Mechanical;Thermodynamics;Time
2919 abstract = "We present a unified framework for extracting kinetic
2920 information from single-molecule pulling experiments at constant force
2921 or constant pulling speed. Our procedure provides estimates of not only
2922 (i) the intrinsic rate coefficient and (ii) the location of the
2923 transition state but also (iii) the free energy of activation. By
2924 analyzing simulated data, we show that the resulting rates of force-
2925 induced rupture are significantly more reliable than those obtained by
2926 the widely used approach based on Bell's formula. We consider the
2927 uniqueness of the extracted kinetic information and suggest guidelines
2928 to avoid over-interpretation of experiments."
2932 author = OKDudko #" and "# JMathe #" and "# ASzabo #" and "# AMeller #" and
2934 title = "Extracting kinetics from single-molecule force spectroscopy:
2935 Nanopore unzipping of {DNA} hairpins",
2942 pages = "4188--4195",
2944 doi = "10.1529/biophysj.106.102855",
2945 eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1877759&blo
2947 keywords = "Computer
2948 Simulation;DNA;Elasticity;Mechanics;Micromanipulation;Microscopy,
2949 Atomic Force;Models, Chemical;Models, Molecular;Nanostructures;Nucleic
2950 Acid Conformation;Porosity;Stress, Mechanical",
2951 abstract = "Single-molecule force experiments provide powerful new tools to
2952 explore biomolecular interactions. Here, we describe a systematic
2953 procedure for extracting kinetic information from force-spectroscopy
2954 experiments, and apply it to nanopore unzipping of individual DNA
2955 hairpins. Two types of measurements are considered: unzipping at
2956 constant voltage, and unzipping at constant voltage-ramp speeds. We
2957 perform a global maximum-likelihood analysis of the experimental data
2958 at low-to-intermediate ramp speeds. To validate the theoretical models,
2959 we compare their predictions with two independent sets of data,
2960 collected at high ramp speeds and at constant voltage, by using a
2961 quantitative relation between the two types of measurements.
2962 Microscopic approaches based on Kramers theory of diffusive barrier
2963 crossing allow us to estimate not only intrinsic rates and transition
2964 state locations, as in the widely used phenomenological approach based
2965 on Bell's formula, but also free energies of activation. The problem of
2966 extracting unique and accurate kinetic parameters of a molecular
2967 transition is discussed in light of the apparent success of the
2968 microscopic theories in reproducing the experimental data."
2972 author = OKDudko #" and "# GHummer #" and "# ASzabo,
2973 title = "Theory, analysis, and interpretation of single-molecule
2974 force spectroscopy experiments.",
2979 address = "Department of Physics and Center for Theoretical
2980 Biological Physics, University of California at San Diego, La
2981 Jolla, CA 92093, USA.
2982 dudko@physics.ucsd.edu",
2985 pages = "15755--15760",
2987 keywords = "Half-Life",
2988 keywords = "Kinetics",
2989 keywords = "Microscopy, Atomic Force",
2990 keywords = "Motion",
2991 keywords = "Nucleic Acid Conformation",
2992 keywords = "Nucleic Acid Denaturation",
2993 keywords = "Protein Folding",
2994 keywords = "Thermodynamics",
2995 abstract = "Dynamic force spectroscopy probes the kinetic and
2996 thermodynamic properties of single molecules and molecular
2997 assemblies. Here, we propose a simple procedure to extract kinetic
2998 information from such experiments. The cornerstone of our method
2999 is a transformation of the rupture-force histograms obtained at
3000 different force-loading rates into the force-dependent lifetimes
3001 measurable in constant-force experiments. To interpret the
3002 force-dependent lifetimes, we derive a generalization of Bell's
3003 formula that is formally exact within the framework of Kramers
3004 theory. This result complements the analytical expression for the
3005 lifetime that we derived previously for a class of model
3006 potentials. We illustrate our procedure by analyzing the nanopore
3007 unzipping of DNA hairpins and the unfolding of a protein attached
3008 by flexible linkers to an atomic force microscope. Our procedure
3009 to transform rupture-force histograms into the force-dependent
3010 lifetimes remains valid even when the molecular extension is a
3011 poor reaction coordinate and higher-dimensional free-energy
3012 surfaces must be considered. In this case the microscopic
3013 interpretation of the lifetimes becomes more challenging because
3014 the lifetimes can reveal richer, and even nonmonotonic, dependence
3017 doi = "10.1073/pnas.0806085105",
3018 URL = "http://www.ncbi.nlm.nih.gov/pubmed/18852468",
3024 title = "Probing the relation between force--lifetime--and chemistry in
3025 single molecular bonds",
3031 doi = "10.1146/annurev.biophys.30.1.105",
3032 url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophys.30.1.105",
3033 keywords = "Biophysics;Kinetics;Microscopy, Atomic Force;Models,
3034 Chemical;Protein Binding;Spectrum Analysis;Time Factors",
3035 abstract = "On laboratory time scales, the energy landscape of a weak bond
3036 along a dissociation pathway is fully explored through Brownian-thermal
3037 excitations, and energy barriers become encoded in a dissociation time
3038 that varies with applied force. Probed with ramps of force over an
3039 enormous range of rates (force/time), this kinetic profile is
3040 transformed into a dynamic spectrum of bond rupture force as a function
3041 of loading rate. On a logarithmic scale in loading rate, the force
3042 spectrum provides an easy-to-read map of the prominent energy barriers
3043 traversed along the force-driven pathway and exposes the differences in
3044 energy between barriers. In this way, the method of dynamic force
3045 spectroscopy (DFS) is being used to probe the complex relation between
3046 force-lifetime-and chemistry in single molecular bonds. Most important,
3047 DFS probes the inner world of molecular interactions to reveal barriers
3048 that are difficult or impossible to detect in assays of near
3049 equilibrium dissociation but that determine bond lifetime and strength
3050 under rapid detachment. To use an ultrasensitive force probe as a
3051 spectroscopic tool, we need to understand the physics of bond
3052 dissociation under force, the impact of experimental technique on the
3053 measurement of detachment force (bond strength), the consequences of
3054 complex interactions in macromolecular bonds, and effects of multiply-
3055 bonded attachments."
3058 @article { evans91a,
3059 author = EEvans #" and "# DBerk #" and "# ALeung,
3060 title = "Detachment of agglutinin-bonded red blood cells. {I}. Forces to
3061 rupture molecular-point attachments",
3069 keywords = "ABO Blood-Group System;Animals;Antibodies,
3070 Monoclonal;Erythrocyte Deformability;Erythrocyte
3071 Membrane;Erythrocytes;Glycophorin;Helix
3072 (Snails);Hemagglutinins;Humans;Immune Sera;Lectins;Mathematics;Models,
3074 abstract = "A simple micromechanical method has been developed to measure
3075 the rupture strength of a molecular-point attachment (focal bond)
3076 between two macroscopically smooth membrane capsules. In the procedure,
3077 one capsule is prepared with a low density coverage of adhesion
3078 molecules, formed as a stiff sphere, and held at fixed position by a
3079 micropipette. The second capsule without adhesion molecules is
3080 pressurized into a spherical shape with low suction by another pipette.
3081 This capsule is maneuvered to initiate point contact at the pole
3082 opposite the stiff capsule which leads to formation of a few (or even
3083 one) molecular attachments. Then, the deformable capsule is slowly
3084 withdrawn by displacement of the pipette. Analysis shows that the end-
3085 to-end extension of the capsule provides a direct measure of the force
3086 at the point contact and, therefore, the rupture strength when
3087 detachment occurs. The range for point forces accessible to this
3088 technique depends on the elastic moduli of the membrane, membrane
3089 tension, and the size of the capsule. For biological and synthetic
3090 vesicle membranes, the range of force lies between 10(-7)-10(-5) dyn
3091 (10(-12)-10(-10) N) which is 100-fold less than presently measurable by
3092 Atomic Force Microscopy! Here, the approach was used to study the
3093 forces required to rupture microscopic attachments between red blood
3094 cells formed by a monoclonal antibody to red cell membrane glycophorin,
3095 anti-A serum, and a lectin from the snail-helix pomatia. Failure of the
3096 attachments appeared to be a stochastic function of the magnitude and
3097 duration of the detachment force. We have correlated the statistical
3098 behavior observed for rupture with a random process model for failure
3099 of small numbers of molecular attachments. The surprising outcome of
3100 the measurements and analysis was that the forces deduced for short-
3101 time failure of 1-2 molecular attachments were nearly the same for all
3102 of the agglutinin, i.e., 1-2 x 10(-6) dyn. Hence, microfluorometric
3103 tests were carried out to determine if labeled agglutinins and/or
3104 labeled surface molecules were transferred between surfaces after
3105 separation of large areas of adhesive contact. The results showed that
3106 the attachments failed because receptors were extracted from the
3110 @article { evans91b,
3111 author = EEvans #" and "# DBerk #" and "# ALeung #" and "# NMohandas,
3112 title = "Detachment of agglutinin-bonded red blood cells. {II}. Mechanical
3113 energies to separate large contact areas",
3121 keywords = "Animals;Antibodies, Monoclonal;Cell Adhesion;Erythrocyte
3122 Membrane;Erythrocytes;Helix
3123 (Snails);Hemagglutination;Hemagglutinins;Humans;Immune
3124 Sera;Kinetics;Lectins;Mathematics",
3125 abstract = "As detailed in a companion paper (Berk, D., and E. Evans. 1991.
3126 Biophys. J. 59:861-872), a method was developed to quantitate the
3127 strength of adhesion between agglutinin-bonded membranes without
3128 ambiguity due to mechanical compliance of the cell body. The
3129 experimental method and analysis were formulated around controlled
3130 assembly and detachment of a pair of macroscopically smooth red blood
3131 cell surfaces. The approach provides precise measurement of the
3132 membrane tension applied at the perimeter of an adhesive contact and
3133 the contact angle theta c between membrane surfaces which defines the
3134 mechanical leverage factor (1-cos theta c) important in the definition
3135 of the work to separate a unit area of contact. Here, the method was
3136 applied to adhesion and detachment of red cells bound together by
3137 different monoclonal antibodies to red cell membrane glycophorin and
3138 the snail-helix pomatia-lectin. For these tests, one of the two red
3139 cells was chemically prefixed in the form of a smooth sphere then
3140 equilibrated with the agglutinin before the adhesion-detachment
3141 procedure. The other cell was not exposed to the agglutinin until it
3142 was forced into contact with the rigid cell surface by mechanical
3143 impingement. Large regions of agglutinin bonding were produced by
3144 impingement but no spontaneous spreading was observed beyond the forced
3145 contact. Measurements of suction force to detach the deformable cell
3146 yielded consistent behavior for all of the agglutinins: i.e., the
3147 strength of adhesion increased progressively with reduction in contact
3148 diameter throughout detachment. This tension-contact diameter behavior
3149 was not altered over a ten-fold range of separation rates. In special
3150 cases, contacts separated smoothly after critical tensions were
3151 reached; these were the highest values attained for tension. Based on
3152 measurements reported in another paper (Evans et al. 1991. Biophys. J.
3153 59:838-848) of the forces required to rupture molecular-point
3154 attachments, the density of cross-bridges was estimated with the
3155 assumption that the tension was proportional to the discrete rupture
3156 force x the number of attachments per unit length. These estimates
3157 showed that only a small fraction of agglutinin formed cross-bridges at
3158 initial assembly and increased progressively with separation. When
3159 critical tension levels were reached, it appeared that nearly all local
3160 agglutinin was involved as cross-bridges. Because one cell surface was
3161 chemically fixed, receptor accumulation was unlikely; thus, microscopic
3162 ``roughness'' and steric repulsion probably modulated formation of
3163 cross-bridges on initial contact.(ABSTRACT TRUNCATED AT 400 WORDS)"
3167 author = EEvans #" and "# KRitchie,
3168 title = "Dynamic strength of molecular adhesion bonds",
3174 pages = "1541--1555",
3176 eprint = "http://www.biophysj.org/cgi/reprint/72/4/1541.pdf",
3177 url = "http://www.biophysj.org/cgi/content/abstract/72/4/1541",
3178 keywords = "Avidin; Biotin; Chemistry, Physical; Computer Simulation;
3179 Mathematics; Monte Carlo Method; Protein Binding",
3180 abstract = "In biology, molecular linkages at, within, and beneath cell
3181 interfaces arise mainly from weak noncovalent interactions. These bonds
3182 will fail under any level of pulling force if held for sufficient time.
3183 Thus, when tested with ultrasensitive force probes, we expect cohesive
3184 material strength and strength of adhesion at interfaces to be time-
3185 and loading rate-dependent properties. To examine what can be learned
3186 from measurements of bond strength, we have extended Kramers' theory
3187 for reaction kinetics in liquids to bond dissociation under force and
3188 tested the predictions by smart Monte Carlo (Brownian dynamics)
3189 simulations of bond rupture. By definition, bond strength is the force
3190 that produces the most frequent failure in repeated tests of breakage,
3191 i.e., the peak in the distribution of rupture forces. As verified by
3192 the simulations, theory shows that bond strength progresses through
3193 three dynamic regimes of loading rate. First, bond strength emerges at
3194 a critical rate of loading (> or = 0) at which spontaneous dissociation
3195 is just frequent enough to keep the distribution peak at zero force. In
3196 the slow-loading regime immediately above the critical rate, strength
3197 grows as a weak power of loading rate and reflects initial coupling of
3198 force to the bonding potential. At higher rates, there is crossover to
3199 a fast regime in which strength continues to increase as the logarithm
3200 of the loading rate over many decades independent of the type of
3201 attraction. Finally, at ultrafast loading rates approaching the domain
3202 of molecular dynamics simulations, the bonding potential is quickly
3203 overwhelmed by the rapidly increasing force, so that only naked
3204 frictional drag on the structure remains to retard separation. Hence,
3205 to expose the energy landscape that governs bond strength, molecular
3206 adhesion forces must be examined over an enormous span of time scales.
3207 However, a significant gap exists between the time domain of force
3208 measurements in the laboratory and the extremely fast scale of
3209 molecular motions. Using results from a simulation of biotin-avidin
3210 bonds (Izrailev, S., S. Stepaniants, M. Balsera, Y. Oono, and K.
3211 Schulten. 1997. Molecular dynamics study of unbinding of the avidin-
3212 biotin complex. Biophys. J., this issue), we describe how Brownian
3213 dynamics can help bridge the gap between molecular dynamics and probe
3215 project = "sawtooth simulation"
3219 author = EEvans #" and "# KRitchie,
3220 title = "Strength of a weak bond connecting flexible polymer chains",
3226 pages = "2439--2447",
3228 eprint = "http://www.biophysj.org/cgi/reprint/76/5/2439.pdf",
3229 url = "http://www.biophysj.org/cgi/content/abstract/76/5/2439",
3230 keywords = "Animals; Biophysics; Biopolymers; Microscopy, Atomic Force;
3231 Models, Chemical; Muscle Proteins; Protein Folding; Protein Kinases;
3232 Stochastic Processes; Stress, Mechanical; Thermodynamics",
3233 abstract = "Bond dissociation under steadily rising force occurs most
3234 frequently at a time governed by the rate of loading (Evans and
3235 Ritchie, 1997 Biophys. J. 72:1541-1555). Multiplied by the loading
3236 rate, the breakage time specifies the force for most frequent failure
3237 (called bond strength) that obeys the same dependence on loading rate.
3238 The spectrum of bond strength versus log(loading rate) provides an
3239 image of the energy landscape traversed in the course of unbonding.
3240 However, when a weak bond is connected to very compliant elements like
3241 long polymers, the load applied to the bond does not rise steadily
3242 under constant pulling speed. Because of nonsteady loading, the most
3243 frequent breakage force can differ significantly from that of a bond
3244 loaded at constant rate through stiff linkages. Using generic models
3245 for wormlike and freely jointed chains, we have analyzed the kinetic
3246 process of failure for a bond loaded by pulling the polymer linkages at
3247 constant speed. We find that when linked by either type of polymer
3248 chain, a bond is likely to fail at lower force under steady separation
3249 than through stiff linkages. Quite unexpectedly, a discontinuous jump
3250 can occur in bond strength at slow separation speed in the case of long
3251 polymer linkages. We demonstrate that the predictions of strength
3252 versus log(loading rate) can rationalize conflicting results obtained
3253 recently for unfolding Ig domains along muscle titin with different
3255 note = "Develops Kramers improvement on Bell model for domain unfolding.
3256 Presents unfolding under variable loading rates. Often cited as the
3257 ``Bell--Evans'' model. They derive a unitless treatment, scaling force
3258 by $f_\beta$, time by $\tau_f$, and elasiticity by compliance
3259 $c(f)$. The appendix has relaxation time formulas for WLC and FJC
3261 project = "sawtooth simulation"
3264 @article { fernandez04,
3265 author = JFernandez #" and "# HLi,
3266 title = "Force-clamp spectroscopy monitors the folding trajectory of a
3274 pages = "1674--1678",
3276 doi = "10.1126/science.1092497",
3277 eprint = "http://www.sciencemag.org/cgi/reprint/303/5664/1674.pdf",
3278 url = "http://www.sciencemag.org/cgi/content/abstract/303/5664/1674",
3279 keywords = "Chemistry, Physical;Microscopy, Atomic Force;Physicochemical
3280 Phenomena;Polyubiquitin;Protein Conformation;Protein
3281 Denaturation;Protein Folding;Protein Structure, Secondary;Time
3283 abstract = "We used force-clamp atomic force microscopy to measure the end-
3284 to-end length of the small protein ubiquitin during its folding
3285 reaction at the single-molecule level. Ubiquitin was first unfolded and
3286 extended at a high force, then the stretching force was quenched and
3287 protein folding was observed. The folding trajectories were continuous
3288 and marked by several distinct stages. The time taken to fold was
3289 dependent on the contour length of the unfolded protein and the
3290 stretching force applied during folding. The folding collapse was
3291 marked by large fluctuations in the end-to-end length of the protein,
3292 but these fluctuations vanished upon the final folding contraction.
3293 These direct observations of the complete folding trajectory of a
3294 protein provide a benchmark to determine the physical basis of the
3299 author = JHoward #" and "# AJHudspeth,
3300 title = {Mechanical relaxation of the hair bundle mediates
3301 adaptation in mechanoelectrical transduction by the
3302 bullfrog's saccular hair cell.},
3308 pages = {3064--3068},
3310 url = {http://www.ncbi.nlm.nih.gov/pubmed/3495007},
3311 keywords = {Acclimatization},
3312 keywords = {Animals},
3313 keywords = {Electric Conductivity},
3314 keywords = {Electric Stimulation},
3315 keywords = {Hair Cells, Auditory},
3316 keywords = {Membrane Potentials},
3317 keywords = {Microelectrodes},
3318 keywords = {Physical Stimulation},
3319 keywords = {Rana catesbeiana},
3320 keywords = {Saccule and Utricle},
3321 abstract = {Mechanoelectrical transduction by hair cells of the
3322 frog's internal ear displays adaptation: the electrical response
3323 to a maintained deflection of the hair bundle declines over a
3324 period of tens of milliseconds. We investigated the role of
3325 mechanics in adaptation by measuring changes in hair-bundle
3326 stiffness following the application of force stimuli. Following
3327 step stimulation with a glass fiber, the hair bundle of a saccular
3328 hair cell initially had a stiffness of approximately equal to
3329 $1\U{mN/m}$. The stiffness then declined to a steady-state level
3330 near $0.6\U{mN/m}$ with a time course comparable to that of
3331 adaptation in the receptor current. The hair bundle may be modeled
3332 as the parallel combination of a spring, which represents the
3333 rotational stiffness of the stereocilia, and a series spring and
3334 dashpot, which respectively, represent the elastic element
3335 responsible for channel gating and the apparatus for adaptation.},
3340 author = JHoward #" and "# AJHudspeth,
3341 title = {Compliance of the Hair Bundle Associated with Gating of
3342 Mechanoelectrical Transduction Channels in the Bullfrog's Saccular
3349 doi = {10.1016/0896-6273(88)90139-0},
3350 url = {http://www.cell.com/neuron/retrieve/pii/0896627388901390},
3351 eprint = {http://download.cell.com/neuron/pdf/PII0896627388901390.pdf},
3352 note = {Initial thermal calibration paper as cited by
3353 \citet{florin95}. This is not an AFM paper, but it uses the
3354 equipartition theorem to calculate the spring constant of hair
3355 fibers by measuring their tip displacement variance. The
3356 discussion occurs in the \emph{Manufacture and Calibration of
3357 Fibers} section on pages 197--198. Actual details are scarce, but
3358 I believe this is the original source of the ``Lorentzian'' and
3359 ``10\% accuracy'' ideas that have haunted themal calibration ever
3364 author = ELFlorin #" and "# VMoy #" and "# HEGaub,
3365 title = {Adhesion forces between individual ligand-receptor pairs},
3373 doi = {10.1126/science.8153628},
3374 url = {http://www.sciencemag.org/content/264/5157/415.abstract},
3375 eprint = {http://www.sciencemag.org/content/264/5157/415.full.pdf},
3376 abstract ={The adhesion force between the tip of an atomic force
3377 microscope cantilever derivatized with avidin and agarose beads
3378 functionalized with biotin, desthiobiotin, or iminobiotin was
3379 measured. Under conditions that allowed only a limited number of
3380 molecular pairs to interact, the force required to separate tip
3381 and bead was found to be quantized in integer multiples of
3382 $160\pm20$ piconewtons for biotin and $85\pm15$ piconewtons for
3383 iminobiotin. The measured force quanta are interpreted as the
3384 unbinding forces of individual molecular pairs.},
3387 @article { florin95,
3388 author = ELFlorin #" and "# MRief #" and "# HLehmann #" and "# MLudwig #"
3389 and "# CDornmair #" and "# VMoy #" and "# HEGaub,
3390 title = "Sensing specific molecular interactions with the atomic force
3398 doi = "10.1016/0956-5663(95)99227-C",
3399 url = "http://dx.doi.org/10.1016/0956-5663(95)99227-C",
3400 abstract = "One of the unique features of the atomic force microscope (AFM)
3401 is its capacity to measure interactions between tip and sample with
3402 high sensitivity and unparal leled spatial resolution. Since the
3403 development of methods for the functionaliza tion of the tips, the
3404 versatility of the AFM has been expanded to experiments wh ere specific
3405 molecular interactions are measured. For illustration, we present m
3406 easurements of the interaction between complementary strands of DNA. A
3407 necessary prerequisite for the quantitative analysis of the interaction
3408 force is knowledg e of the spring constant of the cantilevers. Here, we
3409 compare different techniqu es that allow for the in situ measurement of
3410 the absolute value of the spring co nstant of cantilevers.",
3411 note = {Good review of calibration to 1995, with experimental
3412 comparison between resonance-shift, reference-spring, and
3413 thermal methods. They incorrectly cite \citet{hutter93} as
3414 being published in 1994.},
3415 project = "Cantilever Calibration"
3418 @article{ burnham03,
3419 author = NABurnham #" and "# XiChen #" and "# CSHodges #" and "#
3420 GAMatei #" and "# EJThoreson #" and "# CJRoberts #" and "#
3421 MCDavies #" and "# SJBTendler,
3422 title = {Comparison of calibration methods for atomic-force
3423 microscopy cantilevers},
3430 url = {http://stacks.iop.org/0957-4484/14/i=1/a=301},
3431 abstract = {The scientific community needs a rapid and reliable way
3432 of accurately determining the stiffness of atomic-force microscopy
3433 cantilevers. We have compared the experimentally determined values
3434 of stiffness for ten cantilever probes using four different
3435 methods. For rectangular silicon cantilever beams of well defined
3436 geometry, the approaches all yield values within 17\% of the
3437 manufacturer's nominal stiffness. One of the methods is new, based
3438 on the acquisition and analysis of thermal distribution functions
3439 of the oscillator's amplitude fluctuations. We evaluate this
3440 method in comparison to the three others and recommend it for its
3441 ease of use and broad applicability.},
3442 note = {Contains both the overdamped (\fref{equation}{6}) and
3443 general (\fref{equation}{8}) power spectral densities used in
3444 thermal cantilever calibration, but punts to textbooks for the
3449 author = NRForde #" and "# DIzhaky #" and "# GRWoodcock #" and "# GJLWuite
3450 #" and "# CBustamante,
3451 title = "Using mechanical force to probe the mechanism of pausing and
3452 arrest during continuous elongation by Escherichia coli {RNA}
3460 pages = "11682--11687",
3462 doi = "10.1073/pnas.142417799",
3463 eprint = "http://www.pnas.org/cgi/reprint/99/18/11682.pdf",
3464 url = "http://www.pnas.org/content/99/18/11682",
3465 keywords = "DNA-Directed RNA Polymerases;Escherichia
3466 coli;Kinetics;Transcription, Genetic",
3467 abstract = "Escherichia coli RNA polymerase translocates along the DNA
3468 discontinuously during the elongation phase of transcription, spending
3469 proportionally more time at some template positions, known as pause and
3470 arrest sites, than at others. Current models of elongation suggest that
3471 the enzyme backtracks at these locations, but the dynamics are
3472 unresolved. Here, we study the role of lateral displacement in pausing
3473 and arrest by applying force to individually transcribing molecules. We
3474 find that an assisting mechanical force does not alter the
3475 translocation rate of the enzyme, but does reduce the efficiency of
3476 both pausing and arrest. Moreover, arrested molecules cannot be rescued
3477 by force, suggesting that arrest occurs by a bipartite mechanism: the
3478 enzyme backtracks along the DNA followed by a conformational change of
3479 the ternary complex (RNA polymerase, DNA and transcript), which cannot
3480 be reversed mechanically."
3483 @article { freitag97,
3484 author = SFreitag #" and "# ILTrong #" and "# LKlumb #" and "# PSStayton #"
3486 title = "Structural studies of the streptavidin binding loop.",
3492 pages = "1157--1166",
3494 doi = "10.1002/pro.5560060604",
3495 keywords = "Allosteric Regulation;Bacterial Proteins;Binding
3496 Sites;Biotin;Crystallography, X-Ray;Hydrogen Bonding;Ligands;Models,
3497 Molecular;Molecular Conformation;Streptavidin;Tryptophan",
3498 abstract = "The streptavidin-biotin complex provides the basis for many
3499 important biotechnological applications and is an interesting model
3500 system for studying high-affinity protein-ligand interactions. We
3501 report here crystallographic studies elucidating the conformation of
3502 the flexible binding loop of streptavidin (residues 45 to 52) in the
3503 unbound and bound forms. The crystal structures of unbound streptavidin
3504 have been determined in two monoclinic crystal forms. The binding loop
3505 generally adopts an open conformation in the unbound species. In one
3506 subunit of one crystal form, the flexible loop adopts the closed
3507 conformation and an analysis of packing interactions suggests that
3508 protein-protein contacts stabilize the closed loop conformation. In the
3509 other crystal form all loops adopt an open conformation. Co-
3510 crystallization of streptavidin and biotin resulted in two additional,
3511 different crystal forms, with ligand bound in all four binding sites of
3512 the first crystal form and biotin bound in only two subunits in a
3513 second. The major change associated with binding of biotin is the
3514 closure of the surface loop incorporating residues 45 to 52. Residues
3515 49 to 52 display a 3(10) helical conformation in unbound subunits of
3516 our structures as opposed to the disordered loops observed in other
3517 structure determinations of streptavidin. In addition, the open
3518 conformation is stabilized by a beta-sheet hydrogen bond between
3519 residues 45 and 52, which cannot occur in the closed conformation. The
3520 3(10) helix is observed in nearly all unbound subunits of both the co-
3521 crystallized and ligand-free structures. An analysis of the temperature
3522 factors of the binding loop regions suggests that the mobility of the
3523 closed loops in the complexed structures is lower than in the open
3524 loops of the ligand-free structures. The two biotin bound subunits in
3525 the tetramer found in the MONO-b1 crystal form are those that
3526 contribute Trp 120 across their respective binding pockets, suggesting
3527 a structural link between these binding sites in the tetramer. However,
3528 there are no obvious signatures of binding site communication observed
3529 upon ligand binding, such as quaternary structure changes or shifts in
3530 the region of Trp 120. These studies demonstrate that while
3531 crystallographic packing interactions can stabilize both the open and
3532 closed forms of the flexible loop, in their absence the loop is open in
3533 the unbound state and closed in the presence of biotin. If present in
3534 solution, the helical structure in the open loop conformation could
3535 moderate the entropic penalty associated with biotin binding by
3536 contributing an order-to-disorder component to the loop closure.",
3537 note = "\href{http://www.rcsb.org/pdb/explore.do?structureId=1SWE}{PDB ID:
3539 \href{http://dx.doi.org/10.2210/pdb1swe/pdb}{10.2210/pdb1swe/pdb}."
3542 @article { friddle08,
3543 author = RWFriddle #" and "# PPodsiadlo #" and "# ABArtyukhin #" and "#
3545 title = "Near-Equilibrium Chemical Force Microscopy",
3550 pages = "4986--4990",
3551 doi = "10.1021/jp7095967",
3552 eprint = "http://pubs.acs.org/doi/pdf/10.1021/jp7095967",
3553 url = "http://pubs.acs.org/doi/abs/10.1021/jp7095967"
3557 author = TFujii #" and "# YLSun #" and "# KNAn #" and "# ZPLuo,
3558 title = "Mechanical properties of single hyaluronan molecules",
3566 keywords = "Biomechanics;Cross-Linking Reagents;Elasticity;Extracellular
3567 Matrix;Humans;Hyaluronic Acid;Lasers;Microspheres;Nanotechnology",
3568 abstract = "Hyaluronan (HA) is a major component of the extracellular
3569 matrix. It plays an important role in the mechanical functions of the
3570 extracellular matrix and stabilization of cells. Currently, its
3571 mechanical properties have been investigated only at the gross level.
3572 In this study, the mechanical properties of single HA molecules were
3573 directly measured with an optical tweezer technique, yielding a
3574 persistence length of 4.5 +/- 1.2 nm. This information may help us to
3575 understand the mechanical roles in the extracellular matrix
3576 infrastructure, cell attachment, and to design tissue engineering and
3577 drug delivery systems where the mechanical functions of HA are
3581 @article { ganchev08,
3582 author = DNGanchev #" and "# NJCobb #" and "# KSurewicz #" and "#
3584 title = "Nanomechanical properties of human prion protein amyloid as probed
3585 by force spectroscopy",
3592 pages = "2909--2915",
3594 doi = "10.1529/biophysj.108.133108",
3595 abstract = "Amyloids are associated with a number of protein misfolding
3596 disorders, including prion diseases. In this study, we used single-
3597 molecule force spectroscopy to characterize the nanomechanical
3598 properties and molecular structure of amyloid fibrils formed by human
3599 prion protein PrP90-231. Force-extension curves obtained by specific
3600 attachment of a gold-covered atomic force microscope tip to engineered
3601 Cys residues could be described by the worm-like chain model for
3602 entropic elasticity of a polymer chain, with the size of the N-terminal
3603 segment that could be stretched entropically depending on the tip
3604 attachment site. The data presented here provide direct information
3605 about the forces required to extract an individual monomer from the
3606 core of the PrP90-231 amyloid, and indicate that the beta-sheet core of
3607 this amyloid starts at residue approximately 164-169. The latter
3608 finding has important implications for the ongoing debate regarding the
3609 structure of PrP amyloid."
3613 author = MGao #" and "# DCraig #" and "# OLequin #" and "# ICampbell #" and
3614 "# VVogel #" and "# KSchulten,
3615 title = "Structure and functional significance of mechanically unfolded
3616 fibronectin type {III1} intermediates",
3621 pages = "14784--14789",
3622 doi = "10.1073/pnas.2334390100",
3623 eprint = "http://www.pnas.org/cgi/reprint/100/25/14784.pdf",
3624 url = "http://www.pnas.org/cgi/content/abstract/100/25/14784",
3625 abstract = "Fibronectin (FN) forms fibrillar networks coupling cells to the
3626 extracellular matrix. The formation of FN fibrils, fibrillogenesis, is
3627 a tightly regulated process involving the exposure of cryptic binding
3628 sites in individual FN type III (FN-III) repeats presumably exposed by
3629 mechanical tension. The FN-III1 module has been previously proposed to
3630 contain such cryptic sites that promote the assembly of extracellular
3631 matrix FN fibrils. We have combined NMR and steered molecular dynamics
3632 simulations to study the structure and mechanical unfolding pathway of
3633 FN-III1. This study finds that FN-III1 consists of a {beta}-sandwich
3634 structure that unfolds to a mechanically stable intermediate about four
3635 times the length of the native folded state. Considering previous
3636 experimental findings, our studies provide a structural model by which
3637 mechanical stretching of FN-III1 may induce fibrillogenesis through
3638 this partially unfolded intermediate."
3641 @article { gavrilov01,
3642 author = LAGavrilov #" and "# NSGavrilova,
3643 title = "The reliability theory of aging and longevity",
3652 doi = "10.1006/jtbi.2001.2430",
3653 keywords = "Adult;Aged;Aging;Animals;Humans;Longevity;Middle Aged;Models,
3654 Biological;Survival Rate;Systems Theory",
3655 abstract = "Reliability theory is a general theory about systems failure.
3656 It allows researchers to predict the age-related failure kinetics for a
3657 system of given architecture (reliability structure) and given
3658 reliability of its components. Reliability theory predicts that even
3659 those systems that are entirely composed of non-aging elements (with a
3660 constant failure rate) will nevertheless deteriorate (fail more often)
3661 with age, if these systems are redundant in irreplaceable elements.
3662 Aging, therefore, is a direct consequence of systems redundancy.
3663 Reliability theory also predicts the late-life mortality deceleration
3664 with subsequent leveling-off, as well as the late-life mortality
3665 plateaus, as an inevitable consequence of redundancy exhaustion at
3666 extreme old ages. The theory explains why mortality rates increase
3667 exponentially with age (the Gompertz law) in many species, by taking
3668 into account the initial flaws (defects) in newly formed systems. It
3669 also explains why organisms ``prefer'' to die according to the Gompertz
3670 law, while technical devices usually fail according to the Weibull
3671 (power) law. Theoretical conditions are specified when organisms die
3672 according to the Weibull law: organisms should be relatively free of
3673 initial flaws and defects. The theory makes it possible to find a
3674 general failure law applicable to all adult and extreme old ages, where
3675 the Gompertz and the Weibull laws are just special cases of this more
3676 general failure law. The theory explains why relative differences in
3677 mortality rates of compared populations (within a given species) vanish
3678 with age, and mortality convergence is observed due to the exhaustion
3679 of initial differences in redundancy levels. Overall, reliability
3680 theory has an amazing predictive and explanatory power with a few, very
3681 general and realistic assumptions. Therefore, reliability theory seems
3682 to be a promising approach for developing a comprehensive theory of
3683 aging and longevity integrating mathematical methods with specific
3684 biological knowledge.",
3685 note = "An example of exponential (standard) Gomperz law."
3688 @article { gergely00,
3689 author = CGergely #" and "# JCVoegel #" and "# PSchaaf #" and "# BSenger #"
3690 and "# MMaaloum #" and "# JHorber #" and "# JHemmerle,
3691 title = "Unbinding process of adsorbed proteins under external stress
3692 studied by atomic force microscopy spectroscopy",
3697 pages = "10802--10807",
3698 doi = "10.1073/pnas.180293097",
3699 eprint = "http://www.pnas.org/cgi/reprint/97/20/10802.pdf",
3700 url = "http://www.pnas.org/cgi/content/abstract/97/20/10802"
3703 @article { gompertz25,
3705 title = "On the Nature of the Function Expressive of the Law of Human
3706 Mortality, and on a New Mode of Determining the Value of Life
3715 copyright = "Copyright \copy\ 1825 The Royal Society",
3716 url = "http://www.jstor.org/stable/107756",
3718 jstor_articletype = "primary_article",
3719 jstor_formatteddate = 1825,
3720 jstor_issuetitle = ""
3725 title = {The significance of the difference between two means when
3726 the population variances are unequal},
3733 keywords = "Population",
3735 url = "http://www.jstor.org/stable/2332010",
3741 title = {The generalization of {Student's} problems when several
3742 different population variances are involved},
3749 keywords = "Population",
3751 url = "http://www.ncbi.nlm.nih.gov/pubmed/20287819",
3752 jstor_url = "http://www.jstor.org/stable/2332510",
3756 @article { granzier97,
3757 author = HLGranzier #" and "# MSKellermayer #" and "# MHelmes #" and "#
3759 title = "Titin elasticity and mechanism of passive force development in rat
3760 cardiac myocytes probed by thin-filament extraction",
3766 pages = "2043--2053",
3768 doi = "10.1016/S0006-3495(97)78234-1",
3769 url = "http://www.cell.com/biophysj/retrieve/pii/S0006349597782341",
3770 keywords = "Amino Acid Sequence;Animals;Biomechanics;Biophysical
3771 Phenomena;Biophysics;Cell Fractionation;Elasticity;Gelsolin;Microscopy,
3772 Immunoelectron;Models, Cardiovascular;Molecular Structure;Muscle
3773 Proteins;Myocardial Contraction;Myocardium;Protein
3774 Kinases;Rats;Sarcomeres",
3775 abstract = "Titin (also known as connectin) is a giant filamentous protein
3776 whose elastic properties greatly contribute to the passive force in
3777 muscle. In the sarcomere, the elastic I-band segment of titin may
3778 interact with the thin filaments, possibly affecting the molecule's
3779 elastic behavior. Indeed, several studies have indicated that
3780 interactions between titin and actin occur in vitro and may occur in
3781 the sarcomere as well. To explore the properties of titin alone, one
3782 must first eliminate the modulating effect of the thin filaments by
3783 selectively removing them. In the present work, thin filaments were
3784 selectively removed from the cardiac myocyte by using a gelsolin
3785 fragment. Partial extraction left behind approximately 100-nm-long thin
3786 filaments protruding from the Z-line, whereas the rest of the I-band
3787 became devoid of thin filaments, exposing titin. By applying a much
3788 more extensive gelsolin treatment, we also removed the remaining short
3789 thin filaments near the Z-line. After extraction, the extensibility of
3790 titin was studied by using immunoelectron microscopy, and the passive
3791 force-sarcomere length relation was determined by using mechanical
3792 techniques. Titin's regional extensibility was not detectably affected
3793 by partial thin-filament extraction. Passive force, on the other hand,
3794 was reduced at sarcomere lengths longer than approximately 2.1 microm,
3795 with a 33 +/- 9\% reduction at 2.6 microm. After a complete extraction,
3796 the slack sarcomere length was reduced to approximately 1.7 microm. The
3797 segment of titin near the Z-line, which is otherwise inextensible,
3798 collapsed toward the Z-line in sarcomeres shorter than approximately
3799 2.0 microm, but it was extended in sarcomeres longer than approximately
3800 2.3 microm. Passive force became elevated at sarcomere lengths between
3801 approximately 1.7 and approximately 2.1 microm, but was reduced at
3802 sarcomere lengths of >2.3 microm. These changes can be accounted for by
3803 modeling titin as two wormlike chains in series, one of which increases
3804 its contour length by recruitment of the titin segment near the Z-line
3805 into the elastic pool."
3808 @article { grossman05,
3809 author = CGrossman #" and "# AStout,
3810 title = "Optical Tweezers Advanced Lab",
3814 eprint = "http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf",
3815 note = {Fairly complete overdamped PSD derivation in
3816 \fref{section}{4.3}. Cites \citet{tlusty98} and
3817 \citet{bechhoefer02} for further details. However, Tlusty
3818 (listed as reference 8) doesn't contain the thermal response
3819 fn.\ derivation it was cited for. Also, the single sided PSD
3820 definition credited to reference 9 (listed as Bechhoefer)
3821 looks more like Press (listed as reference 10). I imagine
3822 Grossman and Stout mixed up their references, and meant to
3823 refer to \citet{bechhoefer02} and \citet{press92} respectively
3825 project = "Cantilever Calibration"
3828 @article { halvorsen09,
3829 author = KHalvorsen #" and "# WPWong,
3830 title = "Massively parallel single-molecule manipulation using centrifugal
3834 url = "http://arxiv.org/abs/0912.5370",
3835 abstract = {Precise manipulation of single molecules has already led to
3836 remarkable insights in physics, chemistry, biology and medicine.
3837 However, widespread adoption of single-molecule techniques has been
3838 impeded by equipment cost and the laborious nature of making
3839 measurements one molecule at a time. We have solved these issues with a
3840 new approach: massively parallel single-molecule force measurements
3841 using centrifugal force. This approach is realized in a novel
3842 instrument that we call the Centrifuge Force Microscope (CFM), in which
3843 objects in an orbiting sample are subjected to a calibration-free,
3844 macroscopically uniform force-field while their micro-to-nanoscopic
3845 motions are observed. We demonstrate high-throughput single-molecule
3846 force spectroscopy with this technique by performing thousands of
3847 rupture experiments in parallel, characterizing force-dependent
3848 unbinding kinetics of an antibody-antigen pair in minutes rather than
3849 days. Additionally, we verify the force accuracy of the instrument by
3850 measuring the well-established DNA overstretching transition at 66
3851 $\pm$ 3 pN. With significant benefits in efficiency, cost, simplicity,
3852 and versatility, "single-molecule centrifugation" has the potential to
3853 revolutionize single-molecule experimentation, and open access to a
3854 wider range of researchers and experimental systems.}
3857 @article { hanggi90,
3858 author = PHanggi #" and "# PTalkner #" and "# MBorkovec,
3859 title = "Reaction-rate theory: Fifty years after {K}ramers",
3868 doi = "10.1103/RevModPhys.62.251",
3869 eprint = "http://www.physik.uni-augsburg.de/theo1/hanggi/Papers/112.pdf",
3870 url = "http://prola.aps.org/abstract/RMP/v62/i2/p251_1",
3871 note = "\emph{The} Kramers' theory review article. See pages 268--279 for
3872 the Kramers-specific introduction.",
3873 project = "sawtooth simulation"
3876 @article { hatfield99,
3877 author = JWHatfield #" and "# SRQuake,
3878 title = "Dynamic Properties of an Extended Polymer in Solution",
3884 pages = "3548--3551",
3887 doi = "10.1103/PhysRevLett.82.3548",
3888 url = "http://link.aps.org/abstract/PRL/v82/p3548",
3889 note = "Defines WLC and FJC models, citing textbooks.",
3890 project = "sawtooth simulation"
3893 @article { heymann00,
3894 author = BHeymann #" and "# HGrubmuller,
3895 title = "Dynamic force spectroscopy of molecular adhesion bonds",
3902 pages = "6126--6129",
3904 doi = "10.1103/PhysRevLett.84.6126",
3905 eprint = "http://prola.aps.org/pdf/PRL/v84/i26/p6126_1",
3906 url = "http://prola.aps.org/abstract/PRL/v84/p6126",
3907 abstract = "Recent advances in atomic force microscopy, biomembrane force
3908 probe experiments, and optical tweezers allow one to measure the
3909 response of single molecules to mechanical stress with high precision.
3910 Such experiments, due to limited spatial resolution, typically access
3911 only one single force value in a continuous force profile that
3912 characterizes the molecular response along a reaction coordinate. We
3913 develop a theory that allows one to reconstruct force profiles from
3914 force spectra obtained from measurements at varying loading rates,
3915 without requiring increased resolution. We show that spectra obtained
3916 from measurements with different spring constants contain complementary
3920 @article { hummer01,
3921 author = GHummer #" and "# ASzabo,
3922 title = "From the Cover: Free energy reconstruction from nonequilibrium
3923 single-molecule pulling experiments",
3928 pages = "3658--3661",
3929 doi = "10.1073/pnas.071034098",
3930 eprint = "http://www.pnas.org/cgi/reprint/98/7/3658.pdf",
3931 url = "http://www.pnas.org/cgi/content/abstract/98/7/3658",
3935 @article { hummer03,
3936 author = GHummer #" and "# ASzabo,
3937 title = "Kinetics from nonequilibrium single-molecule pulling experiments",
3945 eprint = "http://www.biophysj.org/cgi/reprint/85/1/5.pdf",
3946 url = "http://www.biophysj.org/cgi/content/abstract/85/1/5",
3947 keywords = "Computer Simulation; Crystallography; Energy Transfer;
3948 Kinetics; Lasers; Micromanipulation; Microscopy, Atomic Force; Models,
3949 Molecular; Molecular Conformation; Motion; Muscle Proteins;
3950 Nanotechnology; Physical Stimulation; Protein Conformation; Protein
3951 Denaturation; Protein Folding; Protein Kinases; Stress, Mechanical",
3952 abstract = "Mechanical forces exerted by laser tweezers or atomic force
3953 microscopes can be used to drive rare transitions in single molecules,
3954 such as unfolding of a protein or dissociation of a ligand. The
3955 phenomenological description of pulling experiments based on Bell's
3956 expression for the force-induced rupture rate is found to be inadequate
3957 when tested against computer simulations of a simple microscopic model
3958 of the dynamics. We introduce a new approach of comparable complexity
3959 to extract more accurate kinetic information about the molecular events
3960 from pulling experiments. Our procedure is based on the analysis of a
3961 simple stochastic model of pulling with a harmonic spring and
3962 encompasses the phenomenological approach, reducing to it in the
3963 appropriate limit. Our approach is tested against computer simulations
3964 of a multimodule titin model with anharmonic linkers and then an
3965 illustrative application is made to the forced unfolding of I27
3966 subunits of the protein titin. Our procedure to extract kinetic
3967 information from pulling experiments is simple to implement and should
3968 prove useful in the analysis of experiments on a variety of systems.",
3970 project = "sawtooth simulation"
3973 @article { hutter05,
3975 title = "Comment on tilt of atomic force microscope cantilevers: Effect on
3976 spring constant and adhesion measurements.",
3983 pages = "2630--2632",
3985 doi = "10.1021/la047670t",
3986 note = "Tilted cantilever corrections (not needed? see Ohler/VEECO note)",
3987 project = "Cantilever Calibration"
3990 @article { hutter93,
3991 author = JHutter #" and "# JBechhoefer,
3992 title = "Calibration of atomic-force microscope tips",
3997 pages = "1868--1873",
3999 doi = "10.1063/1.1143970",
4000 url = "http://link.aip.org/link/?RSI/64/1868/1",
4001 keywords = {atomic force microscopy; calibration; quality factor; probes;
4002 resonance; silicon nitrides; mica; van der waals forces},
4003 note = {Original equipartition-based calibration method (thermal
4004 calibration), after the brief mention in \citet{howard88}.
4005 This is the first paper I've found that works out the theory
4006 in detail, although they punt to page 431 of \citet{heer72}
4007 instead of listing a formula for their ``Lorentzian''. The
4008 experimental data uses high-$Q$ cantilevers in air, and their
4009 figure 2 shows clear water-layer snap-off. There is a
4010 published erratum\citep{hutter93-erratum}.},
4011 project = "Cantilever Calibration"
4014 @article{ hutter93-erratum,
4015 author = JHutter #" and "# JBechhoefer,
4016 title = "Erratum: Calibration of atomic-force microscope tips",
4024 doi = "10.1063/1.1144449",
4025 url = "http://rsi.aip.org/resource/1/rsinak/v64/i11/p3342_s1",
4026 note = {V.~Croquette pointed out that they should calibrate the
4027 response of their optical-detection electronics.},
4028 project = "Cantilever Calibration",
4033 title = {Statistical mechanics, kinetic theory, and stochastic processes},
4036 address = {New York},
4038 isbn = {0-123-36550-3},
4039 language = {English},
4040 keywords = {Statistical mechanics.; Kinetic theory of gases.; Stochastic processes.},
4044 author = CHyeon #" and "# DThirumalai,
4045 title = "Can energy landscape roughness of proteins and {RNA} be measured
4046 by using mechanical unfolding experiments?",
4053 pages = "10249--10253",
4055 doi = "10.1073/pnas.1833310100",
4056 eprint = "http://www.pnas.org/cgi/reprint/100/18/10249.pdf",
4057 url = "http://www.pnas.org/cgi/content/abstract/100/18/10249",
4058 keywords = "Protein Folding; Proteins; RNA; Temperature; Thermodynamics",
4059 abstract = "By considering temperature effects on the mechanical unfolding
4060 rates of proteins and RNA, whose energy landscape is rugged, the
4061 question posed in the title is answered in the affirmative. Adopting a
4062 theory by Zwanzig [Zwanzig, R. (1988) Proc. Natl. Acad. Sci. USA 85,
4063 2029-2030], we show that, because of roughness characterized by an
4064 energy scale epsilon, the unfolding rate at constant force is retarded.
4065 Similarly, in nonequilibrium experiments done at constant loading
4066 rates, the most probable unfolding force increases because of energy
4067 landscape roughness. The effects are dramatic at low temperatures. Our
4068 analysis suggests that, by using temperature as a variable in
4069 mechanical unfolding experiments of proteins and RNA, the ruggedness
4070 energy scale epsilon, can be directly measured.",
4071 note = "Derives the major theory behind my thesis. The Kramers rate
4072 equation is \xref{hanggi90}{equation}{4.56c} (page 275).",
4073 project = "Energy Landscape Roughness"
4076 @article { improta96,
4077 author = SImprota #" and "# ASPolitou #" and "# APastore,
4078 title = "Immunoglobulin-like modules from titin {I}-band: Extensible
4079 components of muscle elasticity.",
4088 doi = "10.1016/S0969-2126(96)00036-6",
4089 keywords = "Amino Acid Sequence;Immunoglobulins;Magnetic Resonance
4090 Spectroscopy;Models, Molecular;Molecular Sequence Data;Molecular
4091 Structure;Muscle Proteins;Protein Kinases;Protein Structure,
4092 Secondary;Protein Structure, Tertiary;Sequence Alignment",
4093 abstract = "BACKGROUND. The giant muscle protein titin forms a filament
4094 which spans half of the sarcomere and performs, along its length, quite
4095 diverse functions. The region of titin located in the sarcomere I-band
4096 is believed to play a major role in extensibility and passive
4097 elasticity of muscle. In the I-band, the titin sequence consists mostly
4098 of repetitive motifs of tandem immunoglobulin-like (Ig) modules
4099 intercalated by a potentially non-globular region. The highly
4100 repetitive titin architecture suggests that the molecular basis of its
4101 mechanical properties be approached through the characterization of the
4102 isolated components of the I-band and their interfaces. In the present
4103 paper, we report on the structure determination in solution of a
4104 representative Ig module from the I-band (I27) as solved by NMR
4105 techniques. RESULTS. The structure of I27 consists of a beta sandwich
4106 formed by two four-stranded sheets (named ABED and A'GFC). This fold
4107 belongs to the intermediate frame (I frame) of the immunoglobulin
4108 superfamily. Comparison of I27 with another titin module from the
4109 region located in the M-line (M5) shows that two loops (between the B
4110 and C and the F and G strands) are shorter in I27, conferring a less
4111 elongated appearance to this structure. Such a feature is specific to
4112 the Ig domains in the I-band and might therefore be related to the
4113 functions of the protein in this region. The structure of tandem Ig
4114 domains as modeled from I27 suggests the presence of hinge regions
4115 connecting contiguous modules. CONCLUSIONS. We suggest that titin Ig
4116 domains in the I-band function as extensible components of muscle
4117 elasticity by stretching the hinge regions.",
4118 note = "\href{http://www.rcsb.org/pdb/explore.do?structureId=1TIT}{PDB ID:
4120 \href{http://dx.doi.org/10.2210/pdb1tit/pdb}{10.2210/pdb1tit/pdb}."
4123 @article { irback05,
4124 author = AIrback #" and "# SMitternacht #" and "# SMohanty,
4125 title = "Dissecting the mechanical unfolding of ubiquitin",
4130 pages = "13427--13432",
4131 doi = "10.1073/pnas.0501581102",
4132 eprint = "http://www.pnas.org/cgi/reprint/102/38/13427.pdf",
4133 url = "http://www.pnas.org/cgi/content/abstract/102/38/13427",
4134 abstract = "The unfolding behavior of ubiquitin under the influence of a
4135 stretching force recently was investigated experimentally by single-
4136 molecule constant-force methods. Many observed unfolding traces had a
4137 simple two-state character, whereas others showed clear evidence of
4138 intermediate states. Here, we use Monte Carlo simulations to
4139 investigate the force-induced unfolding of ubiquitin at the atomic
4140 level. In agreement with experimental data, we find that the unfolding
4141 process can occur either in a single step or through intermediate
4142 states. In addition to this randomness, we find that many quantities,
4143 such as the frequency of occurrence of intermediates, show a clear
4144 systematic dependence on the strength of the applied force. Despite
4145 this diversity, one common feature can be identified in the simulated
4146 unfolding events, which is the order in which the secondary-structure
4147 elements break. This order is the same in two- and three-state events
4148 and at the different forces studied. The observed order remains to be
4149 verified experimentally but appears physically reasonable."
4152 @article{ grubmuller96,
4153 author = HGrubmuller #" and "# BHeymann #" and "# PTavan,
4154 title = {Ligand binding: molecular mechanics calculation of the
4155 streptavidin-biotin rupture force.},
4159 address = {Theoretische Biophysik, Institut f{\"u}r Medizinische
4160 Optik, Ludwig- Maximilians-Universit{\"a}t M{\"u}nchen,
4161 Germany. Helmut.Grubmueller@ Physik.uni-muenchen.de},
4167 url = {http://www.ncbi.nlm.nih.gov/pubmed/8584939},
4168 eprint = {http://pubman.mpdl.mpg.de/pubman/item/escidoc:1690312:2/component/escidoc:1690313/1690312.pdf},
4170 keywords = {Bacterial Proteins},
4171 keywords = {Biotin},
4172 keywords = {Chemistry, Physical},
4173 keywords = {Computer Simulation},
4174 keywords = {Hydrogen Bonding},
4175 keywords = {Ligands},
4176 keywords = {Microscopy, Atomic Force},
4177 keywords = {Models, Chemical},
4178 keywords = {Molecular Conformation},
4179 keywords = {Physicochemical Phenomena},
4180 keywords = {Protein Conformation},
4181 keywords = {Streptavidin},
4182 keywords = {Thermodynamics},
4183 abstract = {The force required to rupture the streptavidin-biotin
4184 complex was calculated here by computer simulations.
4185 The computed force agrees well with that obtained by
4186 recent single molecule atomic force microscope
4187 experiments. These simulations suggest a detailed
4188 multiple-pathway rupture mechanism involving five major
4189 unbinding steps. Binding forces and specificity are
4190 attributed to a hydrogen bond network between the
4191 biotin ligand and residues within the binding pocket of
4192 streptavidin. During rupture, additional water bridges
4193 substantially enhance the stability of the complex and
4194 even dominate the binding interactions. In contrast,
4195 steric restraints do not appear to contribute to the
4196 binding forces, although conformational motions were
4201 @article { izrailev97,
4202 author = SIzrailev #" and "# SStepaniants #" and "# MBalsera #" and "#
4203 YOono #" and "# KSchulten,
4204 title = "Molecular dynamics study of unbinding of the avidin-biotin
4211 pages = "1568--1581",
4213 eprint = "http://www.biophysj.org/cgi/reprint/72/4/1568.pdf",
4214 url = "http://www.biophysj.org/cgi/content/abstract/72/4/1568",
4215 keywords = "Avidin;Binding Sites;Biotin;Computer Simulation;Hydrogen
4216 Bonding;Mathematics;Microscopy, Atomic Force;Microspheres;Models,
4217 Molecular;Molecular Structure;Protein Binding;Protein
4218 Conformation;Protein Folding;Sepharose",
4219 abstract = "We report molecular dynamics simulations that induce, over
4220 periods of 40-500 ps, the unbinding of biotin from avidin by means of
4221 external harmonic forces with force constants close to those of AFM
4222 cantilevers. The applied forces are sufficiently large to reduce the
4223 overall binding energy enough to yield unbinding within the measurement
4224 time. Our study complements earlier work on biotin-streptavidin that
4225 employed a much larger harmonic force constant. The simulations reveal
4226 a variety of unbinding pathways, the role of key residues contributing
4227 to adhesion as well as the spatial range over which avidin binds
4228 biotin. In contrast to the previous studies, the calculated rupture
4229 forces exceed by far those observed. We demonstrate, in the framework
4230 of models expressed in terms of one-dimensional Langevin equations with
4231 a schematic binding potential, the associated Smoluchowski equations,
4232 and the theory of first passage times, that picosecond to nanosecond
4233 simulation of ligand unbinding requires such strong forces that the
4234 resulting protein-ligand motion proceeds far from the thermally
4235 activated regime of millisecond AFM experiments, and that simulated
4236 unbinding cannot be readily extrapolated to the experimentally observed
4240 @article { janshoff00,
4241 author = AJanshoff #" and "# MNeitzert #" and "# YOberdorfer #" and "#
4243 title = "Force Spectroscopy of Molecular Systems-Single Molecule
4244 Spectroscopy of Polymers and Biomolecules.",
4251 pages = "3212--3237",
4253 doi = "10.1002/1521-3773(20000915)39:18<3212::AID-ANIE3212>3.0.CO;2-X",
4255 url = "http://dx.doi.org/10.1002/1521-3773(20000915)39:18<3212::AID-ANIE3212>3.0.CO;2-X",
4256 abstract = "How do molecules interact with each other? What happens if a
4257 neurotransmitter binds to a ligand-operated ion channel? How do
4258 antibodies recognize their antigens? Molecular recognition events play
4259 a pivotal role in nature: in enzymatic catalysis and during the
4260 replication and transcription of the genome; it is also important for
4261 the cohesion of cellular structures and in numerous metabolic reactions
4262 that molecules interact with each other in a specific manner.
4263 Conventional methods such as calorimetry provide very precise values of
4264 binding enthalpies; these are, however, average values obtained from a
4265 large ensemble of molecules without knowledge of the dynamics of the
4266 molecular recognition event. Which forces occur when a single molecular
4267 couple meets and forms a bond? Since the development of the scanning
4268 force microscope and force spectroscopy a couple of years ago, tools
4269 have now become available for measuring the forces between interfaces
4270 with high precision-starting from colloidal forces to the interaction
4271 of single molecules. The manipulation of individual molecules using
4272 force spectroscopy is also possible. In this way, the mechanical
4273 properties on a molecular scale are measurable. The study of single
4274 molecules is not an exclusive domain of force spectroscopy; it can also
4275 be performed with a surface force apparatus, laser tweezers, or the
4276 micropipette technique. Regardless of these techniques, force
4277 spectroscopy has been proven as an extraordinary versatile tool. The
4278 intention of this review article is to present a critical evaluation of
4279 the actual development of static force spectroscopy. The article mainly
4280 focuses on experiments dealing with inter- and intramolecular forces-
4281 starting with ``simple'' electrostatic forces, then ligand-receptor
4282 systems, and finally the stretching of individual molecules."
4285 @article { jollymore09,
4286 author = AJollymore #" and "# CLethias #" and "# QPeng #" and "# YCao #"
4288 title = "Nanomechanical properties of tenascin-{X} revealed by single-
4289 molecule force spectroscopy",
4296 pages = "1277--1286",
4298 doi = "10.1016/j.jmb.2008.11.038",
4299 url = "http://dx.doi.org/10.1016/j.jmb.2008.11.038",
4300 keywords = "Animals;Biomechanics;Cattle;Fibronectins;Kinetics;Microscopy,
4301 Atomic Force;Protein Folding;Protein Structure, Tertiary;Spectrum
4303 abstract = "Tenascin-X is an extracellular matrix protein and binds a
4304 variety of molecules in extracellular matrix and on cell membrane.
4305 Tenascin-X plays important roles in regulating the structure and
4306 mechanical properties of connective tissues. Using single-molecule
4307 atomic force microscopy, we have investigated the mechanical properties
4308 of bovine tenascin-X in detail. Our results indicated that tenascin-X
4309 is an elastic protein and the fibronectin type III (FnIII) domains can
4310 unfold under a stretching force and refold to regain their mechanical
4311 stability upon the removal of the stretching force. All the 30 FnIII
4312 domains of tenascin-X show similar mechanical stability, mechanical
4313 unfolding kinetics, and contour length increment upon domain unfolding,
4314 despite their large sequence diversity. In contrast to the homogeneity
4315 in their mechanical unfolding behaviors, FnIII domains fold at
4316 different rates. Using the 10th FnIII domain of tenascin-X (TNXfn10) as
4317 a model system, we constructed a polyprotein chimera composed of
4318 alternating TNXfn10 and GB1 domains and used atomic force microscopy to
4319 confirm that the mechanical properties of TNXfn10 are consistent with
4320 those of the FnIII domains of tenascin-X. These results lay the
4321 foundation to further study the mechanical properties of individual
4322 FnIII domains and establish the relationship between point mutations
4323 and mechanical phenotypic effect on tenascin-X. Moreover, our results
4324 provided the opportunity to compare the mechanical properties and
4325 design of different forms of tenascins. The comparison between
4326 tenascin-X and tenascin-C revealed interesting common as well as
4327 distinguishing features for mechanical unfolding and folding of
4328 tenascin-C and tenascin-X and will open up new avenues to investigate
4329 the mechanical functions and architectural design of different forms of
4334 author = REJones #" and "# DPHart,
4335 title = "Force interactions between substrates and {SPM} cantilevers
4336 immersed in fluids",
4343 doi = "10.1016/j.triboint.2004.08.016",
4344 url = "http://dx.doi.org/10.1016/j.triboint.2004.08.016",
4345 keywords = "AFM;Liquid;Hydrodynamic;Lubrication",
4346 abstract = "With the availability of equipment used in Scanning Probe
4347 Microscopy (SPM), researchers have been able to probe the local fluid-
4348 substrate force interactions with resolutions of pN using a variety of
4349 SPM cantilevers. When using such methods, it is essential to
4350 differentiate between contributions to the net force on the cantilever.
4351 Specifically, the interaction between the cantilever, substrate and
4352 fluid, quantified while generating force curves, are discussed and
4353 compared with theoretical models for squeeze-film effects and drag on
4354 the SPM cantilevers. In addition we have demonstrated a simple method
4355 for utilizing the system as a micro-viscometer, independently measuring
4356 the viscosity of the lubricant for each test."
4359 @article { juckett93,
4360 author = DAJuckett #" and "# BRosenberg,
4361 title = "Comparison of the {G}ompertz and {W}eibull functions as
4362 descriptors for human mortality distributions and their intersections",
4370 doi = "10.1016/0047-6374(93)90068-3",
4371 keywords = "Adolescent;Adult;Aged;Aged, 80 and
4372 over;Aging;Biometry;Child;Child, Preschool;Data Interpretation,
4373 Statistical;Female;Humans;Infant;Infant, Newborn;Longitudinal
4374 Studies;Male;Middle Aged;Models, Biological;Models,
4375 Statistical;Mortality",
4376 abstract = "The Gompertz and Weibull functions are compared with respect to
4377 goodness-of-fit to human mortality distributions; ability to describe
4378 mortality curve intersections; and, parameter interpretation. The
4379 Gompertz function is shown to be a better descriptor for 'all-causes'
4380 of deaths and combined disease categories while the Weibull function is
4381 shown to be a better descriptor of purer, single causes-of-death. A
4382 modified form of the Weibull function maps directly to the inherent
4383 degrees of freedom of human mortality distributions while the Gompertz
4384 function does not. Intersections in the old-age tails of mortality are
4385 explored in the context of both functions and, in particular, the
4386 relationship between distribution intersections, and the Gompertz
4387 ln[R0] versus alpha regression is examined. Evidence is also presented
4388 that mortality intersections are fundamental to the survivorship form
4389 and not the rate (hazard) form. Finally, comparisons are made to the
4390 parameter estimates in recent longitudinal Gompertzian analyses and the
4391 probable errors in those analyses are discussed.",
4392 note = "Nice table of various functions associated with Gompertz and
4396 @article { kaplan58,
4397 author = ELKaplan #" and "# PMeier,
4398 title = "Nonparametric Estimation from Incomplete Observations",
4407 copyright = "Copyright \copy\ 1958 American Statistical Association",
4408 url = "http://www.jstor.org/stable/2281868",
4412 @article { kellermayer03,
4413 author = MSKellermayer #" and "# CBustamante #" and "# HLGranzier,
4414 title = "Mechanics and structure of titin oligomers explored with atomic
4422 doi = "10.1016/S0005-2728(03)00029-X",
4423 url = "http://dx.doi.org/10.1016/S0005-2728(03)00029-X",
4424 keywords = "Titin;Wormlike chain;Unfolding;Elasticity;AFM;Molecular force
4426 abstract = "Titin is a giant polypeptide that spans half of the striated
4427 muscle sarcomere and generates passive force upon stretch. To explore
4428 the elastic response and structure of single molecules and oligomers of
4429 titin, we carried out molecular force spectroscopy and atomic force
4430 microscopy (AFM) on purified full-length skeletal-muscle titin. From
4431 the force data, apparent persistence lengths as long as ~1.5 nm were
4432 obtained for the single, unfolded titin molecule. Furthermore, data
4433 suggest that titin molecules may globally associate into oligomers
4434 which mechanically behave as independent wormlike chains (WLCs).
4435 Consistent with this, AFM of surface-adsorbed titin molecules revealed
4436 the presence of oligomers. Although oligomers may form globally via
4437 head-to-head association of titin, the constituent molecules otherwise
4438 appear independent from each other along their contour. Based on the
4439 global association but local independence of titin molecules, we
4440 discuss a mechanical model of the sarcomere in which titin molecules
4441 with different contour lengths, corresponding to different isoforms,
4442 are held in a lattice. The net force response of aligned titin
4443 molecules is determined by the persistence length of the tandemly
4444 arranged, different WLC components of the individual molecules, the
4445 ratio of their overall contour lengths, and by domain unfolding events.
4446 Biased domain unfolding in mechanically selected constituent molecules
4447 may serve as a compensatory mechanism for contour- and persistence-
4448 length differences. Variation in the ratio and contour length of the
4449 component chains may provide mechanisms for the fine-tuning of the
4450 sarcomeric passive force response.",
4454 @article { kellermayer97,
4455 author = MSKellermayer #" and "# SBSmith #" and "# HLGranzier #" and "#
4457 title = "Folding-unfolding transitions in single titin molecules
4458 characterized with laser tweezers",
4465 pages = "1112--1116",
4467 keywords = "Amino Acid
4468 Sequence;Elasticity;Entropy;Immunoglobulins;Lasers;Models,
4469 Chemical;Muscle Contraction;Muscle Proteins;Muscle Relaxation;Muscle,
4470 Skeletal;Protein Denaturation;Protein Folding;Protein Kinases;Stress,
4472 abstract = "Titin, a giant filamentous polypeptide, is believed to play a
4473 fundamental role in maintaining sarcomeric structural integrity and
4474 developing what is known as passive force in muscle. Measurements of
4475 the force required to stretch a single molecule revealed that titin
4476 behaves as a highly nonlinear entropic spring. The molecule unfolds in
4477 a high-force transition beginning at 20 to 30 piconewtons and refolds
4478 in a low-force transition at approximately 2.5 piconewtons. A fraction
4479 of the molecule (5 to 40 percent) remains permanently unfolded,
4480 behaving as a wormlike chain with a persistence length (a measure of
4481 the chain's bending rigidity) of 20 angstroms. Force hysteresis arises
4482 from a difference between the unfolding and refolding kinetics of the
4483 molecule relative to the stretch and release rates in the experiments,
4484 respectively. Scaling the molecular data up to sarcomeric dimensions
4485 reproduced many features of the passive force versus extension curve of
4490 author = WKing #" and "# MSu #" and "# GYang,
4491 title = "{M}onte {C}arlo simulation of mechanical unfolding of proteins
4492 based on a simple two-state model",
4496 address = "Department of Physics, Drexel University, 3141
4497 Chestnut Street, Philadelphia, PA 19104, USA.",
4503 alternative_issn = "1879-0003",
4504 doi = "10.1016/j.ijbiomac.2009.12.001",
4505 url = "http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001",
4507 keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
4508 simulation;Worm-like chain;Single molecule methods",
4509 abstract = "Single molecule methods are becoming routine biophysical
4510 techniques for studying biological macromolecules. In mechanical
4511 unfolding of proteins, an externally applied force is used to induce
4512 the unfolding of individual protein molecules. Such experiments have
4513 revealed novel information that has significantly enhanced our
4514 understanding of the function and folding mechanisms of several types
4515 of proteins. To obtain information on the unfolding kinetics and the
4516 free energy landscape of the protein molecule from mechanical unfolding
4517 data, a Monte Carlo simulation based on a simple two-state kinetic
4518 model is often used. In this paper, we provide a detailed description
4519 of the procedure to perform such simulations and discuss the
4520 approximations and assumptions involved. We show that the appearance of
4521 the force versus extension curves from mechanical unfolding of proteins
4522 is affected by a variety of experimental parameters, such as the length
4523 of the protein polymer and the force constant of the cantilever. We
4524 also analyze the errors associated with different methods of data
4525 pooling and present a quantitative measure of how well the simulation
4526 results fit experimental data. These findings will be helpful in
4527 experimental design, artifact identification, and data analysis for
4528 single molecule studies of various proteins using the mechanical
4530 note = "Sawsim is available at \url{http://blog.tremily.us/posts/sawsim/}.",
4533 @article { kleiner07,
4534 author = AKleiner #" and "# EShakhnovich,
4535 title = "The mechanical unfolding of ubiquitin through all-atom Monte Carlo
4536 simulation with a Go-type potential",
4543 pages = "2054--2061",
4545 doi = "10.1529/biophysj.106.081257",
4546 eprint = "http://www.biophysj.org/cgi/reprint/92/6/2054",
4547 url = "http://www.biophysj.org/cgi/content/full/92/6/2054",
4548 keywords = "Computer Simulation; Models, Chemical; Models, Molecular;
4549 Models, Statistical; Monte Carlo Method; Motion; Protein Conformation;
4550 Protein Denaturation; Protein Folding; Ubiquitin",
4551 abstract = "The mechanical unfolding of proteins under a stretching force
4552 has an important role in living systems and is a logical extension of
4553 the more general protein folding problem. Recent advances in
4554 experimental methodology have allowed the stretching of single
4555 molecules, thus rendering this process ripe for computational study. We
4556 use all-atom Monte Carlo simulation with a G?-type potential to study
4557 the mechanical unfolding pathway of ubiquitin. A detailed, robust,
4558 well-defined pathway is found, confirming existing results in this vein
4559 though using a different model. Additionally, we identify the protein's
4560 fundamental stabilizing secondary structure interactions in the
4561 presence of a stretching force and show that this fundamental
4562 stabilizing role does not persist in the absence of mechanical stress.
4563 The apparent success of simulation methods in studying ubiquitin's
4564 mechanical unfolding pathway indicates their potential usefulness for
4565 future study of the stretching of other proteins and the relationship
4566 between protein structure and the response to mechanical deformation."
4569 @article { klimov00,
4570 author = DKlimov #" and "# DThirumalai,
4571 title = "Native topology determines force-induced unfolding pathways in
4579 pages = "7254--7259",
4581 doi = "10.1073/pnas.97.13.7254",
4582 eprint = "http://www.pnas.org/cgi/reprint/97/13/7254.pdf",
4583 url = "http://www.pnas.org/cgi/content/abstract/97/13/7254",
4584 keywords = "Animals; Humans; Protein Folding; Proteins; Spectrin",
4585 abstract = "Single-molecule manipulation techniques reveal that stretching
4586 unravels individually folded domains in the muscle protein titin and
4587 the extracellular matrix protein tenascin. These elastic proteins
4588 contain tandem repeats of folded domains with beta-sandwich
4589 architecture. Herein, we propose by stretching two model sequences (S1
4590 and S2) with four-stranded beta-barrel topology that unfolding forces
4591 and pathways in folded domains can be predicted by using only the
4592 structure of the native state. Thermal refolding of S1 and S2 in the
4593 absence of force proceeds in an all-or-none fashion. In contrast, phase
4594 diagrams in the force-temperature (f,T) plane and steered Langevin
4595 dynamics studies of these sequences, which differ in the native
4596 registry of the strands, show that S1 unfolds in an allor-none fashion,
4597 whereas unfolding of S2 occurs via an obligatory intermediate. Force-
4598 induced unfolding is determined by the native topology. After proving
4599 that the simulation results for S1 and S2 can be calculated by using
4600 native topology alone, we predict the order of unfolding events in Ig
4601 domain (Ig27) and two fibronectin III type domains ((9)FnIII and
4602 (10)FnIII). The calculated unfolding pathways for these proteins, the
4603 location of the transition states, and the pulling speed dependence of
4604 the unfolding forces reflect the differences in the way the strands are
4605 arranged in the native states. We also predict the mechanisms of force-
4606 induced unfolding of the coiled-coil spectrin (a three-helix bundle
4607 protein) for all 20 structures deposited in the Protein Data Bank. Our
4608 approach suggests a natural way to measure the phase diagram in the
4609 (f,C) plane, where C is the concentration of denaturants.",
4610 note = {Simulated unfolding time scales for Ig27-like S1 and S2 domains.},
4613 @article { klimov99,
4614 author = DKlimov #" and "# DThirumalai,
4615 title = "Stretching single-domain proteins: Phase diagram and kinetics of
4616 force-induced unfolding",
4623 pages = "6166--6170",
4625 keywords = "Amino Acid Sequence;Kinetics;Models, Chemical;Protein
4626 Denaturation;Protein Folding;Proteins;Thermodynamics;Time Factors",
4627 abstract = "Single-molecule force spectroscopy reveals unfolding of domains
4628 in titin on stretching. We provide a theoretical framework for these
4629 experiments by computing the phase diagrams for force-induced unfolding
4630 of single-domain proteins using lattice models. The results show that
4631 two-state folders (at zero force) unravel cooperatively, whereas
4632 stretching of non-two-state folders occurs through intermediates. The
4633 stretching rates of individual molecules show great variations
4634 reflecting the heterogeneity of force-induced unfolding pathways. The
4635 approach to the stretched state occurs in a stepwise ``quantized''
4636 manner. Unfolding dynamics and forces required to stretch proteins
4637 depend sensitively on topology. The unfolding rates increase
4638 exponentially with force f till an optimum value, which is determined
4639 by the barrier to unfolding when f = 0. A mapping of these results to
4640 proteins shows qualitative agreement with force-induced unfolding of
4641 Ig-like domains in titin. We show that single-molecule force
4642 spectroscopy can be used to map the folding free energy landscape of
4643 proteins in the absence of denaturants."
4646 @article { kosztin06,
4647 author = IKosztin #" and "# BBarz #" and "# LJanosi,
4648 title = "Calculating potentials of mean force and diffusion coefficients
4649 from nonequilibrium processes without Jarzynski's equality",
4657 doi = "10.1063/1.2166379",
4658 url = "http://link.aip.org/link/?JCPSA6/124/064106/1"
4661 @article { kramers40,
4663 title = "Brownian motion in a field of force and the diffusion model of
4664 chemical reactions",
4672 doi = "10.1016/S0031-8914(40)90098-2",
4673 url = "http://dx.doi.org/10.1016/S0031-8914(40)90098-2",
4674 abstract = "A particle which is caught in a potential hole and which,
4675 through the shuttling action of Brownian motion, can escape over a
4676 potential barrier yields a suitable model for elucidating the
4677 applicability of the transition state method for calculating the rate
4678 of chemical reactions.",
4679 note = "Seminal paper on thermally activated barrier crossings."
4682 @article { krammer99,
4683 author = AKrammer #" and "# HLu #" and "# BIsralewitz #" and "# KSchulten
4685 title = "Forced unfolding of the fibronectin type {III} module reveals a
4686 tensile molecular recognition switch",
4693 pages = "1351--1356",
4695 keywords = "Amino Acid Sequence;Binding Sites;Computer
4696 Simulation;Crystallography, X-Ray;Disulfides;Fibronectins;Hydrogen
4697 Bonding;Integrins;Models, Molecular;Oligopeptides;Protein
4698 Conformation;Protein Denaturation;Protein Folding;Protein Structure,
4699 Secondary;Protein Structure, Tertiary;Software;Tensile Strength",
4700 abstract = "The 10th type III module of fibronectin possesses a beta-
4701 sandwich structure consisting of seven beta-strands (A-G) that are
4702 arranged in two antiparallel sheets. It mediates cell adhesion to
4703 surfaces via its integrin binding motif, Arg78, Gly79, and Asp80 (RGD),
4704 which is placed at the apex of the loop connecting beta-strands F and
4705 G. Steered molecular dynamics simulations in which tension is applied
4706 to the protein's terminal ends reveal that the beta-strand G is the
4707 first to break away from the module on forced unfolding whereas the
4708 remaining fold maintains its structural integrity. The separation of
4709 strand G from the remaining fold results in a gradual shortening of the
4710 distance between the apex of the RGD-containing loop and the module
4711 surface, which potentially reduces the loop's accessibility to surface-
4712 bound integrins. The shortening is followed by a straightening of the
4713 RGD-loop from a tight beta-turn into a linear conformation, which
4714 suggests a further decrease of affinity and selectivity to integrins.
4715 The RGD-loop therefore is located strategically to undergo strong
4716 conformational changes in the early stretching stages of the module and
4717 thus constitutes a mechanosensitive control of ligand recognition."
4720 @article { kreuzer01,
4721 author = HJKreuzer #" and "# SHPayne,
4722 title = "Stretching a macromolecule in an atomic force microscope:
4723 statistical mechanical analysis",
4732 eprint = "http://www.biophysj.org/cgi/reprint/80/6/2505.pdf",
4733 url = "http://www.biophysj.org/cgi/content/abstract/80/6/2505",
4734 keywords = "Biophysics;Macromolecular Substances;Microscopy, Atomic
4735 Force;Models, Statistical;Models, Theoretical;Statistics as Topic",
4736 abstract = "We formulate the proper statistical mechanics to describe the
4737 stretching of a macromolecule under a force provided by the cantilever
4738 of an atomic force microscope. In the limit of a soft cantilever the
4739 generalized ensemble of the coupled molecule/cantilever system reduces
4740 to the Gibbs ensemble for an isolated molecule subject to a constant
4741 force in which the extension is fluctuating. For a stiff cantilever we
4742 obtain the Helmholtz ensemble for an isolated molecule held at a fixed
4743 extension with the force fluctuating. Numerical examples are given for
4744 poly (ethylene glycol) chains."
4748 author = KKroy #" and "# JGlaser,
4749 title = "The glassy wormlike chain",
4755 doi = "10.1088/1367-2630/9/11/416",
4756 eprint = "http://www.iop.org/EJ/article/1367-2630/9/11/416/njp7_11_416.pdf",
4757 url = "http://stacks.iop.org/1367-2630/9/416",
4758 abstract = "We introduce a new model for the dynamics of a wormlike chain
4759 (WLC) in an environment that gives rise to a rough free energy
4760 landscape, which we name the glassy WLC. It is obtained from the common
4761 WLC by an exponential stretching of the relaxation spectrum of its
4762 long-wavelength eigenmodes, controlled by a single parameter
4763 \\boldsymbol{\\cal E} . Predictions for pertinent observables such as
4764 the dynamic structure factor and the microrheological susceptibility
4765 exhibit the characteristics of soft glassy rheology and compare
4766 favourably with experimental data for reconstituted cytoskeletal
4767 networks and live cells. We speculate about the possible microscopic
4768 origin of the stretching, implications for the nonlinear rheology, and
4769 the potential physiological significance of our results.",
4770 note = "Has short section on WLC relaxation time in the weakly bending
4774 @article { labeit03,
4775 author = DLabeit #" and "# KWatanabe #" and "# CWitt #" and "# HFujita #"
4776 and "# YWu #" and "# SLahmers #" and "# TFunck #" and "# SLabeit #" and
4778 title = "Calcium-dependent molecular spring elements in the giant protein
4784 pages = "13716--13721",
4785 doi = "10.1073/pnas.2235652100",
4786 eprint = "http://www.pnas.org/cgi/reprint/100/23/13716.pdf",
4787 url = "http://www.pnas.org/cgi/content/abstract/100/23/13716",
4788 abstract = "Titin (also known as connectin) is a giant protein with a wide
4789 range of cellular functions, including providing muscle cells with
4790 elasticity. Its physiological extension is largely derived from the
4791 PEVK segment, rich in proline (P), glutamate (E), valine (V), and
4792 lysine (K) residues. We studied recombinant PEVK molecules containing
4793 the two conserved elements: {approx}28-residue PEVK repeats and E-rich
4794 motifs. Single molecule experiments revealed that calcium-induced
4795 conformational changes reduce the bending rigidity of the PEVK
4796 fragments, and site-directed mutagenesis identified four glutamate
4797 residues in the E-rich motif that was studied (exon 129), as critical
4798 for this process. Experiments with muscle fibers showed that titin-
4799 based tension is calcium responsive. We propose that the PEVK segment
4800 contains E-rich motifs that render titin a calcium-dependent molecular
4801 spring that adapts to the physiological state of the cell."
4805 author = SLabeit #" and "# BKolmerer,
4806 title = "Titins: Giant proteins in charge of muscle ultrastructure
4812 address = "European Molecular Biology Laboratory, Heidelberg, Germany.",
4816 keywords = "Actin Cytoskeleton",
4817 keywords = "Amino Acid Sequence",
4818 keywords = "Animals",
4819 keywords = "DNA, Complementary",
4820 keywords = "Elasticity",
4821 keywords = "Fibronectins",
4822 keywords = "Humans",
4823 keywords = "Immunoglobulins",
4824 keywords = "Molecular Sequence Data",
4825 keywords = "Muscle Contraction",
4826 keywords = "Muscle Proteins",
4827 keywords = "Muscle, Skeletal",
4828 keywords = "Myocardium",
4829 keywords = "Protein Kinases",
4830 keywords = "Rabbits",
4831 keywords = "Repetitive Sequences, Nucleic Acid",
4832 keywords = "Sarcomeres",
4833 abstract = "In addition to thick and thin filaments, vertebrate
4834 striated muscle contains a third filament system formed by the
4835 giant protein titin. Single titin molecules extend from Z discs to
4836 M lines and are longer than 1 micrometer. The titin filament
4837 contributes to muscle assembly and resting tension, but more
4838 details are not known because of the large size of the
4839 protein. The complete complementary DNA sequence of human cardiac
4840 titin was determined. The 82-kilobase complementary DNA predicts a
4841 3-megadalton protein composed of 244 copies of immunoglobulin and
4842 fibronectin type III (FN3) domains. The architecture of sequences
4843 in the A band region of titin suggests why thick filament
4844 structure is conserved among vertebrates. In the I band region,
4845 comparison of titin sequences from muscles of different passive
4846 tension identifies two elements that correlate with tissue
4847 stiffness. This suggests that titin may act as two springs in
4848 series. The differential expression of the springs provides a
4849 molecular explanation for the diversity of sarcomere length and
4850 resting tension in vertebrate striated muscles.",
4852 URL = "http://www.ncbi.nlm.nih.gov/pubmed/7569978",
4857 author = RLaw #" and "# GLiao #" and "# SHarper #" and "# GYang #" and "#
4858 DSpeicher #" and "# DDischer,
4859 title = "Pathway shifts and thermal softening in temperature-coupled forced
4860 unfolding of spectrin domains",
4861 address = "Biophysical Engineering Lab, Institute for Medicine and
4862 Engineering, and School of Engineering and Applied Science,
4863 University of Pennsylvania, Philadelphia, Pennsylvania
4870 pages = "3286--3293",
4872 keywords = "Circular Dichroism;Elasticity;Heat;Microscopy, Atomic
4873 Force;Physical Stimulation;Protein Conformation;Protein
4874 Denaturation;Protein Folding;Protein Structure,
4875 Tertiary;Spectrin;Stress, Mechanical;Temperature",
4876 abstract = "Pathways of unfolding a protein depend in principle on the
4877 perturbation-whether it is temperature, denaturant, or even forced
4878 extension. Widely-shared, helical-bundle spectrin repeats are known to
4879 melt at temperatures as low as 40-45 degrees C and are also known to
4880 unfold via multiple pathways as single molecules in atomic force
4881 microscopy. Given the varied roles of spectrin family proteins in cell
4882 deformability, we sought to determine the coupled effects of
4883 temperature on forced unfolding. Bimodal distributions of unfolding
4884 intervals are seen at all temperatures for the four-repeat beta(1-4)
4885 spectrin-an alpha-actinin homolog. The major unfolding length
4886 corresponds to unfolding of a single repeat, and a minor peak at twice
4887 the length corresponds to tandem repeats. Increasing temperature shows
4888 fewer tandem events but has no effect on unfolding intervals. As T
4889 approaches T(m), however, mean unfolding forces in atomic force
4890 microscopy also decrease; and circular dichroism studies demonstrate a
4891 nearly proportional decrease of helical content in solution. The
4892 results imply a thermal softening of a helical linker between repeats
4893 which otherwise propagates a helix-to-coil transition to adjacent
4894 repeats. In sum, structural changes with temperature correlate with
4895 both single-molecule unfolding forces and shifts in unfolding
4897 doi = "10.1016/S0006-3495(03)74747-X",
4898 URL = "http://www.ncbi.nlm.nih.gov/pubmed/14581229",
4902 @article { levinthal68,
4903 author = CLevinthal,
4904 title = "Are there pathways for protein folding?",
4911 "http://www.biochem.wisc.edu/courses/biochem704/Reading/Levinthal1968.p
4913 note = "\emph{Not} Levinthal's paradox."
4916 @inproceedings { levinthal69,
4917 editor = PDebrunner #" and "# JCMTsibris #" and "# EMunck,
4918 author = CLevinthal,
4919 title = "How to Fold Graciously.",
4920 booktitle = "Mossbauer Spectroscopy in Biological Systems",
4923 publisher = UIP:Urbana,
4924 address = "Allerton House, Monticello, IL",
4925 url = "http://www-miller.ch.cam.ac.uk/levinthal/levinthal.html"
4929 author = RLevy #" and "# MMaaloum,
4930 title = "Measuring the spring constant of atomic force microscope
4931 cantilevers: Thermal fluctuations and other methods",
4937 doi = "10.1088/0957-4484/13/1/307",
4938 url = "http://stacks.iop.org/0957-4484/13/33",
4939 abstract = "Knowledge of the interaction forces between surfaces gained
4940 using an atomic force microscope (AFM) is crucial in a variety of
4941 industrial and scientific applications and necessitates a precise
4942 knowledge of the cantilever spring constant. Many methods have been
4943 devised to experimentally determine the spring constants of AFM
4944 cantilevers. The thermal fluctuation method is elegant but requires a
4945 theoretical model of the bending modes. For a rectangular cantilever,
4946 this model is available (Butt and Jaschke). Detailed thermal
4947 fluctuation measurements of a series of AFM cantilever beams have been
4948 performed in order to test the validity and accuracy of the recent
4949 theoretical models. The spring constant of rectangular cantilevers can
4950 also be determined easily with the method of Sader and White. We found
4951 very good agreement between the two methods. In the case of the
4952 V-shaped cantilever, we have shown that the thermal fluctuation method
4953 is a valid and accurate approach to the evaluation of the spring
4954 constant. A comparison between this method and those of Sader-
4955 Neumeister and of Ducker has been established. In some cases, we found
4956 disagreement between these two methods; the effect of non-conservation
4957 of material properties over all cantilevers from a single chip is
4958 qualitatively invoked.",
4959 note = "Good review of thermal calibration to 2002, but not much on the
4960 derviation of the Lorentzian fit.",
4961 project = "Cantilever Calibration"
4965 author = HLi #" and "# AOberhauser #" and "# SFowler #" and "# JClarke #"
4967 title = "Atomic force microscopy reveals the mechanical design of a modular
4973 pages = "6527--6531",
4974 doi = "10.1073/pnas.120048697",
4975 eprint = "http://www.pnas.org/cgi/reprint/97/12/6527.pdf",
4976 url = "http://www.pnas.org/cgi/content/abstract/97/12/6527",
4978 note = "Unfolding order not from protein-surface interactions. Mechanical
4979 unfolding of a chain of interleaved domains $ABABAB\ldots$ yielded a
4980 run of $A$ unfoldings followed by a run of $B$ unfoldings."
4984 author = HLi #" and "# AOberhauser #" and "# SRedick #" and "#
4985 MCarrionVazquez #" and "# HErickson #" and "# JFernandez,
4986 title = "Multiple conformations of {PEVK} proteins detected by single-
4987 molecule techniques",
4992 pages = "10682--10686",
4993 doi = "10.1073/pnas.191189098",
4994 eprint = "http://www.pnas.org/cgi/reprint/98/19/10682.pdf",
4995 url = "http://www.pnas.org/cgi/content/abstract/98/19/10682",
4996 abstract = "An important component of muscle elasticity is the PEVK region
4997 of titin, so named because of the preponderance of these amino acids.
4998 However, the PEVK region, similar to other elastomeric proteins, is
4999 thought to form a random coil and therefore its structure cannot be
5000 determined by standard techniques. Here we combine single-molecule
5001 electron microscopy and atomic force microscopy to examine the
5002 conformations of the human cardiac titin PEVK region. In contrast to a
5003 simple random coil, we have found that cardiac PEVK shows a wide range
5004 of elastic conformations with end-to-end distances ranging from 9 to 24
5005 nm and persistence lengths from 0.4 to 2.5 nm. Individual PEVK
5006 molecules retained their distinctive elastic conformations through many
5007 stretch-relaxation cycles, consistent with the view that these PEVK
5008 conformers cannot be interconverted by force. The multiple elastic
5009 conformations of cardiac PEVK may result from varying degrees of
5010 proline isomerization. The single-molecule techniques demonstrated here
5011 may help elucidate the conformation of other proteins that lack a well-
5016 author = HLi #" and "# JFernandez,
5017 title = "Mechanical design of the first proximal Ig domain of human cardiac
5018 titin revealed by single molecule force spectroscopy",
5027 doi = "10.1016/j.jmb.2003.09.036",
5028 keywords = "Amino Acid Sequence;Disulfides;Humans;Immunoglobulins;Models,
5029 Molecular;Molecular Sequence Data;Muscle Proteins;Myocardium;Protein
5030 Denaturation;Protein Engineering;Protein Kinases;Protein Structure,
5031 Tertiary;Spectrum Analysis",
5032 abstract = "The elastic I-band part of muscle protein titin contains two
5033 tandem immunoglobulin (Ig) domain regions of distinct mechanical
5034 properties. Until recently, the only known structure was that of the
5035 I27 module of the distal region, whose mechanical properties have been
5036 reported in detail. Recently, the structure of the first proximal
5037 domain, I1, has been resolved at 2.1A. In addition to the
5038 characteristic beta-sandwich structure of all titin Ig domains, the
5039 crystal structure of I1 showed an internal disulfide bridge that was
5040 proposed to modulate its mechanical extensibility in vivo. Here, we use
5041 single molecule force spectroscopy and protein engineering to examine
5042 the mechanical architecture of this domain. In contrast to the
5043 predictions made from the X-ray crystal structure, we find that the
5044 formation of a disulfide bridge in I1 is a relatively rare event in
5045 solution, even under oxidative conditions. Furthermore, our studies of
5046 the mechanical stability of I1 modules engineered with point mutations
5047 reveal significant differences between the mechanical unfolding of the
5048 I1 and I27 modules. Our study illustrates the varying mechanical
5049 architectures of the titin Ig modules."
5053 author = LeLi #" and "# HHuang #" and "# CBadilla #" and "# JFernandez,
5054 title = "Mechanical unfolding intermediates observed by single-molecule
5055 force spectroscopy in a fibronectin type {III} module",
5064 doi = "10.1016/j.jmb.2004.11.021",
5065 keywords = "Fibronectins;Kinetics;Microscopy, Atomic Force;Models,
5066 Molecular;Mutagenesis, Site-Directed;Protein Denaturation;Protein
5067 Folding;Protein Structure, Tertiary;Recombinant Fusion Proteins",
5068 abstract = "Domain 10 of type III fibronectin (10FNIII) is known to play a
5069 pivotal role in the mechanical interactions between cell surface
5070 integrins and the extracellular matrix. Recent molecular dynamics
5071 simulations have predicted that 10FNIII, when exposed to a stretching
5072 force, unfolds along two pathways, each with a distinct, mechanically
5073 stable intermediate. Here, we use single-molecule force spectroscopy
5074 combined with protein engineering to test these predictions by probing
5075 the mechanical unfolding pathway of 10FNIII. Stretching single
5076 polyproteins containing the 10FNIII module resulted in sawtooth
5077 patterns where 10FNIII was seen unfolding in two consecutive steps. The
5078 native state unfolded at 100(+/-20) pN, elongating (10)FNIII by
5079 12(+/-2) nm and reaching a clearly marked intermediate that unfolded at
5080 50(+/-20) pN. Unfolding of the intermediate completed the elongation of
5081 the molecule by extending another 19(+/-2) nm. Site-directed
5082 mutagenesis of residues in the A and B beta-strands (E9P and L19P)
5083 resulted in sawtooth patterns with all-or-none unfolding events that
5084 elongated the molecule by 19(+/-2) nm. In contrast, mutating residues
5085 in the G beta-strand gave results that were dependent on amino acid
5086 position. The mutation I88P in the middle of the G beta-strand resulted
5087 in native like unfolding sawtooth patterns showing an intact
5088 intermediate state. The mutation Y92P, which is near the end of G beta-
5089 strand, produced sawtooth patterns with all-or-none unfolding events
5090 that lengthened the molecule by 17(+/-2) nm. These results are
5091 consistent with the view that 10FNIII can unfold in two different ways.
5092 Along one pathway, the detachment of the A and B beta-strands from the
5093 body of the folded module constitute the first unfolding event,
5094 followed by the unfolding of the remaining beta-sandwich structure.
5095 Along the second pathway, the detachment of the G beta-strands is
5096 involved in the first unfolding event. These results are in excellent
5097 agreement with the sequence of events predicted by molecular dynamics
5098 simulations of the 10FNIII module."
5102 author = MSLi #" and "# CKHu #" and "# DKlimov #" and "# DThirumalai,
5103 title = "Multiple stepwise refolding of immunoglobulin domain {I27} upon
5104 force quench depends on initial conditions",
5110 doi = "10.1073/pnas.0503758103",
5111 eprint = "http://www.pnas.org/cgi/reprint/103/1/93.pdf",
5112 url = "http://www.pnas.org/cgi/content/abstract/103/1/93",
5113 abstract = "Mechanical folding trajectories for polyproteins starting from
5114 initially stretched conformations generated by single-molecule atomic
5115 force microscopy experiments [Fernandez, J. M. & Li, H. (2004) Science
5116 303, 1674-1678] show that refolding, monitored by the end-to-end
5117 distance, occurs in distinct multiple stages. To clarify the molecular
5118 nature of folding starting from stretched conformations, we have probed
5119 the folding dynamics, upon force quench, for the single I27 domain from
5120 the muscle protein titin by using a C{alpha}-Go model. Upon temperature
5121 quench, collapse and folding of I27 are synchronous. In contrast,
5122 refolding from stretched initial structures not only increases the
5123 folding and collapse time scales but also decouples the two kinetic
5124 processes. The increase in the folding times is associated primarily
5125 with the stretched state to compact random coil transition.
5126 Surprisingly, force quench does not alter the nature of the refolding
5127 kinetics, but merely increases the height of the free-energy folding
5128 barrier. Force quench refolding times scale as f1.gif, where {Delta}xf
5129 {approx} 0.6 nm is the location of the average transition state along
5130 the reaction coordinate given by end-to-end distance. We predict that
5131 {tau}F and the folding mechanism can be dramatically altered by the
5132 initial and/or final values of force. The implications of our results
5133 for design and analysis of experiments are discussed."
5138 title = "Divergence measures based on the {S}hannon entropy",
5146 doi = "10.1109/18.61115",
5147 url = "http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?isnumber=2227&arnumbe
5148 r=61115&count=35&index=9",
5149 keywords = "divergence;dissimilarity measure;discrimintation
5150 information;entropy;probability of error bounds",
5151 abstract = "A novel class of information-theoretic divergence measures
5152 based on the Shannon entropy is introduced. Unlike the well-known
5153 Kullback divergences, the new measures do not require the condition of
5154 absolute continuity to be satisfied by the probability distributions
5155 involved. More importantly, their close relationship with the
5156 variational distance and the probability of misclassification error are
5157 established in terms of bounds. These bounds are crucial in many
5158 applications of divergence measures. The measures are also well
5159 characterized by the properties of nonnegativity, finiteness,
5160 semiboundedness, and boundedness."
5164 author = WALinke #" and "# AGrutzner,
5165 title = "Pulling single molecules of titin by {AFM}--recent advances and
5166 physiological implications",
5175 doi = "10.1007/s00424-007-0389-x",
5176 abstract = "Perturbation of a protein away from its native state by
5177 mechanical stress is a physiological process immanent to many cells.
5178 The mechanical stability and conformational diversity of proteins under
5179 force therefore are important parameters in nature. Molecular-level
5180 investigations of ``mechanical proteins'' have enjoyed major
5181 breakthroughs over the last decade, a development to which atomic force
5182 microscopy (AFM) force spectroscopy has been instrumental. The giant
5183 muscle protein titin continues to be a paradigm model in this field. In
5184 this paper, we review how single-molecule mechanical measurements of
5185 titin using AFM have served to elucidate key aspects of protein
5186 unfolding-refolding and mechanisms by which biomolecular elasticity is
5187 attained. We outline recent work combining protein engineering and AFM
5188 force spectroscopy to establish the mechanical behavior of titin
5189 domains using molecular ``fingerprinting.'' Furthermore, we summarize
5190 AFM force-extension data demonstrating different mechanical stabilities
5191 of distinct molecular-spring elements in titin, compare AFM force-
5192 extension to novel force-ramp/force-clamp studies, and elaborate on
5193 exciting new results showing that AFM force clamp captures the
5194 unfolding and refolding trajectory of single mechanical proteins. Along
5195 the way, we discuss the physiological implications of the findings, not
5196 least with respect to muscle mechanics. These studies help us
5197 understand how proteins respond to forces in cells and how
5198 mechanosensing and mechanosignaling events may proceed in vivo."
5201 @article { linke98a,
5202 author = WALinke #" and "# MRStockmeier #" and "# MIvemeyer #" and "#
5203 HHosser #" and "# PMundel,
5204 title = "Characterizing titin's {I}-band {Ig} domain region as an entropic
5209 volume = "111 (Pt 11)",
5210 pages = "1567--1574",
5213 eprint = "http://jcs.biologists.org/cgi/reprint/111/11/1567",
5214 url = "http://jcs.biologists.org/cgi/content/abstract/111/11/1567",
5215 keywords = "Animals;Elasticity;Immunoglobulins;Male;Muscle Proteins;Muscle,
5216 Skeletal;Protein Kinases;Rats;Rats, Wistar;Structure-Activity
5218 abstract = "The poly-immunoglobulin domain region of titin, located within
5219 the elastic section of this giant muscle protein, determines the
5220 extensibility of relaxed myofibrils mainly at shorter physiological
5221 lengths. To elucidate this region's contribution to titin elasticity,
5222 we measured the elastic properties of the N-terminal I-band Ig region
5223 by using immunofluorescence/immunoelectron microscopy and myofibril
5224 mechanics and tried to simulate the results with a model of entropic
5225 polymer elasticity. Rat psoas myofibrils were stained with titin-
5226 specific antibodies flanking the Ig region at the N terminus and C
5227 terminus, respectively, to record the extension behaviour of that titin
5228 segment. The segment's end-to-end length increased mainly at small
5229 stretch, reaching approximately 90\% of the native contour length of
5230 the Ig region at a sarcomere length of 2.8 microm. At this extension,
5231 the average force per single titin molecule, deduced from the steady-
5232 state passive length-tension relation of myofibrils, was approximately
5233 5 or 2.5 pN, depending on whether we assumed a number of 3 or 6 titins
5234 per half thick filament. When the force-extension curve constructed for
5235 the Ig region was simulated by the wormlike chain model, best fits were
5236 obtained for a persistence length, a measure of the chain's bending
5237 rigidity, of 21 or 42 nm (for 3 or 6 titins/half thick filament), which
5238 correctly reproduced the curve for sarcomere lengths up to 3.4 microm.
5239 Systematic deviations between data and fits above that length indicated
5240 that forces of >30 pN per titin strand may induce unfolding of Ig
5241 modules. We conclude that stretches of at least 5-6 Ig domains, perhaps
5242 coinciding with known super repeat patterns of these titin modules in
5243 the I-band, may represent the unitary lengths of the wormlike chain.
5244 The poly-Ig regions might thus act as compliant entropic springs that
5245 determine the minute levels of passive tension at low extensions of a
5249 @article { linke98b,
5250 author = WALinke #" and "# MIvemeyer #" and "# PMundel #" and "#
5251 MRStockmeier #" and "# BKolmerer,
5252 title = "Nature of {PEVK}-titin elasticity in skeletal muscle",
5259 pages = "8052--8057",
5261 keywords = "Animals;Elasticity;Fluorescent Antibody
5262 Technique;Male;Microscopy, Immunoelectron;Muscle Proteins;Muscle,
5263 Skeletal;Protein Kinases;Rats;Rats, Wistar;Stress, Mechanical",
5264 abstract = "A unique sequence within the giant titin molecule, the PEVK
5265 domain, has been suggested to greatly contribute to passive force
5266 development of relaxed skeletal muscle during stretch. To explore the
5267 nature of PEVK elasticity, we used titin-specific antibodies to stain
5268 both ends of the PEVK region in rat psoas myofibrils and determined the
5269 region's force-extension relation by combining immunofluorescence and
5270 immunoelectron microscopy with isolated myofibril mechanics. We then
5271 tried to fit the results with recent models of polymer elasticity. The
5272 PEVK segment elongated substantially at sarcomere lengths above 2.4
5273 micro(m) and reached its estimated contour length at approximately 3.5
5274 micro(m). In immunofluorescently labeled sarcomeres stretched and
5275 released repeatedly above 3 micro(m), reversible PEVK lengthening could
5276 be readily visualized. At extensions near the contour length, the
5277 average force per titin molecule was calculated to be approximately 45
5278 pN. Attempts to fit the force-extension curve of the PEVK segment with
5279 a standard wormlike chain model of entropic elasticity were successful
5280 only for low to moderate extensions. In contrast, the experimental data
5281 also could be correctly fitted at high extensions with a modified
5282 wormlike chain model that incorporates enthalpic elasticity. Enthalpic
5283 contributions are likely to arise from electrostatic stiffening, as
5284 evidenced by the ionic-strength dependency of titin-based myofibril
5285 stiffness; at high stretch, hydrophobic effects also might become
5286 relevant. Thus, at physiological muscle lengths, the PEVK region does
5287 not function as a pure entropic spring. Rather, PEVK elasticity may
5288 have both entropic and enthalpic origins characterizable by a polymer
5289 persistence length and a stretch modulus."
5293 author = WLiu #" and "# VMontana #" and "# EChapman #" and "# UMohideen #"
5295 title = "Botulinum toxin type {B} micromechanosensor",
5300 pages = "13621--13625",
5301 doi = "10.1073/pnas.2233819100",
5302 eprint = "http://www.pnas.org/cgi/reprint/100/23/13621.pdf",
5303 url = "http://www.pnas.org/cgi/content/abstract/100/23/13621",
5304 abstract = "Botulinum neurotoxin (BoNT) types A, B, E, and F are toxic to
5305 humans; early and rapid detection is essential for adequate medical
5306 treatment. Presently available tests for detection of BoNTs, although
5307 sensitive, require hours to days. We report a BoNT-B sensor whose
5308 properties allow detection of BoNT-B within minutes. The technique
5309 relies on the detection of an agarose bead detachment from the tip of a
5310 micromachined cantilever resulting from BoNT-B action on its
5311 substratum, the synaptic protein synaptobrevin 2, attached to the
5312 beads. The mechanical resonance frequency of the cantilever is
5313 monitored for the detection. To suspend the bead off the cantilever we
5314 use synaptobrevin's molecular interaction with another synaptic
5315 protein, syntaxin 1A, that was deposited onto the cantilever tip.
5316 Additionally, this bead detachment technique is general and can be used
5317 in any displacement reaction, such as in receptor-ligand pairs, where
5318 the introduction of one chemical leads to the displacement of another.
5319 The technique is of broad interest and will find uses outside
5324 author = GLois #" and "# JBlawzdziewicz #" and "# CSOHern,
5325 title = "Reliable protein folding on complex energy landscapes: the free
5326 energy reaction path",
5333 pages = "2692--2701",
5335 doi = "10.1529/biophysj.108.133132",
5336 abstract = "A theoretical framework is developed to study the dynamics of
5337 protein folding. The key insight is that the search for the native
5338 protein conformation is influenced by the rate r at which external
5339 parameters, such as temperature, chemical denaturant, or pH, are
5340 adjusted to induce folding. A theory based on this insight predicts
5341 that 1), proteins with complex energy landscapes can fold reliably to
5342 their native state; 2), reliable folding can occur as an equilibrium or
5343 out-of-equilibrium process; and 3), reliable folding only occurs when
5344 the rate r is below a limiting value, which can be calculated from
5345 measurements of the free energy. We test these predictions against
5346 numerical simulations of model proteins with a single energy scale."
5350 author = HLu #" and "# AKrammer #" and "# BIsralewitz #" and "# VVogel #"
5352 title = "Computer modeling of force-induced titin domain unfolding",
5354 journal = AdvExpMedBiol,
5358 url = {http://www.ncbi.nlm.nih.gov/pubmed/10987071},
5359 keywords = "Amino Acid Sequence;Animals;Computer
5360 Simulation;Elasticity;Fibronectins;Humans;Hydrogen
5361 Bonding;Immunoglobulins;Models, Molecular;Muscle Proteins;Muscle,
5362 Skeletal;Myofibrils;Protein Conformation;Protein Denaturation;Protein
5364 abstract = "Titin, a 1 micron long protein found in striated muscle
5365 myofibrils, possesses unique elastic and extensibility properties, and
5366 is largely composed of a PEVK region and beta-sandwich immunoglobulin
5367 (Ig) and fibronectin type III (FnIII) domains. The extensibility
5368 behavior of titin has been shown in atomic force microscope and optical
5369 tweezer experiments to partially depend on the reversible unfolding of
5370 individual Ig and FnIII domains. We performed steered molecular
5371 dynamics simulations to stretch single titin Ig domains in solution
5372 with pulling speeds of 0.1-1.0 A/ps, and FnIII domains with a pulling
5373 speed of 0.5 A/ps. Resulting force-extension profiles exhibit a single
5374 dominant peak for each domain unfolding, consistent with the
5375 experimentally observed sequential, as opposed to concerted, unfolding
5376 of Ig and FnIII domains under external stretching forces. The force
5377 peaks can be attributed to an initial burst of a set of backbone
5378 hydrogen bonds connected to the domains' terminal beta-strands.
5379 Constant force stretching simulations, applying 500-1000 pN of force,
5380 were performed on Ig domains. The resulting domain extensions are
5381 halted at an initial extension of 10 A until the set of all six
5382 hydrogen bonds connecting terminal beta-strands break simultaneously.
5383 This behavior is accounted for by a barrier separating folded and
5384 unfolded states, the shape of which is consistent with AFM and chemical
5385 denaturation data.",
5386 note = "discussion in journal on pages 161--2"
5390 author = HLu #" and "# KSchulten,
5391 title = "The key event in force-induced unfolding of Titin's immunoglobulin
5400 doi = {10.1016/S0006-3495(00)76273-4},
5401 url = {http://www.cell.com/biophysj/abstract/S0006-3495%2800%2976273-4},
5402 eprint = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300915/pdf/10866937.pdf},
5403 keywords = "Amino Acid Sequence;Computer Simulation;Double Bind
5404 Interaction;Hydrogen Bonding;Immunoglobulins;Microscopy, Atomic
5405 Force;Models, Chemical;Models, Molecular;Molecular Sequence Data;Muscle
5406 Proteins;Protein Folding;Protein Kinases;Protein Structure,
5407 Tertiary;Stress, Mechanical;Water",
5408 abstract = "Steered molecular dynamics simulation of force-induced titin
5409 immunoglobulin domain I27 unfolding led to the discovery of a
5410 significant potential energy barrier at an extension of approximately
5411 14 A on the unfolding pathway that protects the domain against
5412 stretching. Previous simulations showed that this barrier is due to the
5413 concurrent breaking of six interstrand hydrogen bonds (H-bonds) between
5414 beta-strands A' and G that is preceded by the breaking of two to three
5415 hydrogen bonds between strands A and B, the latter leading to an
5416 unfolding intermediate. The simulation results are supported by
5417 Angstrom-resolution atomic force microscopy data. Here we perform a
5418 structural and energetic analysis of the H-bonds breaking. It is
5419 confirmed that H-bonds between strands A and B break rapidly. However,
5420 the breaking of the H-bond between strands A' and G needs to be
5421 assisted by fluctuations of water molecules. In nanosecond simulations,
5422 water molecules are found to repeatedly interact with the protein
5423 backbone atoms, weakening individual interstrand H-bonds until all six
5424 A'-G H-bonds break simultaneously under the influence of external
5425 stretching forces. Only when those bonds are broken can the generic
5426 unfolding take place, which involves hydrophobic interactions of the
5427 protein core and exerts weaker resistance against stretching than the
5432 author = HLu #" and "# BIsralewitz #" and "# AKrammer #" and "# VVogel #"
5434 title = "Unfolding of titin immunoglobulin domains by steered molecular
5435 dynamics simulation",
5443 doi = "10.1016/S0006-3495(98)77556-3",
5444 eprint = "http://download.cell.com/biophysj/pdf/PIIS0006349598775563.pdf",
5445 url = "http://www.cell.com/biophysj/abstract/S0006-3495(98)77556-3",
5446 keywords = "Amino Acid Sequence;Animals;Computer Simulation;Glutamic
5447 Acid;Immunoglobulins;Lysine;Macromolecular Substances;Models,
5448 Molecular;Molecular Sequence Data;Muscle
5449 Proteins;Myocardium;Proline;Protein Denaturation;Protein
5450 Folding;Protein Kinases;Protein Structure, Secondary;Sequence
5451 Alignment;Sequence Homology, Amino Acid;Valine",
5452 abstract = "Titin, a 1-microm-long protein found in striated muscle
5453 myofibrils, possesses unique elastic and extensibility properties in
5454 its I-band region, which is largely composed of a PEVK region (70\%
5455 proline, glutamic acid, valine, and lysine residue) and seven-strand
5456 beta-sandwich immunoglobulin-like (Ig) domains. The behavior of titin
5457 as a multistage entropic spring has been shown in atomic force
5458 microscope and optical tweezer experiments to partially depend on the
5459 reversible unfolding of individual Ig domains. We performed steered
5460 molecular dynamics simulations to stretch single titin Ig domains in
5461 solution with pulling speeds of 0.5 and 1.0 A/ps. Resulting force-
5462 extension profiles exhibit a single dominant peak for each Ig domain
5463 unfolding, consistent with the experimentally observed sequential, as
5464 opposed to concerted, unfolding of Ig domains under external stretching
5465 forces. This force peak can be attributed to an initial burst of
5466 backbone hydrogen bonds, which takes place between antiparallel beta-
5467 strands A and B and between parallel beta-strands A' and G. Additional
5468 features of the simulations, including the position of the force peak
5469 and relative unfolding resistance of different Ig domains, can be
5470 related to experimental observations."
5474 author = HLu #" and "# KSchulten,
5475 title = "Steered molecular dynamics simulations of force-induced protein
5485 doi = "10.1002/(SICI)1097-0134(19990601)35:4<453::AID-PROT9>3.0.CO;2-M",
5486 eprint = "http://www3.interscience.wiley.com/cgi-bin/fulltext/65000328/PDFSTART",
5487 url = "http://www3.interscience.wiley.com/journal/65000328/abstract",
5488 keywords = "Computer Simulation;Fibronectins;Hydrogen Bonding;Microscopy,
5489 Atomic Force;Models, Molecular;Protein Denaturation",
5490 abstract = "Steered molecular dynamics (SMD), a computer simulation method
5491 for studying force-induced reactions in biopolymers, has been applied
5492 to investigate the response of protein domains to stretching apart of
5493 their terminal ends. The simulations mimic atomic force microscopy and
5494 optical tweezer experiments, but proceed on much shorter time scales.
5495 The simulations on different domains for 0.6 nanosecond each reveal two
5496 types of protein responses: the first type, arising in certain beta-
5497 sandwich domains, exhibits nanosecond unfolding only after a force
5498 above 1,500 pN is applied; the second type, arising in a wider class of
5499 protein domain structures, requires significantly weaker forces for
5500 nanosecond unfolding. In the first case, strong forces are needed to
5501 concertedly break a set of interstrand hydrogen bonds which protect the
5502 domains against unfolding through stretching; in the second case,
5503 stretching breaks backbone hydrogen bonds one by one, and does not
5504 require strong forces for this purpose. Stretching of beta-sandwich
5505 (immunoglobulin) domains has been investigated further revealing a
5506 specific relationship between response to mechanical strain and the
5507 architecture of beta-sandwich domains."
5510 @article { makarov01,
5511 author = DEMakarov #" and "# PHansma #" and "# HMetiu,
5512 title = "Kinetic Monte Carlo simulation of titin unfolding",
5518 pages = "9663--9673",
5520 doi = "10.1063/1.1369622",
5521 eprint = "http://hansmalab.physics.ucsb.edu/pdf/297%20-%20Makarov,%20D.E._J
5522 .Chem.Phys._2001.pdf",
5523 url = "http://link.aip.org/link/?JCP/114/9663/1",
5524 keywords = "proteins; hydrogen bonds; digital simulation; Monte Carlo
5525 methods; molecular biophysics; intramolecular mechanics;
5526 macromolecules; atomic force microscopy"
5530 author = JFMarko #" and "# EDSiggia,
5531 title = "Stretching {DNA}",
5537 pages = "8759--8770",
5539 eprint = "http://pubs.acs.org/cgi-
5540 bin/archive.cgi/mamobx/1995/28/i26/pdf/ma00130a008.pdf",
5542 "http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ma00130a008
5545 note = "Derivation of the Worm-like Chain interpolation function."
5548 @article { marszalek02,
5549 author = PMarszalek #" and "# HLi #" and "# AOberhauser #" and "#
5551 title = "Chair-boat transitions in single polysaccharide molecules observed
5552 with force-ramp {AFM}",
5557 pages = "4278--4283",
5558 doi = "10.1073/pnas.072435699",
5559 eprint = "http://www.pnas.org/cgi/reprint/99/7/4278.pdf",
5560 url = "http://www.pnas.org/cgi/content/abstract/99/7/4278",
5561 abstract = "Under a stretching force, the sugar ring of polysaccharide
5562 molecules switches from the chair to the boat-like or inverted chair
5563 conformation. This conformational change can be observed by stretching
5564 single polysaccharide molecules with an atomic force microscope. In
5565 those early experiments, the molecules were stretched at a constant
5566 rate while the resulting force changed over wide ranges. However,
5567 because the rings undergo force-dependent transitions, an experimental
5568 arrangement where the force is the free variable introduces an
5569 undesirable level of complexity in the results. Here we demonstrate the
5570 use of force-ramp atomic force microscopy to capture the conformational
5571 changes in single polysaccharide molecules. Force-ramp atomic force
5572 microscopy readily captures the ring transitions under conditions where
5573 the entropic elasticity of the molecule is separated from its
5574 conformational transitions, enabling a quantitative analysis of the
5575 data with a simple two-state model. This analysis directly provides the
5576 physico-chemical characteristics of the ring transitions such as the
5577 width of the energy barrier, the relative energy of the conformers, and
5578 their enthalpic elasticity. Our experiments enhance the ability of
5579 single-molecule force spectroscopy to make high-resolution measurements
5580 of the conformations of single polysaccharide molecules under a
5581 stretching force, making an important addition to polysaccharide
5585 @article { marszalek99,
5586 author = PMarszalek #" and "# HLu #" and "# HLi #" and "# MCarrionVazquez
5587 #" and "# AOberhauser #" and "# KSchulten #" and "# JFernandez,
5588 title = "Mechanical unfolding intermediates in titin modules",
5597 doi = "10.1038/47083",
5598 eprint = "http://www.nature.com/nature/journal/v402/n6757/pdf/402100a0.pdf",
5599 url = "http://www.nature.com/nature/journal/v402/n6757/abs/402100a0.html",
5600 keywords = "Biomechanics;Computer Simulation;Humans;Hydrogen
5601 Bonding;Microscopy, Atomic Force;Models, Molecular;Muscle
5602 Proteins;Myocardium;Protein Folding;Protein Kinases;Recombinant
5604 abstract = "The modular protein titin, which is responsible for the passive
5605 elasticity of muscle, is subjected to stretching forces. Previous work
5606 on the experimental elongation of single titin molecules has suggested
5607 that force causes consecutive unfolding of each domain in an all-or-
5608 none fashion. To avoid problems associated with the heterogeneity of
5609 the modular, naturally occurring titin, we engineered single proteins
5610 to have multiple copies of single immunoglobulin domains of human
5611 cardiac titin. Here we report the elongation of these molecules using
5612 the atomic force microscope. We find an abrupt extension of each domain
5613 by approximately 7 A before the first unfolding event. This fast
5614 initial extension before a full unfolding event produces a reversible
5615 'unfolding intermediate' Steered molecular dynamics simulations show
5616 that the rupture of a pair of hydrogen bonds near the amino terminus of
5617 the protein domain causes an extension of about 6 A, which is in good
5618 agreement with our observations. Disruption of these hydrogen bonds by
5619 site-directed mutagenesis eliminates the unfolding intermediate. The
5620 unfolding intermediate extends titin domains by approximately 15\% of
5621 their slack length, and is therefore likely to be an important
5622 previously unrecognized component of titin elasticity."
5625 @article { mcpherson01,
5626 author = JDMcPherson #" and "# MMarra #" and "# LHillier #" and "#
5627 RHWaterston #" and "# AChinwalla #" and "# JWallis #" and "# MSekhon #"
5628 and "# KWylie #" and "# ERMardis #" and "# RKWilson #" and "# RFulton
5629 #" and "# TAKucaba #" and "# CWagner-McPherson #" and "# WBBarbazuk #"
5630 and "# SGGregory #" and "# SJHumphray #" and "# LFrench #" and "#
5631 RSEvans #" and "# GBethel #" and "# AWhittaker #" and "# JLHolden #"
5632 and "# OTMcCann #" and "# ADunham #" and "# CSoderlund #" and "#
5633 CEScott #" and "# DRBentley #" and "# GSchuler #" and "# HCChen #" and
5634 "# WJang #" and "# EDGreen #" and "# JRIdol #" and "# VVMaduro #" and
5635 "# KTMontgomery #" and "# ELee #" and "# AMiller #" and "# SEmerling #"
5636 and "# Kucherlapati #" and "# RGibbs #" and "# SScherer #" and "#
5637 JHGorrell #" and "# ESodergren #" and "# KClerc-Blankenburg #" and "#
5638 PTabor #" and "# SNaylor #" and "# DGarcia #" and "# PJdeJong #" and "#
5639 JJCatanese #" and "# NNowak #" and "# KOsoegawa #" and "# SQin #" and
5640 "# LRowen #" and "# AMadan #" and "# MDors #" and "# LHood #" and "#
5641 BTrask #" and "# CFriedman #" and "# HMassa #" and "# VGCheung #" and
5642 "# IRKirsch #" and "# TReid #" and "# RYonescu #" and "# JWeissenbach
5643 #" and "# TBruls #" and "# RHeilig #" and "# EBranscomb #" and "#
5644 AOlsen #" and "# NDoggett #" and "# JFCheng #" and "# THawkins #" and
5645 "# RMMyers #" and "# JShang #" and "# LRamirez #" and "# JSchmutz #"
5646 and "# OVelasquez #" and "# KDixon #" and "# NEStone #" and "# DRCox #"
5647 and "# DHaussler #" and "# WJKent #" and "# TFurey #" and "# SRogic #"
5648 and "# SKennedy #" and "# SJones #" and "# ARosenthal #" and "# GWen #"
5649 and "# MSchilhabel #" and "# GGloeckner #" and "# GNyakatura #" and "#
5650 RSiebert #" and "# BSchlegelberger #" and "# JKorenberg #" and "#
5651 XNChen #" and "# AFujiyama #" and "# MHattori #" and "# AToyoda #" and
5652 "# TYada #" and "# HSPark #" and "# YSakaki #" and "# NShimizu #" and
5653 "# SAsakawa #" and "# KKawasaki #" and "# TSasaki #" and "# AShintani
5654 #" and "# AShimizu #" and "# KShibuya #" and "# JKudoh #" and "#
5655 SMinoshima #" and "# JRamser #" and "# PSeranski #" and "# CHoff #" and
5656 "# APoustka #" and "# RReinhardt #" and "# HLehrach,
5657 title = "A physical map of the human genome.",
5666 doi = "10.1038/35057157",
5667 eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409934a0.pdf",
5668 url = "http://www.nature.com/nature/journal/v409/n6822/full/409934a0.html",
5669 keywords = "Chromosomes, Artificial, Bacterial;Cloning, Molecular;Contig
5670 Mapping;DNA Fingerprinting;Gene Duplication;Genome, Human;Humans;In
5671 Situ Hybridization, Fluorescence;Repetitive Sequences, Nucleic Acid",
5672 abstract = "The human genome is by far the largest genome to be sequenced,
5673 and its size and complexity present many challenges for sequence
5674 assembly. The International Human Genome Sequencing Consortium
5675 constructed a map of the whole genome to enable the selection of clones
5676 for sequencing and for the accurate assembly of the genome sequence.
5677 Here we report the construction of the whole-genome bacterial
5678 artificial chromosome (BAC) map and its integration with previous
5679 landmark maps and information from mapping efforts focused on specific
5680 chromosomal regions. We also describe the integration of sequence data
5685 author = CCMello #" and "# DBarrick,
5686 title = "An experimentally determined protein folding energy landscape",
5693 pages = "14102--14107",
5695 doi = "10.1073/pnas.0403386101",
5696 keywords = "Animals; Ankyrin Repeat; Circular Dichroism; Drosophila
5697 Proteins; Drosophila melanogaster; Gene Deletion; Models, Chemical;
5698 Models, Molecular; Protein Denaturation; Protein Folding; Protein
5699 Structure, Tertiary; Spectrometry, Fluorescence; Thermodynamics; Urea",
5700 abstract = "Energy landscapes have been used to conceptually describe and
5701 model protein folding but have been difficult to measure
5702 experimentally, in large part because of the myriad of partly folded
5703 protein conformations that cannot be isolated and thermodynamically
5704 characterized. Here we experimentally determine a detailed energy
5705 landscape for protein folding. We generated a series of overlapping
5706 constructs containing subsets of the seven ankyrin repeats of the
5707 Drosophila Notch receptor, a protein domain whose linear arrangement of
5708 modular structural units can be fragmented without disrupting
5709 structure. To a good approximation, stabilities of each construct can
5710 be described as a sum of energy terms associated with each repeat. The
5711 magnitude of each energy term indicates that each repeat is
5712 intrinsically unstable but is strongly stabilized by interactions with
5713 its nearest neighbors. These linear energy terms define an equilibrium
5714 free energy landscape, which shows an early free energy barrier and
5715 suggests preferred low-energy routes for folding."
5718 @article { merkel99,
5719 author = RMerkel #" and "# PNassoy #" and "# ALeung #" and "# KRitchie #"
5721 title = "Energy landscapes of receptor-ligand bonds explored with dynamic
5722 force spectroscopy",
5731 doi = "10.1038/16219",
5732 url = "http://www.nature.com/nature/journal/v397/n6714/full/397050a0.html",
5733 keywords = "Biotin;Microscopy, Atomic Force;Protein Binding;Streptavidin",
5734 abstract = "Atomic force microscopy (AFM) has been used to measure the
5735 strength of bonds between biological receptor molecules and their
5736 ligands. But for weak noncovalent bonds, a dynamic spectrum of bond
5737 strengths is predicted as the loading rate is altered, with the
5738 measured strength being governed by the prominent barriers traversed in
5739 the energy landscape along the force-driven bond-dissociation pathway.
5740 In other words, the pioneering early AFM measurements represent only a
5741 single point in a continuous spectrum of bond strengths, because theory
5742 predicts that these will depend on the rate at which the load is
5743 applied. Here we report the strength spectra for the bonds between
5744 streptavidin (or avidin) and biotins-the prototype of receptor-ligand
5745 interactions used in earlier AFM studies, and which have been modelled
5746 by molecular dynamics. We have probed bond formation over six orders of
5747 magnitude in loading rate, and find that the bond survival time
5748 diminished from about 1 min to 0.001 s with increasing loading rate
5749 over this range. The bond strength, meanwhile, increased from about 5
5750 pN to 170 pN. Thus, although they are among the strongest noncovalent
5751 linkages in biology (affinity of 10(13) to 10(15) M(-1)), these bonds
5752 in fact appear strong or weak depending on how fast they are loaded. We
5753 are also able to relate the activation barriers derived from our
5754 strength spectra to the shape of the energy landscape derived from
5755 simulations of the biotin-avidin complex."
5758 @article { metropolis87,
5759 author = NMetropolis,
5760 title = "The Beginning of the {M}onte {C}arlo Method",
5766 url = "http://library.lanl.gov/cgi-bin/getfile?15-12.pdf"
5769 @article { mickler07,
5770 author = MMickler #" and "# RDima #" and "# HDietz #" and "# CHyeon #" and
5771 "# DThirumalai #" and "# MRief,
5772 title = "Revealing the bifurcation in the unfolding pathways of {GFP} by
5773 using single-molecule experiments and simulations",
5778 pages = "20268--20273",
5779 doi = "10.1073/pnas.0705458104",
5780 eprint = "http://www.pnas.org/cgi/reprint/104/51/20268.pdf",
5781 url = "http://www.pnas.org/cgi/content/abstract/104/51/20268",
5782 keywords = "AFM experiments, coarse-grained simulations, cross-link
5783 mutants, pathway bifurcation, plasticity of energy landscape",
5784 abstract = "Nanomanipulation of biomolecules by using single-molecule
5785 methods and computer simulations has made it possible to visualize the
5786 energy landscape of biomolecules and the structures that are sampled
5787 during the folding process. We use simulations and single-molecule
5788 force spectroscopy to map the complex energy landscape of GFP that is
5789 used as a marker in cell biology and biotechnology. By engineering
5790 internal disulfide bonds at selected positions in the GFP structure,
5791 mechanical unfolding routes are precisely controlled, thus allowing us
5792 to infer features of the energy landscape of the wild-type GFP. To
5793 elucidate the structures of the unfolding pathways and reveal the
5794 multiple unfolding routes, the experimental results are complemented
5795 with simulations of a self-organized polymer (SOP) model of GFP. The
5796 SOP representation of proteins, which is a coarse-grained description
5797 of biomolecules, allows us to perform forced-induced simulations at
5798 loading rates and time scales that closely match those used in atomic
5799 force microscopy experiments. By using the combined approach, we show
5800 that forced unfolding of GFP involves a bifurcation in the pathways to
5801 the stretched state. After detachment of an N-terminal {alpha}-helix,
5802 unfolding proceeds along two distinct pathways. In the dominant
5803 pathway, unfolding starts from the detachment of the primary N-terminal
5804 -strand, while in the minor pathway rupture of the last, C-terminal
5805 -strand initiates the unfolding process. The combined approach has
5806 allowed us to map the features of the complex energy landscape of GFP
5807 including a characterization of the structures, albeit at a coarse-
5808 grained level, of the three metastable intermediates.",
5809 note = {Hiccup in unfolding leg corresponds to unfolding
5810 intermediate (\fref{figure}{2}). The unfolding time scale in GFP
5811 is about $6\U{ms}$.},
5815 author = RNevo #" and "# CStroh #" and "# FKienberger #" and "# DKaftan #"
5816 and "# VBrumfeld #" and "# MElbaum #" and "# ZReich #" and "#
5818 title = "A molecular switch between alternative conformational states in
5819 the complex of {Ran} and importin beta1",
5827 doi = "10.1038/nsb940",
5828 eprint = "http://www.nature.com/nsmb/journal/v10/n7/pdf/nsb940.pdf",
5829 url = "http://www.nature.com/nsmb/journal/v10/n7/abs/nsb940.html",
5830 keywords = "Guanosine Diphosphate; Guanosine Triphosphate; Microscopy,
5831 Atomic Force; Protein Binding; Protein Conformation; beta Karyopherins;
5832 ran GTP-Binding Protein",
5833 abstract = "Several million macromolecules are exchanged each minute
5834 between the nucleus and cytoplasm by receptor-mediated transport. Most
5835 of this traffic is controlled by the small GTPase Ran, which regulates
5836 assembly and disassembly of the receptor-cargo complexes in the
5837 appropriate cellular compartment. Here we applied dynamic force
5838 spectroscopy to study the interaction of Ran with the nuclear import
5839 receptor importin beta1 (impbeta) at the single-molecule level. We
5840 found that the complex alternates between two distinct conformational
5841 states of different adhesion strength. The application of an external
5842 mechanical force shifts equilibrium toward one of these states by
5843 decreasing the height of the interstate activation energy barrier. The
5844 other state can be stabilized by a functional Ran mutant that increases
5845 this barrier. These results support a model whereby functional control
5846 of Ran-impbeta is achieved by a population shift between pre-existing
5847 alternative conformations."
5851 author = RNevo #" and "# VBrumfeld #" and "# MElbaum #" and "#
5852 PHinterdorfer #" and "# ZReich,
5853 title = "Direct discrimination between models of protein activation by
5854 single-molecule force measurements",
5860 pages = "2630--2634",
5862 doi = "10.1529/biophysj.104.041889",
5863 eprint = "http://www.biophysj.org/cgi/reprint/87/4/2630.pdf",
5864 url = "http://www.biophysj.org/cgi/content/abstract/87/4/2630",
5865 keywords = "Elasticity; Enzyme Activation; Micromanipulation; Microscopy,
5866 Atomic Force; Models, Chemical; Models, Molecular; Multiprotein
5867 Complexes; Nuclear Proteins; Physical Stimulation; Protein Binding;
5868 Stress, Mechanical; Structure-Activity Relationship; beta Karyopherins;
5869 ran GTP-Binding Protein",
5870 abstract = "The limitations imposed on the analyses of complex chemical and
5871 biological systems by ensemble averaging can be overcome by single-
5872 molecule experiments. Here, we used a single-molecule technique to
5873 discriminate between two generally accepted mechanisms of a key
5874 biological process--the activation of proteins by molecular effectors.
5875 The two mechanisms, namely induced-fit and population-shift, are
5876 normally difficult to discriminate by ensemble approaches. As a model,
5877 we focused on the interaction between the nuclear transport effector,
5878 RanBP1, and two related complexes consisting of the nuclear import
5879 receptor, importin beta, and the GDP- or GppNHp-bound forms of the
5880 small GTPase, Ran. We found that recognition by the effector proceeds
5881 through either an induced-fit or a population-shift mechanism,
5882 depending on the substrate, and that the two mechanisms can be
5883 differentiated by the data."
5887 author = RNevo #" and "# VBrumfeld #" and "# RKapon #" and "# PHinterdorfer
5889 title = "Direct measurement of protein energy landscape roughness",
5897 doi = "10.1038/sj.embor.7400403",
5898 eprint = "http://www.nature.com/embor/journal/v6/n5/pdf/7400403.pdf",
5899 url = "http://www.nature.com/embor/journal/v6/n5/abs/7400403.html",
5900 keywords = "Models, Molecular; Protein Binding; Protein Folding; Spectrum
5901 Analysis; Thermodynamics; beta Karyopherins; ran GTP-Binding Protein",
5902 abstract = "The energy landscape of proteins is thought to have an
5903 intricate, corrugated structure. Such roughness should have important
5904 consequences on the folding and binding kinetics of proteins, as well
5905 as on their equilibrium fluctuations. So far, no direct measurement of
5906 protein energy landscape roughness has been made. Here, we combined a
5907 recent theory with single-molecule dynamic force spectroscopy
5908 experiments to extract the overall energy scale of roughness epsilon
5909 for a complex consisting of the small GTPase Ran and the nuclear
5910 transport receptor importin-beta. The results gave epsilon > 5k(B)T,
5911 indicating a bumpy energy surface, which is consistent with the ability
5912 of importin-beta to accommodate multiple conformations and to interact
5913 with different, structurally distinct ligands.",
5914 note = "Applies \citet{hyeon03} to ligand-receptor binding.",
5915 project = "Energy Landscape Roughness"
5919 author = SNg #" and "# KBillings #" and "# TOhashi #" and "# MAllen #" and
5920 "# RBest #" and "# LRandles #" and "# HErickson #" and "# JClarke,
5921 title = "Designing an extracellular matrix protein with enhanced mechanical
5929 pages = "9633--9637",
5930 doi = "10.1073/pnas.0609901104",
5931 eprint = "http://www.pnas.org/cgi/reprint/104/23/9633.pdf",
5932 url = "http://www.pnas.org/cgi/content/abstract/104/23/9633",
5933 abstract = "The extracellular matrix proteins tenascin and fibronectin
5934 experience significant mechanical forces in vivo. Both contain a number
5935 of tandem repeating homologous fibronectin type III (fnIII) domains,
5936 and atomic force microscopy experiments have demonstrated that the
5937 mechanical strength of these domains can vary significantly. Previous
5938 work has shown that mutations in the core of an fnIII domain from human
5939 tenascin (TNfn3) reduce the unfolding force of that domain
5940 significantly: The composition of the core is apparently crucial to the
5941 mechanical stability of these proteins. Based on these results, we have
5942 used rational redesign to increase the mechanical stability of the 10th
5943 fnIII domain of human fibronectin, FNfn10, which is directly involved
5944 in integrin binding. The hydrophobic core of FNfn10 was replaced with
5945 that of the homologous, mechanically stronger TNfn3 domain. Despite the
5946 extensive substitution, FNoTNc retains both the three-dimensional
5947 structure and the cell adhesion activity of FNfn10. Atomic force
5948 microscopy experiments reveal that the unfolding forces of the
5949 engineered protein FNoTNc increase by {approx}20% to match those of
5950 TNfn3. Thus, we have specifically designed a protein with increased
5951 mechanical stability. Our results demonstrate that core engineering can
5952 be used to change the mechanical strength of proteins while retaining
5953 functional surface interactions."
5957 author = SNg #" and "# JClarke,
5958 title = "Experiments Suggest that Simulations May Overestimate
5959 Electrostatic Contributions to the Mechanical Stability of a
5960 Fibronectin Type {III} Domain",
5964 pages = "851–854",
5969 doi = "10.1016/j.jmb.2007.06.015",
5970 url = "http://dx.doi.org/10.1016/j.jmb.2007.06.015",
5972 keywords = "MD simulations",
5974 keywords = "forced unfolding",
5975 keywords = "extracellular matrix",
5976 abstract = "Steered molecular dynamics simulations have previously
5977 been used to investigate the mechanical properties of the
5978 extracellular matrix protein fibronectin. The simulations
5979 suggest that the mechanical stability of the tenth type III
5980 domain from fibronectin (FNfn10) is largely determined by a
5981 number of critical hydrogen bonds in the peripheral
5982 strands. Interestingly, the simulations predict that lowering
5983 the pH from 7 to ∼4.7 will increase the mechanical stability
5984 of FNfn10 significantly (by ∼33 %) due to the protonation of a
5985 few key acidic residues in the A and B strands. To test this
5986 simulation prediction, we used single-molecule atomic force
5987 microscopy (AFM) to investigate the mechanical stability of
5988 FNfn10 at neutral pH and at lower pH where these key residues
5989 have been shown to be protonated. Our AFM experimental results
5990 show no difference in the mechanical stability of FNfn10 at
5991 these different pH values. These results suggest that some
5992 simulations may overestimate the role played by electrostatic
5993 interactions in determining the mechanical stability of
5998 author = RNome #" and "# JZhao #" and "# WHoff #" and "# NScherer,
5999 title = "Axis-dependent anisotropy in protein unfolding from integrated
6000 nonequilibrium single-molecule experiments, analysis, and simulation",
6007 pages = "20799--20804",
6009 doi = "10.1073/pnas.0701281105",
6010 eprint = "http://www.pnas.org/cgi/reprint/104/52/20799.pdf",
6011 url = "http://www.pnas.org/cgi/content/abstract/104/52/20799",
6012 keywords = "Anisotropy; Bacterial Proteins; Biophysics; Computer
6013 Simulation; Cysteine; Halorhodospira halophila; Hydrogen Bonding;
6014 Kinetics; Luminescent Proteins; Microscopy, Atomic Force; Molecular
6015 Conformation; Protein Binding; Protein Conformation; Protein
6016 Denaturation; Protein Folding; Protein Structure, Secondary",
6017 abstract = "We present a comprehensive study that integrates experimental
6018 and theoretical nonequilibrium techniques to map energy landscapes
6019 along well defined pull-axis specific coordinates to elucidate
6020 mechanisms of protein unfolding. Single-molecule force-extension
6021 experiments along two different axes of photoactive yellow protein
6022 combined with nonequilibrium statistical mechanical analysis and
6023 atomistic simulation reveal energetic and mechanistic anisotropy.
6024 Steered molecular dynamics simulations and free-energy curves
6025 constructed from the experimental results reveal that unfolding along
6026 one axis exhibits a transition-state-like feature where six hydrogen
6027 bonds break simultaneously with weak interactions observed during
6028 further unfolding. The other axis exhibits a constant (unpeaked) force
6029 profile indicative of a noncooperative transition, with enthalpic
6030 (e.g., H-bond) interactions being broken throughout the unfolding
6031 process. Striking qualitative agreement was found between the force-
6032 extension curves derived from steered molecular dynamics calculations
6033 and the equilibrium free-energy curves obtained by JarzynskiHummerSzabo
6034 analysis of the nonequilibrium work data. The anisotropy persists
6035 beyond pulling distances of more than twice the initial dimensions of
6036 the folded protein, indicating a rich energy landscape to the
6037 mechanically fully unfolded state. Our findings challenge the notion
6038 that cooperative unfolding is a universal feature in protein
6044 title = "Handbook of Molecular Force Spectroscopy",
6046 isbn = "978-0-387-49987-1",
6047 publisher = SPRINGER,
6048 note = "The first book about force spectroscopy. Discusses the scaffold
6049 effect in section 8.4.1."
6052 @article { nummela07,
6053 author = JNummela #" and "# IAndricioaei,
6054 title = "{Exact Low-Force Kinetics from High-Force Single-Molecule
6060 pages = "3373--3381",
6061 doi = "10.1529/biophysj.107.111658",
6062 eprint = "http://www.biophysj.org/cgi/reprint/93/10/3373.pdf",
6063 url = "http://www.biophysj.org/cgi/content/abstract/93/10/3373",
6064 abstract = "Mechanical forces play a key role in crucial cellular processes
6065 involving force-bearing biomolecules, as well as in novel single-
6066 molecule pulling experiments. We present an exact method that enables
6067 one to extrapolate, to low (or zero) forces, entire time-correlation
6068 functions and kinetic rate constants from the conformational dynamics
6069 either simulated numerically or measured experimentally at a single,
6070 relatively higher, external force. The method has twofold relevance:
6071 1), to extrapolate the kinetics at physiological force conditions from
6072 molecular dynamics trajectories generated at higher forces that
6073 accelerate conformational transitions; and 2), to extrapolate unfolding
6074 rates from experimental force-extension single-molecule curves. The
6075 theoretical formalism, based on stochastic path integral weights of
6076 Langevin trajectories, is presented for the constant-force, constant
6077 loading rate, and constant-velocity modes of the pulling experiments.
6078 For the first relevance, applications are described for simulating the
6079 conformational isomerization of alanine dipeptide; and for the second
6080 relevance, the single-molecule pulling of RNA is considered. The
6081 ability to assign a weight to each trace in the single-molecule data
6082 also suggests a means to quantitatively compare unfolding pathways
6083 under different conditions."
6086 @article { oberhauser01,
6087 author = AOberhauser #" and "# PHansma #" and "# MCarrionVazquez #" and "#
6089 title = "Stepwise unfolding of titin under force-clamp atomic force
6096 doi = "10.1073/pnas.021321798",
6097 eprint = "http://www.pnas.org/cgi/reprint/98/2/468.pdf",
6098 url = "http://www.pnas.org/cgi/content/abstract/98/2/468",
6104 title = "Cantilever spring constant calibration using laser Doppler
6114 doi = "10.1063/1.2743272",
6115 url = "http://link.aip.org/link/?RSI/78/063701/1",
6116 keywords = "calibration; vibration measurement; measurement by laser beam;
6117 Doppler measurement; measurement uncertainty; atomic force microscopy",
6118 note = "Excellent review of thermal calibration to 2007, but nothing in the
6119 way of derivations. Compares thermal tune and Sader method with laser
6120 Doppler vibrometry.",
6121 project = "Cantilever Calibration"
6124 @article { olshansky97,
6125 author = SJOlshansky #" and "# BACarnes,
6126 title = "Ever since {G}ompertz",
6129 journal = Demography,
6134 url = "http://www.jstor.org/stable/2061656",
6135 keywords = "Aging;Biometry;History, 19th Century;History, 20th
6136 Century;Humans;Life Tables;Mortality;Sexual Maturation",
6137 abstract = "In 1825 British actuary Benjamin Gompertz made a simple but
6138 important observation that a law of geometrical progression pervades
6139 large portions of different tables of mortality for humans. The simple
6140 formula he derived describing the exponential rise in death rates
6141 between sexual maturity and old age is commonly, referred to as the
6142 Gompertz equation-a formula that remains a valuable tool in demography
6143 and in other scientific disciplines. Gompertz's observation of a
6144 mathematical regularity in the life table led him to believe in the
6145 presence of a low of mortality that explained why common age patterns
6146 of death exist. This law of mortality has captured the attention of
6147 scientists for the past 170 years because it was the first among what
6148 are now several reliable empirical tools for describing the dying-out
6149 process of many living organisms during a significant portion of their
6150 life spans. In this paper we review the literature on Gompertz's law of
6151 mortality and discuss the importance of his observations and insights
6152 in light of research on aging that has taken place since then.",
6153 note = "Hardly any actual math, but the references might be interesting.
6154 I'll look into them if I have the time. Available through several
6158 @article { onuchic96,
6159 author = JNOnuchic #" and "# NDSocci #" and "# ZLuthey-Schulten #" and "#
6161 title = "Protein folding funnels: the nature of the transition state
6169 keywords = "Animals; Cytochrome c Group; Humans; Infant; Protein Folding",
6170 abstract = "BACKGROUND: Energy landscape theory predicts that the folding
6171 funnel for a small fast-folding alpha-helical protein will have a
6172 transition state half-way to the native state. Estimates of the
6173 position of the transition state along an appropriate reaction
6174 coordinate can be obtained from linear free energy relationships
6175 observed for folding and unfolding rate constants as a function of
6176 denaturant concentration. The experimental results of Huang and Oas for
6177 lambda repressor, Fersht and collaborators for C12, and Gray and
6178 collaborators for cytochrome c indicate a free energy barrier midway
6179 between the folded and unfolded regions. This barrier arises from an
6180 entropic bottleneck for the folding process. RESULTS: In keeping with
6181 the experimental results, lattice simulations based on the folding
6182 funnel description show that the transition state is not just a single
6183 conformation, but rather an ensemble of a relatively large number of
6184 configurations that can be described by specific values of one or a few
6185 order parameters (e.g. the fraction of native contacts). Analysis of
6186 this transition state or bottleneck region from our lattice simulations
6187 and from atomistic models for small alpha-helical proteins by Boczko
6188 and Brooks indicates a broad distribution for native contact
6189 participation in the transition state ensemble centered around 50\%.
6190 Importantly, however, the lattice-simulated transition state ensemble
6191 does include some particularly hot contacts, as seen in the
6192 experiments, which have been termed by others a folding nucleus.
6193 CONCLUSIONS: Linear free energy relations provide a crude spectroscopy
6194 of the transition state, allowing us to infer the values of a reaction
6195 coordinate based on the fraction of native contacts. This bottleneck
6196 may be thought of as a collection of delocalized nuclei where different
6197 native contacts will have different degrees of participation. The
6198 agreement between the experimental results and the theoretical
6199 predictions provides strong support for the landscape analysis."
6203 author = COpitz #" and "# MKulke #" and "# MLeake #" and "# CNeagoe #" and
6204 "# HHinssen #" and "# RHajjar #" and "# WALinke,
6205 title = "Damped elastic recoil of the titin spring in myofibrils of human
6211 pages = "12688--12693",
6212 doi = "10.1073/pnas.2133733100",
6213 eprint = "http://www.pnas.org/cgi/reprint/100/22/12688.pdf",
6214 url = "http://www.pnas.org/cgi/content/abstract/100/22/12688",
6215 abstract = "The giant protein titin functions as a molecular spring in
6216 muscle and is responsible for most of the passive tension of
6217 myocardium. Because the titin spring is extended during diastolic
6218 stretch, it will recoil elastically during systole and potentially may
6219 influence the overall shortening behavior of cardiac muscle. Here,
6220 titin elastic recoil was quantified in single human heart myofibrils by
6221 using a high-speed charge-coupled device-line camera and a
6222 nanonewtonrange force sensor. Application of a slack-test protocol
6223 revealed that the passive shortening velocity (Vp) of nonactivated
6224 cardiomyofibrils depends on: (i) initial sarcomere length, (ii)
6225 release-step amplitude, and (iii) temperature. Selective digestion of
6226 titin, with low doses of trypsin, decelerated myofibrillar passive
6227 recoil and eventually stopped it. Selective extraction of actin
6228 filaments with a Ca2+-independent gelsolin fragment greatly reduced the
6229 dependency of Vp on release-step size and temperature. These results
6230 are explained by the presence of viscous forces opposing myofibrillar
6231 passive recoil that are caused mainly by weak actin-titin interactions.
6232 Thus, Vp is determined by two distinct factors: titin elastic recoil
6233 and internal viscous drag forces. The recoil could be modeled as that
6234 of a damped entropic spring consisting of independent worm-like chains.
6235 The functional importance of myofibrillar elastic recoil was addressed
6236 by comparing instantaneous Vp to unloaded shortening velocity, which
6237 was measured in demembranated, fully Ca2+-activated, human cardiac
6238 fibers. Titin-driven passive recoil was much faster than active
6239 unloaded shortening velocity in early phases of isotonic contraction.
6240 Damped myofibrillar elastic recoil could help accelerate active
6241 contraction speed of human myocardium during early systolic
6245 @article { oroudjev02,
6246 author = EOroudjev #" and "# JSoares #" and "# SArcidiacono #" and "#
6247 JThompson #" and "# SFossey #" and "# HHansma,
6248 title = "Segmented nanofibers of spider dragline silk: Atomic force
6249 microscopy and single-molecule force spectroscopy",
6254 pages = "6460--6465",
6255 doi = "10.1073/pnas.082526499",
6256 eprint = "http://www.pnas.org/cgi/reprint/99/suppl_2/6460.pdf",
6257 url = "http://www.pnas.org/cgi/content/abstract/99/suppl_2/6460",
6258 abstract = "Despite its remarkable materials properties, the structure of
6259 spider dragline silk has remained unsolved. Results from two probe
6260 microscopy techniques provide new insights into the structure of spider
6261 dragline silk. A soluble synthetic protein from dragline silk
6262 spontaneously forms nanofibers, as observed by atomic force microscopy.
6263 These nanofibers have a segmented substructure. The segment length and
6264 amino acid sequence are consistent with a slab-like shape for
6265 individual silk protein molecules. The height and width of nanofiber
6266 segments suggest a stacking pattern of slab-like molecules in each
6267 nanofiber segment. This stacking pattern produces nano-crystals in an
6268 amorphous matrix, as observed previously by NMR and x-ray diffraction
6269 of spider dragline silk. The possible importance of nanofiber formation
6270 to native silk production is discussed. Force spectra for single
6271 molecules of the silk protein demonstrate that this protein unfolds
6272 through a number of rupture events, indicating a modular substructure
6273 within single silk protein molecules. A minimal unfolding module size
6274 is estimated to be around 14 nm, which corresponds to the extended
6275 length of a single repeated module, 38 amino acids long. The structure
6276 of this spider silk protein is distinctly different from the structures
6277 of other proteins that have been analyzed by single-molecule force
6278 spectroscopy, and the force spectra show correspondingly novel
6283 author = EPaci #" and "# MKarplus,
6284 title = "Unfolding proteins by external forces and temperature: The
6285 importance of topology and energetics",
6290 pages = "6521--6526",
6291 doi = "10.1073/pnas.100124597",
6292 eprint = "http://www.pnas.org/cgi/reprint/97/12/6521.pdf",
6293 url = "http://www.pnas.org/cgi/content/abstract/97/12/6521"
6297 author = EPaci #" and "# MKarplus,
6298 title = "Forced unfolding of fibronectin type 3 modules: an analysis by
6299 biased molecular dynamics simulations",
6308 doi = "10.1006/jmbi.1999.2670",
6309 keywords = "Dimerization;Fibronectins;Humans;Hydrogen Bonding;Microscopy,
6310 Atomic Force;Protein Denaturation;Protein Folding",
6311 abstract = "Titin, an important constituent of vertebrate muscles, is a
6312 protein of the order of a micrometer in length in the folded state.
6313 Atomic force microscopy and laser tweezer experiments have been used to
6314 stretch titin molecules to more than ten times their folded lengths. To
6315 explain the observed relation between force and extension, it has been
6316 suggested that the immunoglobulin and fibronectin domains unfold one at
6317 a time in an all-or-none fashion. We use molecular dynamics simulations
6318 to study the forced unfolding of two different fibronectin type 3
6319 domains (the ninth, 9Fn3, and the tenth, 10Fn3, from human fibronectin)
6320 and of their heterodimer of known structure. An external biasing
6321 potential on the N to C distance is employed and the protein is treated
6322 in the polar hydrogen representation with an implicit solvation model.
6323 The latter provides an adiabatic solvent response, which is important
6324 for the nanosecond unfolding simulation method used here. A series of
6325 simulations is performed for each system to obtain meaningful results.
6326 The two different fibronectin domains are shown to unfold in the same
6327 way along two possible pathways. These involve the partial separation
6328 of the ``beta-sandwich'', an essential structural element, and the
6329 unfolding of the individual sheets in a stepwise fashion. The biasing
6330 potential results are confirmed by constant force unfolding
6331 simulations. For the two connected domains, there is complete unfolding
6332 of one domain (9Fn3) before major unfolding of the second domain
6333 (10Fn3). Comparison of different models for the potential energy
6334 function demonstrates that the dominant cohesive element in both
6335 proteins is due to the attractive van der Waals interactions;
6336 electrostatic interactions play a structural role but appear to make
6337 only a small contribution to the stabilization of the domains, in
6338 agreement with other studies of beta-sheet stability. The unfolding
6339 forces found in the simulations are of the order of those observed
6340 experimentally, even though the speed of the former is more than six
6341 orders of magnitude greater than that used in the latter."
6345 author = QPeng #" and "# HLi,
6346 title = "Atomic force microscopy reveals parallel mechanical unfolding
6347 pathways of T4 lysozyme: Evidence for a kinetic partitioning mechanism",
6352 pages = "1885--1890",
6353 doi = "10.1073/pnas.0706775105",
6354 eprint = "http://www.pnas.org/cgi/reprint/105/6/1885.pdf",
6355 url = "http://www.pnas.org/cgi/content/abstract/105/6/1885",
6356 abstract = "Kinetic partitioning is predicted to be a general mechanism for
6357 proteins to fold into their well defined native three-dimensional
6358 structure from unfolded states following multiple folding pathways.
6359 However, experimental evidence supporting this mechanism is still
6360 limited. By using single-molecule atomic force microscopy, here we
6361 report experimental evidence supporting the kinetic partitioning
6362 mechanism for mechanical unfolding of T4 lysozyme, a small protein
6363 composed of two subdomains. We observed that on stretching from its N
6364 and C termini, T4 lysozyme unfolds by multiple distinct unfolding
6365 pathways: the majority of T4 lysozymes unfold in an all-or-none fashion
6366 by overcoming a dominant unfolding kinetic barrier; and a small
6367 fraction of T4 lysozymes unfold in three-state fashion involving
6368 unfolding intermediate states. The three-state unfolding pathways do
6369 not follow well defined routes, instead they display variability and
6370 diversity in individual unfolding pathways. The unfolding intermediate
6371 states are local energy minima along the mechanical unfolding pathways
6372 and are likely to result from the residual structures present in the
6373 two subdomains after crossing the main unfolding barrier. These results
6374 provide direct evidence for the kinetic partitioning of the mechanical
6375 unfolding pathways of T4 lysozyme, and the complex unfolding behaviors
6376 reflect the stochastic nature of kinetic barrier rupture in mechanical
6377 unfolding processes. Our results demonstrate that single-molecule
6378 atomic force microscopy is an ideal tool to investigate the
6379 folding/unfolding dynamics of complex multimodule proteins that are
6380 otherwise difficult to study using traditional methods."
6384 author = WPress #" and "# STeukolsky #" and "# WVetterling #" and "#
6386 title = "Numerical Recipies in {C}: The Art of Scientific Computing",
6390 address = "New York",
6391 eprint = "http://www.nrbook.com/a/bookcpdf.php",
6392 note = "See Sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
6393 Fourier transforms and power spectrum estimation.",
6394 project = "Cantilever Calibration"
6397 @article { puchner08,
6398 author = EPuchner #" and "# GFranzen #" and "# MGautel #" and "# HEGaub,
6399 title = "Comparing proteins by their unfolding pattern.",
6407 doi = "10.1529/biophysj.108.129999",
6408 eprint = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/pdf/426.pdf",
6409 url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2426622/",
6410 keywords = "Algorithms;Computer Simulation;Microscopy, Atomic Force;Models,
6411 Chemical;Models, Molecular;Protein Denaturation;Protein
6413 abstract = "Single molecule force spectroscopy has evolved into an
6414 important and extremely powerful technique for investigating the
6415 folding potentials of biomolecules. Mechanical tension is applied to
6416 individual molecules, and the subsequent, often stepwise unfolding is
6417 recorded in force extension traces. However, because the energy
6418 barriers of the folding potentials are often close to the thermal
6419 energy, both the extensions and the forces at which these barriers are
6420 overcome are subject to marked fluctuations. Therefore, force extension
6421 traces are an inadequate representation despite widespread use
6422 particularly when large populations of proteins need to be compared and
6423 analyzed. We show in this article that contour length, which is
6424 independent of fluctuations and alterable experimental parameters, is a
6425 more appropriate variable than extension. By transforming force
6426 extension traces into contour length space, histograms are obtained
6427 that directly represent the energy barriers. In contrast to force
6428 extension traces, such barrier position histograms can be averaged to
6429 investigate details of the unfolding potential. The cross-superposition
6430 of barrier position histograms allows us to detect and visualize the
6431 order of unfolding events. We show with this approach that in contrast
6432 to the sequential unfolding of bacteriorhodopsin, two main steps in the
6433 unfolding of the enzyme titin kinase are independent of each other. The
6434 potential of this new method for accurate and automated analysis of
6435 force spectroscopy data and for novel automated screening techniques is
6436 shown with bacteriorhodopsin and with protein constructs containing GFP
6438 note = {Contour length space and barrier position fingerprinting.
6439 There are errors in \fref{equation}{3}, propagated from
6440 \citet{livadaru03}. I contacted Elias Puchner and pointed out the
6441 typos, and he revised his FRC fit parameters from $\gamma=22\dg$
6442 and $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The
6443 combined effect on \fref{figure}{3} of fixing the equation typos
6444 and adjusting the fit parameters was small, so their conclusions
6448 @article { raible04,
6449 author = MRaible #" and "# MEvstigneev #" and "# PReimann #" and "#
6450 FWBartels #" and "# RRos,
6451 title = "Theoretical analysis of dynamic force spectroscopy experiments on
6452 ligand-receptor complexes",
6461 doi = "10.1016/j.jbiotec.2004.04.017",
6462 keywords = "Binding Sites;Computer Simulation;DNA;DNA-Binding
6463 Proteins;Elasticity;Ligands;Macromolecular
6464 Substances;Micromanipulation;Microscopy, Atomic Force;Models,
6465 Chemical;Molecular Biology;Nucleic Acid Conformation;Physical
6466 Stimulation;Protein Binding;Protein Conformation;Stress, Mechanical",
6467 abstract = "The forced rupture of single chemical bonds in biomolecular
6468 compounds (e.g. ligand-receptor systems) as observed in dynamic force
6469 spectroscopy experiments is addressed. Under the assumption that the
6470 probability of bond rupture depends only on the instantaneously acting
6471 force, a data collapse onto a single master curve is predicted. For
6472 rupture data obtained experimentally by dynamic AFM force spectroscopy
6473 of a ligand-receptor bond between a DNA and a regulatory protein we do
6474 not find such a collapse. We conclude that the above mentioned,
6475 generally accepted assumption is not satisfied and we discuss possible
6479 @article { raible06,
6480 author = MRaible #" and "# MEvstigneev #" and "# FWBartels #" and "# REckel
6481 #" and "# MNguyen-Duong #" and "# RMerkel #" and "# RRos #" and "#
6482 DAnselmetti #" and "# PReimann,
6483 title = "Theoretical analysis of single-molecule force spectroscopy
6484 experiments: heterogeneity of chemical bonds",
6491 pages = "3851--3864",
6493 doi = "10.1529/biophysj.105.077099",
6494 eprint = "http://www.biophysj.org/cgi/reprint/90/11/3851.pdf",
6495 url = "http://www.biophysj.org/cgi/content/abstract/90/11/3851",
6496 keywords = "Biomechanics;Microscopy, Atomic Force;Models,
6497 Molecular;Statistical Distributions;Thermodynamics",
6498 abstract = "We show that the standard theoretical framework in single-
6499 molecule force spectroscopy has to be extended to consistently describe
6500 the experimental findings. The basic amendment is to take into account
6501 heterogeneity of the chemical bonds via random variations of the force-
6502 dependent dissociation rates. This results in a very good agreement
6503 between theory and rupture data from several different experiments."
6506 @article{ bartels03,
6507 author = FWBartels #" and "# BBaumgarth #" and "# DAnselmetti
6508 #" and "# RRos #" and "# ABecker,
6509 title = "Specific binding of the regulatory protein Exp{G} to
6510 promoter regions of the galactoglucan biosynthesis gene cluster of
6511 Sinorhizobium meliloti--a combined molecular biology and force
6512 spectroscopy investigation.",
6513 journal = JStructBiol,
6516 address = "Experimentelle Biophysik, Fakult{\"a}t f{\"u}r Physik,
6517 Universit{\"a}t Bielefeld, 33615 Bielefeld, Germany.",
6521 keywords = "Base Sequence",
6522 keywords = "Binding Sites",
6523 keywords = "Conserved Sequence",
6524 keywords = "Fungal Proteins",
6525 keywords = "Galactans",
6526 keywords = "Glucans",
6527 keywords = "Kinetics",
6528 keywords = "Microscopy, Atomic Force",
6529 keywords = "Multigene Family",
6530 keywords = "Polysaccharides, Bacterial",
6531 keywords = "Promoter Regions, Genetic",
6532 keywords = "Protein Binding",
6533 keywords = "Sinorhizobium meliloti",
6534 keywords = "Trans-Activators",
6535 abstract = "Specific protein-DNA interaction is fundamental for all
6536 aspects of gene transcription. We focus on a regulatory
6537 DNA-binding protein in the Gram-negative soil bacterium
6538 Sinorhizobium meliloti 2011, which is capable of fixing molecular
6539 nitrogen in a symbiotic interaction with alfalfa plants. The ExpG
6540 protein plays a central role in regulation of the biosynthesis of
6541 the exopolysaccharide galactoglucan, which promotes the
6542 establishment of symbiosis. ExpG is a transcriptional activator of
6543 exp gene expression. We investigated the molecular mechanism of
6544 binding of ExpG to three associated target sequences in the exp
6545 gene cluster with standard biochemical methods and single molecule
6546 force spectroscopy based on the atomic force microscope
6547 (AFM). Binding of ExpG to expA1, expG-expD1, and expE1 promoter
6548 fragments in a sequence specific manner was demonstrated, and a 28
6549 bp conserved region was found. AFM force spectroscopy experiments
6550 confirmed the specific binding of ExpG to the promoter regions,
6551 with unbinding forces ranging from 50 to 165 pN in a logarithmic
6552 dependence from the loading rates of 70-79000 pN/s. Two different
6553 regimes of loading rate-dependent behaviour were
6554 identified. Thermal off-rates in the range of k(off)=(1.2+/-1.0) x
6555 10(-3)s(-1) were derived from the lower loading rate regime for
6556 all promoter regions. In the upper loading rate regime, however,
6557 these fragments exhibited distinct differences which are
6558 attributed to the molecular binding mechanism.",
6560 URL = "http://www.ncbi.nlm.nih.gov/pubmed/12972351",
6565 author = MRief #" and "# HGrubmuller,
6566 title = "Force spectroscopy of single biomolecules",
6575 doi = "10.1002/1439-7641(20020315)3:3<255::AID-CPHC255>3.0.CO;2-M",
6576 url = "http://www3.interscience.wiley.com/journal/91016383/abstract",
6577 keywords = "Ligands;Microscopy, Atomic Force;Polysaccharides;Protein
6578 Denaturation;Proteins",
6579 abstract = "Many processes in the body are effected and regulated by highly
6580 specialized protein molecules: These molecules certainly deserve the
6581 name ``biochemical nanomachines''. Recent progress in single-molecule
6582 experiments and corresponding simulations with supercomputers enable us
6583 to watch these ``nanomachines'' at work, revealing a host of astounding
6584 mechanisms. Examples are the fine-tuned movements of the binding pocket
6585 of a receptor protein locking into its ligand molecule and the forced
6586 unfolding of titin, which acts as a molecular shock absorber to protect
6587 muscle cells. At present, we are not capable of designing such high
6588 precision machines, but we are beginning to understand their working
6589 principles and to simulate and predict their function.",
6590 note = "Nice, general review of force spectroscopy to 2002, but not much
6596 title = "Fundamentals of Statistical and Thermal Physics",
6598 publisher = McGraw-Hill,
6599 address = "New York",
6600 note = "Thermal noise for simple harmonic oscillators, in Chapter
6601 15, Sections 6 and 10.",
6602 project = "Cantilever Calibration"
6606 author = MRief #" and "# MGautel #" and "# FOesterhelt #" and "# JFernandez
6608 title = "Reversible Unfolding of Individual Titin Immunoglobulin Domains by
6614 pages = "1109--1112",
6615 doi = "10.1126/science.276.5315.1109",
6616 eprint = "http://www.sciencemag.org/cgi/reprint/276/5315/1109.pdf",
6617 url = "http://www.sciencemag.org/cgi/content/abstract/276/5315/1109",
6618 note = "Seminal paper for force spectroscopy on Titin. Cited by
6619 \citet{dietz04} (ref 9) as an example of how unfolding large proteins
6620 is easily interpreted (vs.\ confusing unfolding in bulk), but Titin is
6621 a rather simple example of that, because of its globular-chain
6623 project = "Energy Landscape Roughness"
6627 author = MRief #" and "# FOesterhelt #" and "# BHeymann #" and "# HEGaub,
6628 title = "Single Molecule Force Spectroscopy on Polysaccharides by Atomic
6636 pages = "1295--1297",
6638 doi = "10.1126/science.275.5304.1295",
6639 eprint = "http://www.sciencemag.org/cgi/reprint/275/5304/1295.pdf",
6640 url = "http://www.sciencemag.org/cgi/content/abstract/275/5304/1295",
6641 abstract = "Recent developments in piconewton instrumentation allow the
6642 manipulation of single molecules and measurements of intermolecular as
6643 well as intramolecular forces. Dextran filaments linked to a gold
6644 surface were probed with the atomic force microscope tip by vertical
6645 stretching. At low forces the deformation of dextran was found to be
6646 dominated by entropic forces and can be described by the Langevin
6647 function with a 6 angstrom Kuhn length. At elevated forces the strand
6648 elongation was governed by a twist of bond angles. At higher forces the
6649 dextran filaments underwent a distinct conformational change. The
6650 polymer stiffened and the segment elasticity was dominated by the
6651 bending of bond angles. The conformational change was found to be
6652 reversible and was corroborated by molecular dynamics calculations."
6656 author = MRief #" and "# JFernandez #" and "# HEGaub,
6657 title = "Elastically Coupled Two-Level Systems as a Model for Biopolymer
6664 pages = "4764--4767",
6667 doi = "10.1103/PhysRevLett.81.4764",
6668 eprint = "http://prola.aps.org/pdf/PRL/v81/i21/p4764_1",
6669 url = "http://prola.aps.org/abstract/PRL/v81/i21/p4764_1",
6670 note = "Original details on mechanical unfolding analysis via Monte Carlo
6675 author = MRief #" and "# HClausen-Schaumann #" and "# HEGaub,
6676 title = "Sequence-dependent mechanics of single {DNA} molecules",
6684 doi = "10.1038/7582",
6685 eprint = "http://www.nature.com/nsmb/journal/v6/n4/pdf/nsb0499_346.pdf",
6686 url = "http://www.nature.com/nsmb/journal/v6/n4/abs/nsb0499_346.html",
6687 keywords = "Bacteriophage lambda;Base Pairing;DNA;DNA, Single-Stranded;DNA,
6688 Viral;Gold;Mechanics;Microscopy, Atomic Force;Nucleotides;Spectrum
6689 Analysis;Thermodynamics",
6690 abstract = "Atomic force microscope-based single-molecule force
6691 spectroscopy was employed to measure sequence-dependent mechanical
6692 properties of DNA by stretching individual DNA double strands attached
6693 between a gold surface and an AFM tip. We discovered that in lambda-
6694 phage DNA the previously reported B-S transition, where 'S' represents
6695 an overstretched conformation, at 65 pN is followed by a nonequilibrium
6696 melting transition at 150 pN. During this transition the DNA is split
6697 into single strands that fully recombine upon relaxation. The sequence
6698 dependence was investigated in comparative studies with poly(dG-dC) and
6699 poly(dA-dT) DNA. Both the B-S and the melting transition occur at
6700 significantly lower forces in poly(dA-dT) compared to poly(dG-dC). We
6701 made use of the melting transition to prepare single poly(dG-dC) and
6702 poly(dA-dT) DNA strands that upon relaxation reannealed into hairpins
6703 as a result of their self-complementary sequence. The unzipping of
6704 these hairpins directly revealed the base pair-unbinding forces for G-C
6705 to be 20 +/- 3 pN and for A-T to be 9 +/- 3 pN."
6708 @article{ schmitt00,
6709 author = LSchmitt #" and "# MLudwig #" and "# HEGaub #" and "# RTampe,
6710 title = "A metal-chelating microscopy tip as a new toolbox for
6711 single-molecule experiments by atomic force microscopy.",
6715 address = "Institut f{\"u}r Physiologische Chemie,
6716 Philipps-Universit{\"a}t Marburg, 35033 Marburg,
6717 Germany. schmittl@mailer.uni-marburg.de",
6720 pages = "3275--3285",
6721 keywords = "Chelating Agents",
6722 keywords = "Edetic Acid",
6723 keywords = "Histidine",
6724 keywords = "Metals",
6725 keywords = "Microscopy, Atomic Force",
6726 keywords = "Nitrilotriacetic Acid",
6727 keywords = "Peptides",
6728 keywords = "Recombinant Fusion Proteins",
6729 abstract = "In recent years, the atomic force microscope (AFM) has
6730 contributed much to our understanding of the molecular forces
6731 involved in various high-affinity receptor-ligand
6732 systems. However, a universal anchor system for such measurements
6733 is still required. This would open up new possibilities for the
6734 study of biological recognition processes and for the
6735 establishment of high-throughput screening applications. One such
6736 candidate is the N-nitrilo-triacetic acid (NTA)/His-tag system,
6737 which is widely used in molecular biology to isolate and purify
6738 histidine-tagged fusion proteins. Here the histidine tag acts as a
6739 high-affinity recognition site for the NTA chelator. Accordingly,
6740 we have investigated the possibility of using this approach in
6741 single-molecule force measurements. Using a histidine-peptide as a
6742 model system, we have determined the binding force for various
6743 metal ions. At a loading rate of 0.5 microm/s, the determined
6744 forces varied from 22 +/- 4 to 58 +/- 5 pN. Most importantly, no
6745 interaction was detected for Ca(2+) and Mg(2+) up to
6746 concentrations of 10 mM. Furthermore, EDTA and a metal ion
6747 reloading step demonstrated the reversibility of the
6748 approach. Here the molecular interactions were turned off (EDTA)
6749 and on (metal reloading) in a switch-like fashion. Our results
6750 show that the NTA/His-tag system will expand the ``molecular
6751 toolboxes'' with which receptor-ligand systems can be investigated
6752 at the single-molecule level.",
6754 doi = "10.1016/S0006-3495(00)76863-9",
6755 URL = "http://www.ncbi.nlm.nih.gov/pubmed/10828003",
6759 @article { roters96,
6760 author = ARoters #" and "# DJohannsmann,
6761 title = "Distance-dependent noise measurements in scanning force
6767 pages = "7561-7577",
6768 doi = "10.1088/0953-8984",
6769 eprint = "http://www.iop.org/EJ/article/0953-8984/8/41/006/c64103.pdf",
6770 url = "http://stacks.iop.org/0953-8984/8/7561",
6771 abstract = "The changes in the thermal noise spectrum of a scanning-force-
6772 microscope cantilever upon approach of the tip to the sample were used
6773 to investigate the interactions between the cantilever and the sample.
6774 The investigation of thermal noise is the natural choice for dynamic
6775 measurements with little disturbance of the sample. In particular, the
6776 small amplitudes involved ensure linear dynamic response. It is
6777 possible to discriminate between viscous coupling, elastic coupling and
6778 changes in the effective mass. The technique is versatile in terms of
6779 substrates and environments. Hydrodynamic long-range interactions
6780 depending on the sample, the geometry and the ambient medium are
6781 observed. The dependence of hydrodynamic interaction on various
6782 parameters such as the viscosity and the density of the medium is
6783 described. For sufficiently soft surfaces, the method is sensitive to
6784 viscoelastic properties of the surface. For example, the viscous
6785 coupling to the surface is strongly increased when the surface is
6786 covered with a swollen `polymer brush'.",
6787 note = "They actually write down a Lagrangian formula and give a decent
6788 derivation of PSD, but don't show or work out the integrals.",
6789 project = "Cantilever Calibration"
6793 author = FGittes #" and "# CFSchmidt,
6794 title = {Thermal noise limitations on micromechanical experiments},
6801 doi = {10.1007/s002490050113},
6802 url = {http://dx.doi.org/10.1007/s002490050113},
6804 publisher = SPRINGER:V,
6805 keywords = {Key words Thermal noise; Optical tweezers; Atomic force
6806 microscopy; Single molecules; Micromechanics},
6807 language = {English},
6810 @article { ryckaert77,
6811 author = JPRyckaert #" and "# GCiccotti #" and "# HJCBerendsen,
6812 title = "Numerical integration of the cartesian equations of motion of a
6813 system with constraints: molecular dynamics of n-alkanes",
6820 doi = "10.1016/0021-9991(77)90098-5",
6821 url = "http://dx.doi.org/10.1016/0021-9991(77)90098-5",
6822 abstract = "A numerical algorithm integrating the 3N Cartesian equations of
6823 motion of a system of N points subject to holonomic constraints is
6824 formulated. The relations of constraint remain perfectly fulfilled at
6825 each step of the trajectory despite the approximate character of
6826 numerical integration. The method is applied to a molecular dynamics
6827 simulation of a liquid of 64 n-butane molecules and compared to a
6828 simulation using generalized coordinates. The method should be useful
6829 for molecular dynamics calculations on large molecules with internal
6830 degrees of freedom.",
6831 note = "Entry-level explaination of MD with rigid constraints. Explicit
6832 Verlet integrator example."
6835 @article { sarkar04,
6836 author = ASarkar #" and "# RRobertson #" and "# JFernandez,
6837 title = "Simultaneous atomic force microscope and fluorescence measurements
6838 of protein unfolding using a calibrated evanescent wave",
6843 pages = "12882--12886",
6844 doi = "10.1073/pnas.0403534101",
6845 eprint = "http://www.pnas.org/cgi/reprint/101/35/12882.pdf",
6846 url = "http://www.pnas.org/cgi/content/abstract/101/35/12882",
6847 abstract = "Fluorescence techniques for monitoring single-molecule dynamics
6848 in the vertical dimension currently do not exist. Here we use an atomic
6849 force microscope to calibrate the distance-dependent intensity decay of
6850 an evanescent wave. The measured evanescent wave transfer function was
6851 then used to convert the vertical motions of a fluorescent particle
6852 into displacement ($SD =< 1$ nm). We demonstrate the use of the
6853 calibrated evanescent wave to resolve the 20.1 {+/-} 0.5-nm step
6854 increases in the length of the small protein ubiquitin during forced
6855 unfolding. The experiments that we report here make an important
6856 contribution to fluorescence microscopy by demonstrating the
6857 unambiguous optical tracking of a single molecule with a resolution
6858 comparable to that of an atomic force microscope."
6862 author = TSato #" and "# MEsaki #" and "# JFernandez #" and "# TEndo,
6863 title = "{Comparison of the protein-unfolding pathways between
6864 mitochondrial protein import and atomic-force microscopy measurements}",
6869 pages = "17999--18004",
6870 doi = "10.1073/pnas.0504495102",
6871 eprint = "http://www.pnas.org/cgi/reprint/102/50/17999.pdf",
6872 url = "http://www.pnas.org/cgi/content/abstract/102/50/17999",
6873 abstract = "Many newly synthesized proteins have to become unfolded during
6874 translocation across biological membranes. We have analyzed the effects
6875 of various stabilization/destabilization mutations in the Ig-like
6876 module of the muscle protein titin upon its import from the N terminus
6877 or C terminus into mitochondria. The effects of mutations on the import
6878 of the titin module from the C terminus correlate well with those on
6879 forced mechanical unfolding in atomic-force microscopy (AFM)
6880 measurements. On the other hand, as long as turnover of the
6881 mitochondrial Hsp70 system is not rate-limiting for the import, import
6882 of the titin module from the N terminus is sensitive to mutations in
6883 the N-terminal region but not the ones in the C-terminal region that
6884 affect resistance to global unfolding in AFM experiments. We propose
6885 that the mitochondrial-import system can catalyze precursor-unfolding
6886 by reducing the stability of unfolding intermediates."
6889 @article { schlierf04,
6890 author = MSchlierf #" and "# HLi #" and "# JFernandez,
6891 title = "The unfolding kinetics of ubiquitin captured with single-molecule
6892 force-clamp techniques",
6899 pages = "7299--7304",
6901 doi = "10.1073/pnas.0400033101",
6902 eprint = "http://www.pnas.org/cgi/reprint/101/19/7299.pdf",
6903 url = "http://www.pnas.org/cgi/content/abstract/101/19/7299",
6904 keywords = "Kinetics;Microscopy, Atomic Force;Probability;Ubiquitin",
6905 abstract = "We use single-molecule force spectroscopy to study the kinetics
6906 of unfolding of the small protein ubiquitin. Upon a step increase in
6907 the stretching force, a ubiquitin polyprotein extends in discrete steps
6908 of 20.3 +/- 0.9 nm marking each unfolding event. An average of the time
6909 course of these unfolding events was well described by a single
6910 exponential, which is a necessary condition for a memoryless Markovian
6911 process. Similar ensemble averages done at different forces showed that
6912 the unfolding rate was exponentially dependent on the stretching force.
6913 Stretching a ubiquitin polyprotein with a force that increased at a
6914 constant rate (force-ramp) directly measured the distribution of
6915 unfolding forces. This distribution was accurately reproduced by the
6916 simple kinetics of an all-or-none unfolding process. Our force-clamp
6917 experiments directly demonstrate that an ensemble average of ubiquitin
6918 unfolding events is well described by a two-state Markovian process
6919 that obeys the Arrhenius equation. However, at the single-molecule
6920 level, deviant behavior that is not well represented in the ensemble
6921 average is readily observed. Our experiments make an important addition
6922 to protein spectroscopy by demonstrating an unambiguous method of
6923 analysis of the kinetics of protein unfolding by a stretching force."
6926 @article { schlierf06,
6927 author = MSchlierf #" and "# MRief,
6928 title = "Single-molecule unfolding force distributions reveal a funnel-
6929 shaped energy landscape",
6938 doi = "10.1529/biophysj.105.077982",
6939 url = "http://www.biophysj.org/cgi/content/abstract/90/4/L33",
6940 keywords = "Models, Molecular; Protein Folding; Proteins; Thermodynamics",
6941 abstract = "The protein folding process is described as diffusion on a
6942 high-dimensional energy landscape. Experimental data showing details of
6943 the underlying energy surface are essential to understanding folding.
6944 So far in single-molecule mechanical unfolding experiments a simplified
6945 model assuming a force-independent transition state has been used to
6946 extract such information. Here we show that this so-called Bell model,
6947 although fitting well to force velocity data, fails to reproduce full
6948 unfolding force distributions. We show that by applying Kramers'
6949 diffusion model, we were able to reconstruct a detailed funnel-like
6950 curvature of the underlying energy landscape and establish full
6951 agreement with the data. We demonstrate that obtaining spatially
6952 resolved details of the unfolding energy landscape from mechanical
6953 single-molecule protein unfolding experiments requires models that go
6954 beyond the Bell model.",
6955 note = {The inspiration behind my sawtooth simulation. Bell model
6956 fit to $f_{unfold}(v)$, but Kramers model fit to unfolding
6957 distribution for a given $v$. \fref{equation}{3} in the
6958 supplement is \xref{evans99}{equation}{2}, but it is just
6959 $[\text{dying percent}] \cdot [\text{surviving population}]
6961 $\nu \equiv k$ is the force/time-dependent off rate. The Kramers'
6962 rate equation (on page L34, the second equation in the paper) is
6963 \xref{hanggi90}{equation}{4.56b} (page 275) and
6964 \xref{socci96}{equation}{2} but \citet{schlierf06} gets the minus
6965 sign wrong in the exponent. $U_F(x=0)\gg 0$ and
6966 $U_F(x_\text{max})\ll 0$ (\cf~\xref{schlierf06}{figure}{1}).
6967 Schlierf's integral (as written) contains
6968 $\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, which is huge, when
6969 it should contain $\exp{U_F(x_\text{max})}\cdot\exp{-U_F(0)}$,
6970 which is tiny. For more details and a picture of the peak that
6971 forms the bulk of the integrand, see
6972 \cref{eq:kramers,fig:kramers:integrand}. I pointed out this
6973 problem to Michael Schlierf, but he was unconvinced.},
6976 @article { schwaiger04,
6977 author = ISchwaiger #" and "# AKardinal #" and "# MSchleicher #" and "#
6978 AANoegel #" and "# MRief,
6979 title = "A mechanical unfolding intermediate in an actin-crosslinking
6989 doi = "10.1038/nsmb705",
6990 eprint = "http://www.nature.com/nsmb/journal/v11/n1/pdf/nsmb705.pdf",
6991 url = "http://www.nature.com/nsmb/journal/v11/n1/full/nsmb705.html",
6992 keywords = "Actins; Animals; Contractile Proteins; Cross-Linking Reagents;
6993 Dictyostelium; Dimerization; Microfilament Proteins; Microscopy, Atomic
6994 Force; Mutagenesis, Site-Directed; Protein Denaturation; Protein
6995 Folding; Protein Structure, Tertiary; Protozoan Proteins",
6996 abstract = "Many F-actin crosslinking proteins consist of two actin-binding
6997 domains separated by a rod domain that can vary considerably in length
6998 and structure. In this study, we used single-molecule force
6999 spectroscopy to investigate the mechanics of the immunoglobulin (Ig)
7000 rod domains of filamin from Dictyostelium discoideum (ddFLN). We find
7001 that one of the six Ig domains unfolds at lower forces than do those of
7002 all other domains and exhibits a stable unfolding intermediate on its
7003 mechanical unfolding pathway. Amino acid inserts into various loops of
7004 this domain lead to contour length changes in the single-molecule
7005 unfolding pattern. These changes allowed us to map the stable core of
7006 approximately 60 amino acids that constitutes the unfolding
7007 intermediate. Fast refolding in combination with low unfolding forces
7008 suggest a potential in vivo role for this domain as a mechanically
7009 extensible element within the ddFLN rod.",
7010 note = "ddFLN unfolding with WLC params for sacrificial domains. Gives
7011 persistence length $p = 0.5\mbox{ nm}$ in ``high force regime'', $p =
7012 0.9\mbox{ nm}$ in ``low force regime'', with a transition at $F =
7014 project = "sawtooth simulation"
7017 @article { schwaiger05,
7018 author = ISchwaiger #" and "# MSchleicher #" and "# AANoegel #" and "#
7020 title = "The folding pathway of a fast-folding immunoglobulin domain
7021 revealed by single-molecule mechanical experiments",
7029 doi = "10.1038/sj.embor.7400317",
7030 eprint = "http://www.nature.com/embor/journal/v6/n1/pdf/7400317.pdf",
7031 url = "http://www.nature.com/embor/journal/v6/n1/index.html",
7032 keywords = "Animals; Contractile Proteins; Dictyostelium; Immunoglobulins;
7033 Kinetics; Microfilament Proteins; Models, Molecular; Protein Folding;
7034 Protein Structure, Tertiary",
7035 abstract = "The F-actin crosslinker filamin from Dictyostelium discoideum
7036 (ddFLN) has a rod domain consisting of six structurally similar
7037 immunoglobulin domains. When subjected to a stretching force, domain 4
7038 unfolds at a lower force than all the other domains in the chain.
7039 Moreover, this domain shows a stable intermediate along its mechanical
7040 unfolding pathway. We have developed a mechanical single-molecule
7041 analogue to a double-jump stopped-flow experiment to investigate the
7042 folding kinetics and pathway of this domain. We show that an obligatory
7043 and productive intermediate also occurs on the folding pathway of the
7044 domain. Identical mechanical properties suggest that the unfolding and
7045 refolding intermediates are closely related. The folding process can be
7046 divided into two consecutive steps: in the first step 60 C-terminal
7047 amino acids form an intermediate at the rate of 55 s(-1); and in the
7048 second step the remaining 40 amino acids are packed on this core at the
7049 rate of 179 s(-1). This division increases the overall folding rate of
7050 this domain by a factor of ten compared with all other homologous
7051 domains of ddFLN that lack the folding intermediate."
7054 @article { sharma07,
7055 author = DSharma #" and "# OPerisic #" and "# QPeng #" and "# YCao #" and
7056 "# CLam #" and "# HLu #" and "# HLi,
7057 title = "Single-molecule force spectroscopy reveals a mechanically stable
7058 protein fold and the rational tuning of its mechanical stability",
7063 pages = "9278--9283",
7064 doi = "10.1073/pnas.0700351104",
7065 eprint = "http://www.pnas.org/cgi/reprint/104/22/9278.pdf",
7066 url = "http://www.pnas.org/cgi/content/abstract/104/22/9278",
7067 abstract = "It is recognized that shear topology of two directly connected
7068 force-bearing terminal [beta]-strands is a common feature among the
7069 vast majority of mechanically stable proteins known so far. However,
7070 these proteins belong to only two distinct protein folds, Ig-like
7071 [beta] sandwich fold and [beta]-grasp fold, significantly hindering
7072 delineating molecular determinants of mechanical stability and rational
7073 tuning of mechanical properties. Here we combine single-molecule atomic
7074 force microscopy and steered molecular dynamics simulation to reveal
7075 that the de novo designed Top7 fold [Kuhlman B, Dantas G, Ireton GC,
7076 Varani G, Stoddard BL, Baker D (2003) Science 302:13641368] represents
7077 a mechanically stable protein fold that is distinct from Ig-like [beta]
7078 sandwich and [beta]-grasp folds. Although the two force-bearing [beta]
7079 strands of Top7 are not directly connected, Top7 displays significant
7080 mechanical stability, demonstrating that the direct connectivity of
7081 force-bearing [beta] strands in shear topology is not mandatory for
7082 mechanical stability. This finding broadens our understanding of the
7083 design of mechanically stable proteins and expands the protein fold
7084 space where mechanically stable proteins can be screened. Moreover, our
7085 results revealed a substructure-sliding mechanism for the mechanical
7086 unfolding of Top7 and the existence of two possible unfolding pathways
7087 with different height of energy barrier. Such insights enabled us to
7088 rationally tune the mechanical stability of Top7 by redesigning its
7089 mechanical unfolding pathway. Our study demonstrates that computational
7090 biology methods (including de novo design) offer great potential for
7091 designing proteins of defined topology to achieve significant and
7092 tunable mechanical properties in a rational and systematic fashion."
7096 author = YJSheng #" and "# SJiang #" and "# HKTsao,
7097 title = "Forced Kramers escape in single-molecule pulling experiments",
7107 doi = "10.1063/1.2046632",
7108 url = "http://link.aip.org/link/?JCP/123/091102/1",
7109 keywords = "molecular biophysics; bonds (chemical); proteins",
7110 note = "Gives appropriate Einstein-S... relation for diffusion to damping",
7111 project = "sawtooth simulation"
7114 @article { shillcock98,
7115 author = JShillcock #" and "# USeifert,
7116 title = "Escape from a metastable well under a time-ramped force",
7122 pages = "7301--7304",
7125 doi = "10.1103/PhysRevE.57.7301",
7126 eprint = "http://prola.aps.org/pdf/PRE/v57/i6/p7301_1",
7127 url = "http://link.aps.org/abstract/PRE/v57/p7301",
7128 project = "sawtooth simulation"
7132 author = GESims #" and "# SRJun #" and "# GAWu #" and "# SHKim,
7133 title = "Alignment-free genome comparison with feature frequency profiles
7134 ({FFP}) and optimal resolutions",
7141 pages = "2677--2682",
7143 doi = "10.1073/pnas.0813249106",
7144 eprint = "http://www.pnas.org/cgi/reprint/106/31/12826",
7145 url = "http://www.pnas.org/content/106/8/2677",
7146 keywords = "Genome;Introns;Phylogeny",
7147 abstract = "For comparison of whole-genome (genic + nongenic) sequences,
7148 multiple sequence alignment of a few selected genes is not appropriate.
7149 One approach is to use an alignment-free method in which feature (or
7150 l-mer) frequency profiles (FFP) of whole genomes are used for
7151 comparison-a variation of a text or book comparison method, using word
7152 frequency profiles. In this approach it is critical to identify the
7153 optimal resolution range of l-mers for the given set of genomes
7154 compared. The optimum FFP method is applicable for comparing whole
7155 genomes or large genomic regions even when there are no common genes
7156 with high homology. We outline the method in 3 stages: (i) We first
7157 show how the optimal resolution range can be determined with English
7158 books which have been transformed into long character strings by
7159 removing all punctuation and spaces. (ii) Next, we test the robustness
7160 of the optimized FFP method at the nucleotide level, using a mutation
7161 model with a wide range of base substitutions and rearrangements. (iii)
7162 Finally, to illustrate the utility of the method, phylogenies are
7163 reconstructed from concatenated mammalian intronic genomes; the FFP
7164 derived intronic genome topologies for each l within the optimal range
7165 are all very similar. The topology agrees with the established
7166 mammalian phylogeny revealing that intron regions contain a similar
7167 level of phylogenic signal as do coding regions."
7171 author = SBSmith #" and "# LFinzi #" and "# CBustamante,
7172 title = "Direct mechanical measurements of the elasticity of single {DNA}
7173 molecules by using magnetic beads",
7180 pages = "1122--1126",
7182 doi = "10.1126/science.1439819",
7183 eprint = "http://www.sciencemag.org/cgi/reprint/258/5085/1122.pdf",
7184 url = "http://www.sciencemag.org/cgi/content/abstract/258/5085/1122",
7185 keywords = "Chemistry,
7186 Physical;Cisplatin;DNA;Elasticity;Ethidium;Glass;Indoles;Intercalating
7187 Agents;Magnetics;Mathematics;Microspheres",
7188 abstract = "Single DNA molecules were chemically attached by one end to a
7189 glass surface and by their other end to a magnetic bead. Equilibrium
7190 positions of the beads were observed in an optical microscope while the
7191 beads were acted on by known magnetic and hydrodynamic forces.
7192 Extension versus force curves were obtained for individual DNA
7193 molecules at three different salt concentrations with forces between
7194 10(-14) and 10(-11) newtons. Deviations from the force curves predicted
7195 by the freely jointed chain model suggest that DNA has significant
7196 local curvature in solution. Ethidium bromide and
7197 4',6-diamidino-2-phenylindole had little effect on the elastic response
7198 of the molecules, but their extent of intercalation was directly
7199 measured. Conversely, the effect of bend-inducing cis-
7200 diamminedichloroplatinum (II) was large and supports the hypothesis of
7201 natural curvature in DNA."
7205 author = SBSmith #" and "# YCui #" and "# CBustamante,
7206 title = "Overstretching {B}-{DNA}: the elastic response of individual
7207 double-stranded and single-stranded {DNA} molecules",
7216 keywords = "Base Composition;Chemistry, Physical;DNA;DNA, Single-
7217 Stranded;Elasticity;Nucleic Acid Conformation;Osmolar
7218 Concentration;Thermodynamics",
7219 abstract = "Single molecules of double-stranded DNA (dsDNA) were stretched
7220 with force-measuring laser tweezers. Under a longitudinal stress of
7221 approximately 65 piconewtons (pN), dsDNA molecules in aqueous buffer
7222 undergo a highly cooperative transition into a stable form with 5.8
7223 angstroms rise per base pair, that is, 70\% longer than B form dsDNA.
7224 When the stress was relaxed below 65 pN, the molecules rapidly and
7225 reversibly contracted to their normal contour lengths. This transition
7226 was affected by changes in the ionic strength of the medium and the
7227 water activity or by cross-linking of the two strands of dsDNA.
7228 Individual molecules of single-stranded DNA were also stretched giving
7229 a persistence length of 7.5 angstroms and a stretch modulus of 800 pN.
7230 The overstretched form may play a significant role in the energetics of
7235 author = NDSocci #" and "# JNOnuchic #" and "# PGWolynes,
7236 title = "Diffusive dynamics of the reaction coordinate for protein folding
7243 pages = "5860--5868",
7245 doi = "10.1063/1.471317",
7246 eprint = "http://arxiv.org/pdf/cond-mat/9601091",
7247 url = "http://link.aip.org/link/?JCP/104/5860/1",
7248 keywords = "PROTEINS; FOLDS; DIFFUSION; MONTE CARLO METHOD; SIMULATION;
7250 abstract = "The quantitative description of model protein folding kinetics
7251 using a diffusive collective reaction coordinate is examined. Direct
7252 folding kinetics, diffusional coefficients and free energy profiles are
7253 determined from Monte Carlo simulations of a 27-mer, 3 letter code
7254 lattice model, which corresponds roughly to a small helical protein.
7255 Analytic folding calculations, using simple diffusive rate theory,
7256 agree extremely well with the full simulation results. Folding in this
7257 system is best seen as a diffusive, funnel-like process.",
7258 note = "A nice introduction to some quantitative ramifications of the
7259 funnel energy landscape. There's also a bit of Kramers' theory and
7260 graph theory thrown in for good measure."
7264 author = NDSocci #" and "# JNOnuchic #" and "# PGWolynes,
7265 title = "Stretching lattice models of protein folding",
7272 pages = "2031--2035",
7274 keywords = "Amino Acid Sequence;Drug Stability;Kinetics;Models,
7275 Theoretical;Molecular Sequence Data;Peptides;Protein
7276 Denaturation;Protein Folding",
7277 abstract = "A new class of experiments that probe folding of individual
7278 protein domains uses mechanical stretching to cause the transition. We
7279 show how stretching forces can be incorporated in lattice models of
7280 folding. For fast folding proteins, the analysis suggests a complex
7281 relation between the force dependence and the reaction coordinate for
7285 @article { staple08,
7286 author = DBStaple #" and "# SHPayne #" and "# ALCReddin #" and "# HJKreuzer,
7287 title = "Model for stretching and unfolding the giant multidomain muscle
7288 protein using single-molecule force spectroscopy.",
7297 doi = "10.1103/PhysRevLett.101.248301",
7298 url = "http://dx.doi.org/10.1103/PhysRevLett.101.248301",
7299 keywords = "Kinetics;Microscopy, Atomic Force;Models, Chemical;Muscle
7300 Proteins;Protein Conformation;Protein Folding;Protein Kinases;Protein
7301 Structure, Tertiary;Thermodynamics",
7302 abstract = "Single-molecule manipulation has allowed the forced unfolding
7303 of multidomain proteins. Here we outline a theory that not only
7304 explains these experiments but also points out a number of difficulties
7305 in their interpretation and makes suggestions for further experiments.
7306 For titin we reproduce force-extension curves, the dependence of break
7307 force on pulling speed, and break-force distributions and also validate
7308 two common experimental views: Unfolding titin Ig domains can be
7309 explained as stepwise increases in contour length, and increasing force
7310 peaks in native Ig sequences represent a hierarchy of bond strengths.
7311 Our theory is valid for essentially any molecule that can be unfolded
7312 in atomic force microscopy; as a further example, we present force-
7313 extension curves for the unfolding of RNA hairpins."
7317 author = RStark #" and "# TDrobek #" and "# WHeckl,
7318 title = "Thermomechanical noise of a free v-shaped cantilever for atomic-
7327 doi = "http://dx.doi.org/10.1016/S0304-3991(00)00077-2",
7328 abstract = "We have calculated the thermal noise of a v-shaped AFM
7329 cantilever (Microlever, Type E, Thermomicroscopes) by means of a finite
7330 element analysis. The modal shapes of the first 10 eigenmodes are
7331 displayed as well as the numerical constants, which are needed for the
7332 calibration using the thermal noise method. In the first eigenmode,
7333 values for the thermomechanical noise of the z-displacement at 22
7334 degrees C temperature of square root of u2(1) = A/square root of
7335 c(cant) and the photodiode signal (normal-force) of S2(1) = A/square
7336 root of c(cant) were obtained. The results also indicate a systematic
7337 deviation ofthe spectral density of the thermomechanical noise of
7338 v-shaped cantilevers as compared to rectangular beam-shaped
7340 note = "Higher mode adjustments for v-shaped cantilevers from simulation.",
7341 project = "Cantilever Calibration"
7344 @article { strick96,
7345 author = TRStrick #" and "# JFAllemand #" and "# DBensimon #" and "#
7346 ABensimon #" and "# VCroquette,
7347 title = "The elasticity of a single supercoiled {DNA} molecule",
7354 pages = "1835--1837",
7356 keywords = "Bacteriophage lambda;DNA, Superhelical;DNA,
7357 Viral;Elasticity;Magnetics;Nucleic Acid Conformation;Temperature",
7358 abstract = "Single linear DNA molecules were bound at multiple sites at one
7359 extremity to a treated glass cover slip and at the other to a magnetic
7360 bead. The DNA was therefore torsionally constrained. A magnetic field
7361 was used to rotate the beads and thus to coil and pull the DNA. The
7362 stretching force was determined by analysis of the Brownian
7363 fluctuations of the bead. Here the elastic behavior of individual
7364 lambda DNA molecules over- and underwound by up to 500 turns was
7365 studied. A sharp transition was discovered from a low to a high
7366 extension state at a force of approximately 0.45 piconewtons for
7367 underwound molecules and at a force of approximately 3 piconewtons for
7368 overwound ones. These transitions, probably reflecting the formation of
7369 alternative structures in stretched coiled DNA molecules, might be
7370 relevant for DNA transcription and replication."
7373 @article { strunz99,
7374 author = TStrunz #" and "# KOroszlan #" and "# RSchafer #" and "#
7376 title = "Dynamic force spectroscopy of single {DNA} molecules",
7381 pages = "11277--11282",
7382 doi = "10.1073/pnas.96.20.11277",
7383 eprint = "http://www.pnas.org/cgi/reprint/96/20/11277.pdf",
7384 url = "http://www.pnas.org/cgi/content/abstract/96/20/11277"
7388 author = ASzabo #" and "# KSchulten #" and "# ZSchulten,
7389 title = "First passage time approach to diffusion controlled reactions",
7395 pages = "4350--4357",
7397 doi = "10.1063/1.439715",
7398 url = "http://link.aip.org/link/?JCP/72/4350/1",
7399 keywords = "DIFFUSION; CHEMICAL REACTIONS; CHEMICAL REACTION KINETICS;
7400 PROBABILITY; DIFFERENTIAL EQUATIONS"
7403 @article { talaga00,
7404 author = DTalaga #" and "# WLau #" and "# HRoder #" and "# JTang #" and "#
7405 YJia #" and "# WDeGrado #" and "# RHochstrasser,
7406 title = "Dynamics and folding of single two-stranded coiled-coil peptides
7407 studied by fluorescent energy transfer confocal microscopy",
7412 pages = "13021--13026",
7413 doi = "10.1073/pnas.97.24.13021",
7414 eprint = "http://www.pnas.org/cgi/reprint/97/24/13021.pdf",
7415 url = "http://www.pnas.org/cgi/content/abstract/97/24/13021"
7418 @article { thirumalai05,
7419 author = DThirumalai #" and "# CHyeon,
7420 title = "{RNA} and Protein Folding: Common Themes and Variations",
7421 affiliation = "Biophysics Program, and Department of Chemistry and
7422 Biochemistry, Institute for Physical Science and Technology, University
7423 of Maryland, College Park, Maryland 20742",
7428 pages = "4957--4970",
7431 "http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/bi047314+",
7432 abstract = "Visualizing the navigation of an ensemble of unfolded molecules
7433 through the bumpy energy landscape in search of the native state gives
7434 a pictorial view of biomolecular folding. This picture, when combined
7435 with concepts in polymer theory, provides a unified theory of RNA and
7436 protein folding. Just as for proteins, the major folding free energy
7437 barrier for RNA scales sublinearly with the number of nucleotides,
7438 which allows us to extract the elusive prefactor for RNA folding.
7439 Several folding scenarios can be anticipated by considering variations
7440 in the energy landscape that depend on sequence, native topology, and
7441 external conditions. RNA and protein folding mechanism can be described
7442 by the kinetic partitioning mechanism (KPM) according to which a
7443 fraction () of molecules reaches the native state directly, whereas the
7444 remaining fraction gets kinetically trapped in metastable
7445 conformations. For two-state folders 1. Molecular chaperones are
7446 recruited to assist protein folding whenever is small. We show that the
7447 iterative annealing mechanism, introduced to describe chaperonin-
7448 mediated folding, can be generalized to understand protein-assisted RNA
7449 folding. The major differences between the folding of proteins and RNA
7450 arise in the early stages of folding. For RNA, folding can only begin
7451 after the polyelectrolyte problem is solved, whereas protein collapse
7452 requires burial of hydrophobic residues. Cross-fertilization of ideas
7453 between the two fields should lead to an understanding of how RNA and
7454 proteins solve their folding problems.",
7455 note = "unfolding-refolding"
7459 author = SThornton #" and "# JMarion,
7460 title = "Classical Dynamics of Particles and Systems",
7463 isbn = "0-534-40896-6",
7464 publisher = BrooksCole,
7465 address = "Belmont, CA"
7468 @article { tlusty98,
7469 author = TTlusty #" and "# AMeller #" and "# RBar-Ziv,
7470 title = "Optical Gradient Forces of Strongly Localized Fields",
7476 pages = "1738--1741",
7479 doi = "10.1103/PhysRevLett.81.1738",
7480 eprint = "http://prola.aps.org/pdf/PRL/v81/i8/p1738_1",
7482 \url{http://nanoscience.bu.edu/papers/p1738_1_Meller.pdf}.
7483 Cited by \citet{grossman05} for derivation of thermal response
7484 functions. However, I only see a referenced thermal energy when
7485 they list the likelyhood of a small partical (radius $<R_c$)
7486 escaping due to thermal energy, where $R_c$ is roughly $R_c \sim
7487 (k_B T / \alpha I_0)^{1/3}$, $\alpha$ is a dielectric scaling
7488 term, and $I_0$ is the maximum beam energy density. I imagine
7489 Grossman and Stout mixed up this reference.",
7490 project = "Cantilever Calibration"
7493 @article { tshiprut08,
7494 author = ZTshiprut #" and "# JKlafter #" and "# MUrbakh,
7495 title = "Single-molecule pulling experiments: when the stiffness of the
7496 pulling device matters",
7505 doi = "10.1529/biophysj.108.141580",
7506 eprint = "http://www.biophysj.org/cgi/reprint/95/6/L42.pdf",
7507 abstract = "Using Langevin modeling, we investigate the role of the
7508 experimental setup on the unbinding forces measured in single-molecule
7509 pulling experiments. We demonstrate that the stiffness of the pulling
7510 device, K(eff), may influence the unbinding forces through its effect
7511 on the barrier heights for both unbinding and rebinding processes.
7512 Under realistic conditions the effect of K(eff) on the rebinding
7513 barrier is shown to play the most important role. This results in a
7514 significant increase of the mean unbinding force with the stiffness for
7515 a given loading rate. Thus, in contrast to the phenomenological Bell
7516 model, we find that the loading rate (the multiplicative value K(eff)V,
7517 V being the pulling velocity) is not the only control parameter that
7518 determines the mean unbinding force. If interested in intrinsic
7519 properties of a molecular system, we recommend probing the system in
7520 the parameter range corresponding to a weak spring and relatively high
7521 loading rates where rebinding is negligible.",
7522 note = "Cites \citet{dudko03} for Kramers' description of irreversible
7523 rupture, and claims it is required to explain the deviations in
7524 $\avg{F}$ at the same loading rate. Proposes Moese equation as an
7525 example potential. Cites \citet{walton08} for experimental evidence of
7526 $\avg{F}$ increasing with linker stiffness."
7529 @article { uniprot10,
7530 author = UniProtConsort,
7532 title = "The Universal Protein Resource (UniProt) in 2010.",
7538 number = "Database issue",
7539 pages = "D142--D148",
7541 doi = "10.1093/nar/gkp846",
7542 url = "http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_1/D142",
7543 keywords = "Algorithms;Animals;Computational Biology;Databases, Nucleic
7544 Acid;Databases, Protein;Europe;Genome, Fungal;Genome,
7545 Viral;Humans;Information Storage and Retrieval;Internet;Protein
7546 Isoforms;Proteome;Proteomics;Software",
7547 abstract = "The primary mission of UniProt is to support biological
7548 research by maintaining a stable, comprehensive, fully classified,
7549 richly and accurately annotated protein sequence knowledgebase, with
7550 extensive cross-references and querying interfaces freely accessible to
7551 the scientific community. UniProt is produced by the UniProt Consortium
7552 which consists of groups from the European Bioinformatics Institute
7553 (EBI), the Swiss Institute of Bioinformatics (SIB) and the Protein
7554 Information Resource (PIR). UniProt is comprised of four major
7555 components, each optimized for different uses: the UniProt Archive, the
7556 UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt
7557 Metagenomic and Environmental Sequence Database. UniProt is updated and
7558 distributed every 3 weeks and can be accessed online for searches or
7559 download at http://www.uniprot.org."
7562 @misc { uniprot:STRAV,
7563 key = "uniprot:STRAV",
7564 url = "http://www.uniprot.org/uniprot/P22629"
7567 @book { vanKampen07,
7568 author = NGvanKampen,
7569 title = "Stochastic Processes in Physics and Chemistry",
7573 address = "Amsterdam",
7575 project = "sawtooth simulation"
7578 @article { venter01,
7579 author = JCVenter #" and "# MDAdams #" and "# EWMyers #" and "# PWLi #" and
7580 "# RJMural #" and "# GGSutton #" and "# HOSmith #" and "# MYandell #"
7581 and "# CAEvans #" and "# RAHolt #" and "# JDGocayne #" and "#
7582 PAmanatides #" and "# RMBallew #" and "# DHHuson #" and "# JRWortman #"
7583 and "# QZhang #" and "# CDKodira #" and "# XHZheng #" and "# LChen #"
7584 and "# MSkupski #" and "# GSubramanian #" and "# PDThomas #" and "#
7585 JZhang #" and "# GLGaborMiklos #" and "# CNelson #" and "# SBroder #"
7586 and "# AGClark #" and "# JNadeau #" and "# VAMcKusick #" and "# NZinder
7587 #" and "# AJLevine #" and "# RJRoberts #" and "# MSimon #" and "#
7588 CSlayman #" and "# MHunkapiller #" and "# RBolanos #" and "# ADelcher
7589 #" and "# IDew #" and "# DFasulo #" and "# MFlanigan #" and "# LFlorea
7590 #" and "# AHalpern #" and "# SHannenhalli #" and "# SKravitz #" and "#
7591 SLevy #" and "# CMobarry #" and "# KReinert #" and "# KRemington #" and
7592 "# JAbu-Threideh #" and "# EBeasley #" and "# KBiddick #" and "#
7593 VBonazzi #" and "# RBrandon #" and "# MCargill #" and "#
7594 IChandramouliswaran #" and "# RCharlab #" and "# KChaturvedi #" and "#
7595 ZDeng #" and "# VDiFrancesco #" and "# PDunn #" and "# KEilbeck #" and
7596 "# CEvangelista #" and "# AEGabrielian #" and "# WGan #" and "# WGe #"
7597 and "# FGong #" and "# ZGu #" and "# PGuan #" and "# TJHeiman #" and "#
7598 MEHiggins #" and "# RRJi #" and "# ZKe #" and "# KAKetchum #" and "#
7599 ZLai #" and "# YLei #" and "# ZLi #" and "# JLi #" and "# YLiang #" and
7600 "# XLin #" and "# FLu #" and "# GVMerkulov #" and "# NMilshina #" and
7601 "# HMMoore #" and "# AKNaik #" and "# VANarayan #" and "# BNeelam #"
7602 and "# DNusskern #" and "# DBRusch #" and "# SSalzberg #" and "# WShao
7603 #" and "# BShue #" and "# JSun #" and "# ZWang #" and "# AWang #" and
7604 "# XWang #" and "# JWang #" and "# MWei #" and "# RWides #" and "#
7605 CXiao #" and "# CYan #" and "# AYao #" and "# JYe #" and "# MZhan #"
7606 and "# WZhang #" and "# HZhang #" and "# QZhao #" and "# LZheng #" and
7607 "# FZhong #" and "# WZhong #" and "# SZhu #" and "# SZhao #" and "#
7608 DGilbert #" and "# SBaumhueter #" and "# GSpier #" and "# CCarter #"
7609 and "# ACravchik #" and "# TWoodage #" and "# FAli #" and "# HAn #" and
7610 "# AAwe #" and "# DBaldwin #" and "# HBaden #" and "# MBarnstead #" and
7611 "# IBarrow #" and "# KBeeson #" and "# DBusam #" and "# ACarver #" and
7612 "# ACenter #" and "# MLCheng #" and "# LCurry #" and "# SDanaher #" and
7613 "# LDavenport #" and "# RDesilets #" and "# SDietz #" and "# KDodson #"
7614 and "# LDoup #" and "# SFerriera #" and "# NGarg #" and "# AGluecksmann
7615 #" and "# BHart #" and "# JHaynes #" and "# CHaynes #" and "# CHeiner
7616 #" and "# SHladun #" and "# DHostin #" and "# JHouck #" and "# THowland
7617 #" and "# CIbegwam #" and "# JJohnson #" and "# FKalush #" and "#
7618 LKline #" and "# SKoduru #" and "# ALove #" and "# FMann #" and "# DMay
7619 #" and "# SMcCawley #" and "# TMcIntosh #" and "# IMcMullen #" and "#
7620 MMoy #" and "# LMoy #" and "# BMurphy #" and "# KNelson #" and "#
7621 CPfannkoch #" and "# EPratts #" and "# VPuri #" and "# HQureshi #" and
7622 "# MReardon #" and "# RRodriguez #" and "# YHRogers #" and "# DRomblad
7623 #" and "# BRuhfel #" and "# RScott #" and "# CSitter #" and "#
7624 MSmallwood #" and "# EStewart #" and "# RStrong #" and "# ESuh #" and
7625 "# RThomas #" and "# NNTint #" and "# STse #" and "# CVech #" and "#
7626 GWang #" and "# JWetter #" and "# SWilliams #" and "# MWilliams #" and
7627 "# SWindsor #" and "# EWinn-Deen #" and "# KWolfe #" and "# JZaveri #"
7628 and "# KZaveri #" and "# JFAbril #" and "# RGuigo #" and "# MJCampbell
7629 #" and "# KVSjolander #" and "# BKarlak #" and "# AKejariwal #" and "#
7630 HMi #" and "# BLazareva #" and "# THatton #" and "# ANarechania #" and
7631 "# KDiemer #" and "# AMuruganujan #" and "# NGuo #" and "# SSato #" and
7632 "# VBafna #" and "# SIstrail #" and "# RLippert #" and "# RSchwartz #"
7633 and "# BWalenz #" and "# SYooseph #" and "# DAllen #" and "# ABasu #"
7634 and "# JBaxendale #" and "# LBlick #" and "# MCaminha #" and "#
7635 JCarnes-Stine #" and "# PCaulk #" and "# YHChiang #" and "# MCoyne #"
7636 and "# CDahlke #" and "# AMays #" and "# MDombroski #" and "# MDonnelly
7637 #" and "# DEly #" and "# SEsparham #" and "# CFosler #" and "# HGire #"
7638 and "# SGlanowski #" and "# KGlasser #" and "# AGlodek #" and "#
7639 MGorokhov #" and "# KGraham #" and "# BGropman #" and "# MHarris #" and
7640 "# JHeil #" and "# SHenderson #" and "# JHoover #" and "# DJennings #"
7641 and "# CJordan #" and "# JJordan #" and "# JKasha #" and "# LKagan #"
7642 and "# CKraft #" and "# ALevitsky #" and "# MLewis #" and "# XLiu #"
7643 and "# JLopez #" and "# DMa #" and "# WMajoros #" and "# JMcDaniel #"
7644 and "# SMurphy #" and "# MNewman #" and "# TNguyen #" and "# NNguyen #"
7645 and "# MNodell #" and "# SPan #" and "# JPeck #" and "# MPeterson #"
7646 and "# WRowe #" and "# RSanders #" and "# JScott #" and "# MSimpson #"
7647 and "# TSmith #" and "# ASprague #" and "# TStockwell #" and "# RTurner
7648 #" and "# EVenter #" and "# MWang #" and "# MWen #" and "# DWu #" and
7649 "# MWu #" and "# AXia #" and "# AZandieh #" and "# XZhu,
7650 title = "The sequence of the human genome.",
7657 pages = "1304--1351",
7659 doi = "10.1126/science.1058040",
7660 eprint = "http://www.sciencemag.org/cgi/content/pdf/291/5507/1304",
7661 url = "http://www.sciencemag.org/cgi/content/short/291/5507/1304",
7662 keywords = "Algorithms;Animals;Chromosome Banding;Chromosome
7663 Mapping;Chromosomes, Artificial, Bacterial;Computational
7664 Biology;Consensus Sequence;CpG Islands;DNA, Intergenic;Databases,
7665 Factual;Evolution, Molecular;Exons;Female;Gene
7666 Duplication;Genes;Genetic Variation;Genome, Human;Human Genome
7667 Project;Humans;Introns;Male;Phenotype;Physical Chromosome
7668 Mapping;Polymorphism, Single Nucleotide;Proteins;Pseudogenes;Repetitive
7669 Sequences, Nucleic Acid;Retroelements;Sequence Analysis, DNA;Species
7671 abstract = "A 2.91-billion base pair (bp) consensus sequence of the
7672 euchromatic portion of the human genome was generated by the whole-
7673 genome shotgun sequencing method. The 14.8-billion bp DNA sequence was
7674 generated over 9 months from 27,271,853 high-quality sequence reads
7675 (5.11-fold coverage of the genome) from both ends of plasmid clones
7676 made from the DNA of five individuals. Two assembly strategies-a whole-
7677 genome assembly and a regional chromosome assembly-were used, each
7678 combining sequence data from Celera and the publicly funded genome
7679 effort. The public data were shredded into 550-bp segments to create a
7680 2.9-fold coverage of those genome regions that had been sequenced,
7681 without including biases inherent in the cloning and assembly procedure
7682 used by the publicly funded group. This brought the effective coverage
7683 in the assemblies to eightfold, reducing the number and size of gaps in
7684 the final assembly over what would be obtained with 5.11-fold coverage.
7685 The two assembly strategies yielded very similar results that largely
7686 agree with independent mapping data. The assemblies effectively cover
7687 the euchromatic regions of the human chromosomes. More than 90\% of the
7688 genome is in scaffold assemblies of 100,000 bp or more, and 25\% of the
7689 genome is in scaffolds of 10 million bp or larger. Analysis of the
7690 genome sequence revealed 26,588 protein-encoding transcripts for which
7691 there was strong corroborating evidence and an additional approximately
7692 12,000 computationally derived genes with mouse matches or other weak
7693 supporting evidence. Although gene-dense clusters are obvious, almost
7694 half the genes are dispersed in low G+C sequence separated by large
7695 tracts of apparently noncoding sequence. Only 1.1\% of the genome is
7696 spanned by exons, whereas 24\% is in introns, with 75\% of the genome
7697 being intergenic DNA. Duplications of segmental blocks, ranging in size
7698 up to chromosomal lengths, are abundant throughout the genome and
7699 reveal a complex evolutionary history. Comparative genomic analysis
7700 indicates vertebrate expansions of genes associated with neuronal
7701 function, with tissue-specific developmental regulation, and with the
7702 hemostasis and immune systems. DNA sequence comparisons between the
7703 consensus sequence and publicly funded genome data provided locations
7704 of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of
7705 human haploid genomes differed at a rate of 1 bp per 1250 on average,
7706 but there was marked heterogeneity in the level of polymorphism across
7707 the genome. Less than 1\% of all SNPs resulted in variation in
7708 proteins, but the task of determining which SNPs have functional
7709 consequences remains an open challenge."
7712 @article { verdier70,
7714 title = "Relaxation Behavior of the Freely Jointed Chain",
7720 pages = "5512--5517",
7722 doi = "10.1063/1.1672818",
7723 url = "http://link.aip.org/link/?JCP/52/5512/1"
7726 @article { walther07,
7727 author = KWalther #" and "# FGrater #" and "# LDougan #" and "# CBadilla #"
7728 and "# BBerne #" and "# JFernandez,
7729 title = "Signatures of hydrophobic collapse in extended proteins captured
7730 with force spectroscopy",
7735 pages = "7916--7921",
7736 doi = "10.1073/pnas.0702179104",
7737 eprint = "http://www.pnas.org/cgi/reprint/104/19/7916.pdf",
7738 url = "http://www.pnas.org/cgi/content/abstract/104/19/7916",
7739 abstract = "We unfold and extend single proteins at a high force and then
7740 linearly relax the force to probe their collapse mechanisms. We observe
7741 a large variability in the extent of their recoil. Although chain
7742 entropy makes a small contribution, we show that the observed
7743 variability results from hydrophobic interactions with randomly varying
7744 magnitude from protein to protein. This collapse mechanism is common to
7745 highly extended proteins, including nonfolding elastomeric proteins
7746 like PEVK from titin. Our observations explain the puzzling differences
7747 between the folding behavior of highly extended proteins, from those
7748 folding after chemical or thermal denaturation. Probing the collapse of
7749 highly extended proteins with force spectroscopy allows separation of
7750 the different driving forces in protein folding."
7753 @mastersthesis{ lee05,
7755 title = {Chemical Functionalization of AFM Cantilevers},
7759 url = {http://dspace.mit.edu/handle/1721.1/34205},
7760 abstract = {Atomic force microscopy (AFM) has been a powerful
7761 instrument that provides nanoscale imaging of surface features,
7762 mainly of rigid metal or ceramic surfaces that can be insulators
7763 as well as conductors. Since it has been demonstrated that AFM
7764 could be used in aqueous environment such as in water or various
7765 buffers from which physiological condition can be maintained, the
7766 scope of the application of this imaging technique has been
7767 expanded to soft biological materials. In addition, the main usage
7768 of AFM has been to image the material and provide the shape of
7769 surface, which has also been diversified to molecular-recognition
7770 imaging - functional force imaging through force spectroscopy and
7771 modification of AFM cantilevers. By immobilizing of certain
7772 molecules at the end of AFM cantilever, specific molecules or
7773 functionalities can be detected by the combination of intrinsic
7774 feature of AFM and chemical modification technique of AFM
7775 cantilever. The surface molecule that is complementary to the
7776 molecule at the end of AFM probe can be investigated via
7777 specificity of molecule-molecule interaction.(cont.) Thus, this
7778 AFM cantilever chemistry, or chemical functionalization of AFM
7779 cantilever for the purpose of chemomechanical surface
7780 characterization, can be considered as an infinite source of
7781 applications important to understanding biological materials and
7782 material interactions. This thesis is mainly focused on three
7783 parts: (1) AFM cantilever chemistry that introduces specific
7784 protocols in details such as adsorption method, gold chemistry,
7785 and silicon nitride cantilever modification; (2) validation of
7786 cantilever chemistry such as X-ray photoelectron spectroscopy
7787 (XPS), AFM blocking experiment, and fluorescence microscopy,
7788 through which various AFM cantilever chemistry is verified; and
7789 (3) application of cantilever chemistry, especially toward the
7790 potential of force spectroscopy and the imaging of biological
7791 material surfaces.},
7793 note = {Binding proteins to gold-coated cantilevers via EDC (among
7794 other things in this thesis.},
7797 @article { walton08,
7798 author = EBWalton #" and "# SLee #" and "# KJVanVliet,
7799 title = "Extending {B}ell's model: How force transducer stiffness alters
7800 measured unbinding forces and kinetics of molecular complexes",
7807 pages = "2621--2630",
7809 doi = "10.1529/biophysj.107.114454",
7810 keywords = "Biotin;Computer
7811 Simulation;Elasticity;Kinetics;Mechanotransduction, Cellular;Models,
7812 Chemical;Models, Molecular;Molecular Motor
7813 Proteins;Motion;Streptavidin;Stress, Mechanical;Transducers",
7814 abstract = "Forced unbinding of complementary macromolecules such as
7815 ligand-receptor complexes can reveal energetic and kinetic details
7816 governing physiological processes ranging from cellular adhesion to
7817 drug metabolism. Although molecular-level experiments have enabled
7818 sampling of individual ligand-receptor complex dissociation events,
7819 disparities in measured unbinding force F(R) among these methods lead
7820 to marked variation in inferred binding energetics and kinetics at
7821 equilibrium. These discrepancies are documented for even the ubiquitous
7822 ligand-receptor pair, biotin-streptavidin. We investigated these
7823 disparities and examined atomic-level unbinding trajectories via
7824 steered molecular dynamics simulations, as well as via molecular force
7825 spectroscopy experiments on biotin-streptavidin. In addition to the
7826 well-known loading rate dependence of F(R) predicted by Bell's model,
7827 we find that experimentally accessible parameters such as the effective
7828 stiffness of the force transducer k can significantly perturb the
7829 energy landscape and the apparent unbinding force of the complex for
7830 sufficiently stiff force transducers. Additionally, at least 20\%
7831 variation in unbinding force can be attributed to minute differences in
7832 initial atomic positions among energetically and structurally
7833 comparable complexes. For force transducers typical of molecular force
7834 spectroscopy experiments and atomistic simulations, this energy barrier
7835 perturbation results in extrapolated energetic and kinetic parameters
7836 of the complex that depend strongly on k. We present a model that
7837 explicitly includes the effect of k on apparent unbinding force of the
7838 ligand-receptor complex, and demonstrate that this correction enables
7839 prediction of unbinding distances and dissociation rates that are
7840 decoupled from the stiffness of actual or simulated molecular linkers.",
7841 note = "Some detailed estimates at U(x)."
7844 @article { walton86,
7846 title = "The Abbe theory of imaging: an alternative derivation of the
7853 url = "http://stacks.iop.org/0143-0807/7/62"
7856 @article { watanabe05,
7857 author = HWatanabe #" and "# TInoue,
7858 title = "Conformational dynamics of Rouse chains during creep/recovery
7859 processes: a review",
7864 pages = "R607--R636",
7865 doi = "10.1088/0953-8984/17/19/R01",
7866 eprint = "http://www.iop.org/EJ/article/0953-8984/17/19/R01/cm5_19_R01.pdf",
7867 url = "http://stacks.iop.org/0953-8984/17/R607",
7868 abstract = "The Rouse model is a well-established model for non-entangled
7869 polymer chains and also serves as a fundamental model for entangled
7870 chains. The dynamic behaviour of this model under strain-controlled
7871 conditions has been fully analysed in the literature. However, despite
7872 the importance of the Rouse model, no analysis has been made so far of
7873 the orientational anisotropy of the Rouse eigenmodes during the stress-
7874 controlled, creep and recovery processes. For completeness of the
7875 analysis of the model, the Rouse equation of motion is solved to
7876 calculate this anisotropy for monodisperse chains and their binary
7877 blends during the creep/recovery processes. The calculation is simple
7878 and straightforward, but the result is intriguing in the sense that
7879 each Rouse eigenmode during these processes has a distribution in the
7880 retardation times. This behaviour, reflecting the interplay/correlation
7881 among the Rouse eigenmodes of different orders (and for different
7882 chains in the blends) under the constant stress condition, is quite
7883 different from the behaviour under rate-controlled flow (where each
7884 eigenmode exhibits retardation/relaxation associated with a single
7885 characteristic time). Furthermore, the calculation indicates that the
7886 Rouse chains exhibit affine deformation on sudden imposition/removal of
7887 the stress and the magnitude of this deformation is inversely
7888 proportional to the number of bond vectors per chain. In relation to
7889 these results, a difference between the creep and relaxation properties
7890 is also discussed for chains obeying multiple relaxation mechanisms
7891 (Rouse and reptation mechanisms).",
7892 note = "Middly-detailed Rouse model review."
7896 author = AWiita #" and "# SAinavarapu #" and "# HHuang #" and "# JFernandez,
7897 title = "From the Cover: Force-dependent chemical kinetics of disulfide
7898 bond reduction observed with single-molecule techniques",
7903 pages = "7222--7227",
7904 doi = "10.1073/pnas.0511035103",
7905 eprint = "http://www.pnas.org/cgi/reprint/103/19/7222.pdf",
7906 url = "http://www.pnas.org/cgi/content/abstract/103/19/7222",
7907 abstract = "The mechanism by which mechanical force regulates the kinetics
7908 of a chemical reaction is unknown. Here, we use single-molecule force-
7909 clamp spectroscopy and protein engineering to study the effect of force
7910 on the kinetics of thiol/disulfide exchange. Reduction of disulfide
7911 bonds through the thiol/disulfide exchange chemical reaction is crucial
7912 in regulating protein function and is known to occur in mechanically
7913 stressed proteins. We apply a constant stretching force to single
7914 engineered disulfide bonds and measure their rate of reduction by DTT.
7915 Although the reduction rate is linearly dependent on the concentration
7916 of DTT, it is exponentially dependent on the applied force, increasing
7917 10-fold over a 300-pN range. This result predicts that the disulfide
7918 bond lengthens by 0.34 A at the transition state of the thiol/disulfide
7919 exchange reaction. Our work at the single bond level directly
7920 demonstrates that thiol/disulfide exchange in proteins is a force-
7921 dependent chemical reaction. Our findings suggest that mechanical force
7922 plays a role in disulfide reduction in vivo, a property that has never
7923 been explored by traditional biochemistry. Furthermore, our work also
7924 indicates that the kinetics of any chemical reaction that results in
7925 bond lengthening will be force-dependent."
7928 @article { wilcox05,
7929 author = AWilcox #" and "# JChoy #" and "# CBustamante #" and "#
7931 title = "Effect of protein structure on mitochondrial import",
7936 pages = "15435--15440",
7937 doi = "10.1073/pnas.0507324102",
7938 eprint = "http://www.pnas.org/cgi/reprint/102/43/15435.pdf",
7939 url = "http://www.pnas.org/cgi/content/abstract/102/43/15435",
7940 abstract = "Most proteins that are to be imported into the mitochondrial
7941 matrix are synthesized as precursors, each composed of an N-terminal
7942 targeting sequence followed by a mature domain. Precursors are
7943 recognized through their targeting sequences by receptors at the
7944 mitochondrial surface and are then threaded through import channels
7945 into the matrix. Both the targeting sequence and the mature domain
7946 contribute to the efficiency with which proteins are imported into
7947 mitochondria. Precursors must be in an unfolded conformation during
7948 translocation. Mitochondria can unfold some proteins by changing their
7949 unfolding pathways. The effectiveness of this unfolding mechanism
7950 depends on the local structure of the mature domain adjacent to the
7951 targeting sequence. This local structure determines the extent to which
7952 the unfolding pathway can be changed and, therefore, the unfolding rate
7953 increased. Atomic force microscopy studies find that the local
7954 structures of proteins near their N and C termini also influence their
7955 resistance to mechanical unfolding. Thus, protein unfolding during
7956 import resembles mechanical unfolding, and the specificity of import is
7957 determined by the resistance of the mature domain to unfolding as well
7958 as by the properties of the targeting sequence."
7961 @article { wolfsberg01,
7962 author = TGWolfsberg #" and "# JMcEntyre #" and "# GDSchuler,
7963 title = "Guide to the draft human genome.",
7972 doi = "10.1038/35057000",
7973 eprint = "http://www.nature.com/nature/journal/v409/n6822/pdf/409824a0.pdf",
7974 url = "http://www.nature.com/nature/journal/v409/n6822/full/409824a0.html",
7975 keywords = "Amino Acid Sequence;Chromosome Mapping;Computational
7976 Biology;Genes;Genetic Variation;Genome, Human;Human Genome
7977 Project;Humans;Internet;Molecular Sequence Data;Sequence Analysis, DNA",
7978 abstract = "There are a number of ways to investigate the structure,
7979 function and evolution of the human genome. These include examining the
7980 morphology of normal and abnormal chromosomes, constructing maps of
7981 genomic landmarks, following the genetic transmission of phenotypes and
7982 DNA sequence variations, and characterizing thousands of individual
7983 genes. To this list we can now add the elucidation of the genomic DNA
7984 sequence, albeit at 'working draft' accuracy. The current challenge is
7985 to weave together these disparate types of data to produce the
7986 information infrastructure needed to support the next generation of
7987 biomedical research. Here we provide an overview of the different
7988 sources of information about the human genome and how modern
7989 information technology, in particular the internet, allows us to link
7994 author = JWWu #" and "# WLHung #" and "# CHTsai,
7995 title = "Estimation of parameters of the {G}ompertz distribution using the
7996 least squares method",
8005 doi = "10.1016/j.amc.2003.08.086",
8006 url = "http://dx.doi.org/10.1016/j.amc.2003.08.086",
8007 keywords = "Gompertz distribution; Least squares estimate; Maximum
8008 likelihood estimate; First failure-censored; Series system",
8009 abstract = "The Gompertz distribution has been used to describe human
8010 mortality and establish actuarial tables. Recently, this distribution
8011 has been again studied by some authors. The maximum likelihood
8012 estimates for the parameters of the Gompertz distribution has been
8013 discussed by Garg et al. [J. R. Statist. Soc. C 19 (1970) 152]. The
8014 purpose of this paper is to propose unweighted and weighted least
8015 squares estimates for parameters of the Gompertz distribution under the
8016 complete data and the first failure-censored data (series systems; see
8017 [J. Statist. Comput. Simulat. 52 (1995) 337]). A simulation study is
8018 carried out to compare the proposed estimators and the maximum
8019 likelihood estimators. Results of the simulation studies show that the
8020 performance of the weighted least squares estimators is acceptable."
8024 author = GYang #" and "# CCecconi #" and "# WBaase #" and "# IVetter #" and
8025 "# WBreyer #" and "# JHaack #" and "# BMatthews #" and "# FDahlquist #"
8027 title = "Solid-state synthesis and mechanical unfolding of polymers of {T4}
8034 doi = "10.1073/pnas.97.1.139",
8035 eprint = "http://www.pnas.org/cgi/reprint/97/1/139.pdf",
8036 url = "http://www.pnas.org/cgi/content/abstract/97/1/139"
8040 author = YYang #" and "# FCLin #" and "# GYang,
8041 title = "Temperature control device for single molecule measurements using
8042 the atomic force microscope",
8052 doi = "10.1063/1.2204580",
8053 url = "http://link.aip.org/link/?RSI/77/063701/1",
8054 keywords = "temperature control; atomic force microscopy; thermocouples;
8056 note = "Introduces our temperature control system",
8057 project = "Energy Landscape Roughness"
8061 author = WYu #" and "# JLamb #" and "# FHan #" and "# JBirchler,
8062 title = "Telomere-mediated chromosomal truncation in maize",
8067 pages = "17331--17336",
8068 doi = "10.1073/pnas.0605750103",
8069 eprint = "http://www.pnas.org/cgi/reprint/103/46/17331.pdf",
8070 url = "http://www.pnas.org/cgi/content/abstract/103/46/17331",
8071 abstract = "Direct repeats of Arabidopsis telomeric sequence were
8072 constructed to test telomere-mediated chromosomal truncation in maize.
8073 Two constructs with 2.6 kb of telomeric sequence were used to transform
8074 maize immature embryos by Agrobacterium-mediated transformation. One
8075 hundred seventy-six transgenic lines were recovered in which 231
8076 transgene loci were revealed by a FISH analysis. To analyze chromosomal
8077 truncations that result in transgenes located near chromosomal termini,
8078 Southern hybridization analyses were performed. A pattern of smear in
8079 truncated lines was seen as compared with discrete bands for internal
8080 integrations, because telomeres in different cells are elongated
8081 differently by telomerase. When multiple restriction enzymes were used
8082 to map the transgene positions, the size of the smears shifted in
8083 accordance with the locations of restriction sites on the construct.
8084 This result demonstrated that the transgene was present at the end of
8085 the chromosome immediately before the integrated telomere sequence.
8086 Direct evidence for chromosomal truncation came from the results of
8087 FISH karyotyping, which revealed broken chromosomes with transgene
8088 signals at the ends. These results demonstrate that telomere-mediated
8089 chromosomal truncation operates in plant species. This technology will
8090 be useful for chromosomal engineering in maize as well as other plant
8095 author = JZhao #" and "# HLee #" and "# RNome #" and "# SMajid #" and "#
8096 NScherer #" and "# WHoff,
8097 title = "Single-molecule detection of structural changes during
8098 {P}er-{A}rnt-{S}im ({PAS}) domain activation",
8103 pages = "11561--11566",
8104 doi = "10.1073/pnas.0601567103",
8105 eprint = "http://www.pnas.org/cgi/reprint/103/31/11561.pdf",
8106 url = "http://www.pnas.org/cgi/content/abstract/103/31/11561",
8107 abstract = "The Per-Arnt-Sim (PAS) domain is a ubiquitous protein module
8108 with a common three-dimensional fold involved in a wide range of
8109 regulatory and sensory functions in all domains of life. The activation
8110 of these functions is thought to involve partial unfolding of N- or
8111 C-terminal helices attached to the PAS domain. Here we use atomic force
8112 microscopy to probe receptor activation in single molecules of
8113 photoactive yellow protein (PYP), a prototype of the PAS domain family.
8114 Mechanical unfolding of Cys-linked PYP multimers in the presence and
8115 absence of illumination reveals that, in contrast to previous studies,
8116 the PAS domain itself is extended by {approx}3 nm (at the 10-pN
8117 detection limit of the measurement) and destabilized by {approx}30% in
8118 the light-activated state of PYP. Comparative measurements and steered
8119 molecular dynamics simulations of two double-Cys PYP mutants that probe
8120 different regions of the PAS domain quantify the anisotropy in
8121 stability and changes in local structure, thereby demonstrating the
8122 partial unfolding of their PAS domain upon activation. These results
8123 establish a generally applicable single-molecule approach for mapping
8124 functional conformational changes to selected regions of a protein. In
8125 addition, the results have profound implications for the molecular
8126 mechanism of PAS domain activation and indicate that stimulus-induced
8127 partial protein unfolding can be used as a signaling mechanism."
8130 @article { zhuang06,
8131 author = WZhuang #" and "# DAbramavicius #" and "# SMukamel,
8132 title = "Two-dimensional vibrational optical probes for peptide fast
8133 folding investigation",
8138 pages = "18934--18938",
8139 doi = "10.1073/pnas.0606912103",
8140 eprint = "http://www.pnas.org/cgi/reprint/103/50/18934.pdf",
8141 url = "http://www.pnas.org/cgi/content/abstract/103/50/18934",
8142 abstract = "A simulation study shows that early protein folding events may
8143 be investigated by using a recently developed family of nonlinear
8144 infrared techniques that combine the high temporal and spatial
8145 resolution of multidimensional spectroscopy with the chirality-specific
8146 sensitivity of amide vibrations to structure. We demonstrate how the
8147 structural sensitivity of cross-peaks in two-dimensional correlation
8148 plots of chiral signals of an {alpha} helix and a [beta] hairpin may be
8149 used to clearly resolve structural and dynamical details undetectable
8150 by one-dimensional techniques (e.g. circular dichroism) and identify
8151 structures indistinguishable by NMR."
8154 @article { zinober02,
8155 author = RCZinober #" and "# DJBrockwell #" and "# GSBeddard #" and "#
8156 AWBlake #" and "# PDOlmsted #" and "# SERadford #" and "# DASmith,
8157 title = "Mechanically unfolding proteins: the effect of unfolding history
8158 and the supramolecular scaffold",
8164 pages = "2759--2765",
8166 doi = "10.1110/ps.0224602",
8167 eprint = "http://www.proteinscience.org/cgi/reprint/11/12/2759.pdf",
8168 url = "http://www.proteinscience.org/cgi/content/abstract/11/12/2759",
8169 keywords = "Computer Simulation; Models, Molecular; Monte Carlo Method;
8170 Protein Folding; Protein Structure, Tertiary; Proteins",
8171 abstract = "The mechanical resistance of a folded domain in a polyprotein
8172 of five mutant I27 domains (C47S, C63S I27)(5)is shown to depend on the
8173 unfolding history of the protein. This observation can be understood on
8174 the basis of competition between two effects, that of the changing
8175 number of domains attempting to unfold, and the progressive increase in
8176 the compliance of the polyprotein as domains unfold. We present Monte
8177 Carlo simulations that show the effect and experimental data that
8178 verify these observations. The results are confirmed using an
8179 analytical model based on transition state theory. The model and
8180 simulations also predict that the mechanical resistance of a domain
8181 depends on the stiffness of the surrounding scaffold that holds the
8182 domain in vivo, and on the length of the unfolded domain. Together,
8183 these additional factors that influence the mechanical resistance of
8184 proteins have important consequences for our understanding of natural
8185 proteins that have evolved to withstand force.",
8186 note = "Introduces unfolding-order \emph{scaffold effect} on average
8188 project = "sawtooth simulation"
8191 @article { zwanzig92,
8192 author = RZwanzig #" and "# ASzabo #" and "# BBagchi,
8193 title = "Levinthal's paradox.",
8203 "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/pdf/pnas01075-0036.p
8205 url = "http://www.ncbi.nlm.nih.gov/pmc/articles/PMC48166/",
8206 keywords = "Mathematics;Models, Theoretical;Protein Conformation;Proteins",
8207 abstract = "Levinthal's paradox is that finding the native folded state of
8208 a protein by a random search among all possible configurations can take
8209 an enormously long time. Yet proteins can fold in seconds or less.
8210 Mathematical analysis of a simple model shows that a small and
8211 physically reasonable energy bias against locally unfavorable
8212 configurations, of the order of a few kT, can reduce Levinthal's time
8213 to a biologically significant size."
8217 author = XHong #" and "# XChu #" and "# PZou #" and "# YLiu
8219 title = "Magnetic-field-assisted rapid ultrasensitive
8220 immunoassays using Fe3{O4}/Zn{O}/Au nanorices as Raman
8226 address = "Centre for Advanced Optoelectronic Functional
8227 Materials Research, Key Laboratory for UV
8228 Light-Emitting Materials and Technology of Ministry of
8229 Education, Northeast Normal University, Changchun
8234 keywords = "Biosensing Techniques",
8235 keywords = "Electromagnetic Fields",
8236 keywords = "Equipment Design",
8237 keywords = "Equipment Failure Analysis",
8238 keywords = "Immunoassay",
8239 keywords = "Magnetite Nanoparticles",
8240 keywords = "Spectrum Analysis, Raman",
8241 keywords = "Zinc Oxide",
8242 abstract = "Rapid and ultrasensitive immunoassays were developed
8243 by using biofunctional Fe3O4/ZnO/Au nanorices as Raman
8244 probes. Taking advantage of the superparamagnetic
8245 property of the nanorices, the labeled proteins can
8246 rapidly be separated and purified with a commercial
8247 permanent magnet. The unsusceptible multiphonon
8248 resonant Raman scattering of the nanorices provided a
8249 characteristic spectroscopic fingerprint function,
8250 which allowed an accurate detection of the analyte.
8251 High specificity and selectivity of the assay were
8252 demonstrated. It was found that the diffusion barriers
8253 and the boundary layer effects had a great influence on
8254 the detection limit. Manipulation of the nanorice
8255 probes using an external magnetic field can enhance the
8256 assay sensitivity by several orders of magnitude, and
8257 reduce the detection time from 1 h to 3 min. This
8258 magnetic-field-assisted rapid and ultrasensitive
8259 immunoassay based on the resonant Raman scatting of
8260 semiconductor shows significant value for potential
8261 applications in biomedicine, food safety, and
8262 environmental defence.",
8264 doi = "10.1016/j.bios.2010.06.066",
8265 URL = "http://www.ncbi.nlm.nih.gov/pubmed/20667438",
8270 author = LZhao #" and "# ABulhassan #" and "# GYang #" and "#
8272 title = "Real-time detection of the morphological change in
8273 cellulose by a nanomechanical sensor.",
8278 address = "Department of Physics, Drexel University,
8279 Philadelphia, Pennsylvania, USA.",
8283 keywords = "Cellulose",
8284 keywords = "Computer Systems",
8285 keywords = "Equipment Design",
8286 keywords = "Equipment Failure Analysis",
8287 keywords = "Micro-Electrical-Mechanical Systems",
8288 keywords = "Molecular Conformation",
8289 keywords = "Nanotechnology",
8290 keywords = "Transducers",
8291 abstract = "Up to now, experimental limitations have prevented
8292 researchers from achieving the molecular-level
8293 understanding for the initial steps of the enzymatic
8294 hydrolysis of cellulose, where cellulase breaks down
8295 the crystal structure on the surface region of
8296 cellulose and exposes cellulose chains for the
8297 subsequent hydrolysis by cellulase. Because one of
8298 these non-hydrolytic enzymatic steps could be the
8299 rate-limiting step for the entire enzymatic hydrolysis
8300 of crystalline cellulose by cellulase, being able to
8301 analyze and understand these steps is instrumental in
8302 uncovering novel leads for improving the efficiency of
8303 cellulase. In this communication, we report an
8304 innovative application of the microcantilever technique
8305 for a real-time assessment of the morphological change
8306 of cellulose induced by a treatment of sodium chloride.
8307 This sensitive nanomechanical approach to define
8308 changes in surface structure of cellulose has the
8309 potential to permit a real-time assessment of the
8310 effect of the non-hydrolytic activities of cellulase on
8311 cellulose and thereby to provide a comprehensive
8312 understanding of the initial steps of the enzymatic
8313 hydrolysis of cellulose.",
8315 doi = "10.1002/bit.22754",
8316 URL = "http://www.ncbi.nlm.nih.gov/pubmed/20653025",
8321 author = RLiu #" and "# MRoman #" and "# GYang,
8322 title = "Correction of the viscous drag induced errors in
8323 macromolecular manipulation experiments using atomic
8328 address = "Department of Physics, Drexel University,
8329 Philadelphia, Pennsylvania 19104, USA.",
8333 keywords = "Algorithms",
8334 keywords = "Artifacts",
8335 keywords = "Macromolecular Substances",
8336 keywords = "Mechanical Processes",
8337 keywords = "Microscopy, Atomic Force",
8338 keywords = "Models, Theoretical",
8339 keywords = "Motion",
8340 keywords = "Protein Folding",
8341 keywords = "Signal Processing, Computer-Assisted",
8342 keywords = "Viscosity",
8343 abstract = "We describe a method to correct the errors induced by
8344 viscous drag on the cantilever in macromolecular
8345 manipulation experiments using the atomic force
8346 microscope. The cantilever experiences a viscous drag
8347 force in these experiments because of its motion
8348 relative to the surrounding liquid. This viscous force
8349 superimposes onto the force generated by the
8350 macromolecule under study, causing ambiguity in the
8351 experimental data. To remove this artifact, we analyzed
8352 the motions of the cantilever and the liquid in
8353 macromolecular manipulation experiments, and developed
8354 a novel model to treat the viscous drag on the
8355 cantilever as the superposition of the viscous force on
8356 a static cantilever in a moving liquid and that on a
8357 bending cantilever in a static liquid. The viscous
8358 force was measured under both conditions and the
8359 results were used to correct the viscous drag induced
8360 errors from the experimental data. The method will be
8361 useful for many other cantilever based techniques,
8362 especially when high viscosity and high cantilever
8363 speed are involved.",
8365 doi = "10.1063/1.3436646",
8366 URL = "http://www.ncbi.nlm.nih.gov/pubmed/20590242",
8370 @phdthesis { roman12,
8372 title = "Macromolecular crowding effects in the mechanical unfolding
8373 forces of proteins",
8377 url = "http://hdl.handle.net/1860/3854",
8378 eprint = "http://idea.library.drexel.edu/bitstream/1860/3854/1/Roman_Marisa.pdf",
8379 keywords = "Physics",
8380 keywords = "Biophysics",
8381 keywords = "Protein folding",
8382 abstract = "Macromolecules can occupy a large fraction of the volume
8383 of a cell and this crowded environment influences the behavior and
8384 properties of the proteins, such as mechanical unfolding forces,
8385 thermal stability and rates of folding and diffusion. Although
8386 much is already known about molecular crowding, it is not well
8387 understood how it affects a protein’s resistance to mechanical
8388 stress in a crowded environment and how the size of the crowders
8389 affect those changes. An atomic force microscope-based single
8390 molecule method was used to measure the effects of the crowding on
8391 the mechanical stability of a model protein, in this case I-27. As
8392 proteins tend to aggregate, single molecule methods provided a way
8393 to prevent aggregation because of the very low concentration of
8394 proteins in the solution under study. Dextran was used as the
8395 crowding agent with three different molecular weights 6kDa, 10 kDa
8396 and 40 kDa, with concentrations varying from zero to 300 grams per
8397 liter in a pH neutral buffer solution at room temperature. Results
8398 showed that the forces required to unfold biomolecules were
8399 increased when a high concentration of crowder molecules were
8400 added to the buffer solution and that the maximum force required
8401 to unfold a domain was when the crowder size was 10 kDa, which is
8402 comparable to the protein size. Unfolding rates obtained from
8403 Monte Carlo simulations showed that they were also affected in the
8404 presence of crowders. As a consequence, the energy barrier was
8405 also affected. These effects were most notable when the size of
8406 the crowder was 10 kDa, comparable to the size of the protein. On
8407 the other hand, distances to the transition state did not seem to
8408 change when crowders were added to the solution. The effect of
8409 Dextran on the energy barrier was modeled by using established
8410 theories such as Ogston’s and scaled particle theory, neither of
8411 which was completely convincing at describing the results. It can
8412 be hypothesized that the composition of Dextran plays a role in
8413 the deviation of the predicted behavior with respect to the
8414 experimental data.",
8418 @article { measey09,
8419 author = TMeasey #" and "# KBSmith #" and "# SDecatur #" and "#
8420 LZhao #" and "# GYang #" and "# RSchweitzerStenner,
8421 title = "Self-aggregation of a polyalanine octamer promoted by
8422 its {C}-terminal tyrosine and probed by a strongly
8423 enhanced vibrational circular dichroism signal.",
8428 address = "Department of Chemistry, Drexel University, 3141
8429 Chestnut Street, Philadelphia, Pennsylvania 19104,
8433 pages = "18218--18219",
8434 keywords = "Amyloid",
8435 keywords = "Circular Dichroism",
8436 keywords = "Dimerization",
8437 keywords = "Oligopeptides",
8438 keywords = "Peptides",
8439 keywords = "Protein Conformation",
8440 keywords = "Tyrosine",
8441 abstract = "The eight-residue alanine oligopeptide
8442 Ac-A(4)KA(2)Y-NH(2) (AKY8) was found to form
8443 amyloid-like fibrils upon incubation at room
8444 temperature in acidified aqueous solution at peptide
8445 concentrations >10 mM. The fibril solution exhibits an
8446 enhanced vibrational circular dichroism (VCD) couplet
8447 in the amide I' band region that is nearly 2 orders of
8448 magnitude larger than typical polypeptide/protein
8449 signals in this region. The UV-CD spectrum of the
8450 fibril solution shows CD in the region associated with
8451 the tyrosine side chain absorption. A similar peptide,
8452 Ac-A(4)KA(2)-NH(2) (AK7), which lacks a terminal
8453 tyrosine residue, does not aggregate. These results
8454 suggest a pivotal role for the C-terminal tyrosine
8455 residue in stabilizing the aggregation state of this
8456 peptide. It is speculated that interactions between the
8457 lysine and tyrosine side chains of consecutive strands
8458 in an antiparallel arrangement (e.g., cation-pi
8459 interactions) are responsible for the stabilization of
8460 the resulting fibrils. These results offer
8461 considerations and insight regarding the de novo design
8462 of self-assembling oligopeptides for biomedical and
8463 biotechnological applications and highlight the
8464 usefulness of VCD as a tool for probing amyloid fibril
8467 doi = "10.1021/ja908324m",
8468 URL = "http://www.ncbi.nlm.nih.gov/pubmed/19958029",
8473 author = GShan #" and "# SWang #" and "# XFei #" and "# YLiu
8475 title = "Heterostructured Zn{O}/Au nanoparticles-based resonant
8476 Raman scattering for protein detection.",
8481 address = "Center for Advanced Optoelectronic Functional
8482 Materials Research, Northeast Normal University,
8483 Changchun 130024, P. R. China.",
8486 pages = "1468--1472",
8487 keywords = "Animals",
8489 keywords = "Humans",
8490 keywords = "Immunoglobulin G",
8491 keywords = "Metal Nanoparticles",
8492 keywords = "Microscopy, Electron, Transmission",
8493 keywords = "Spectrum Analysis, Raman",
8494 keywords = "Zinc Oxide",
8495 abstract = "A new method of protein detection was explored on the
8496 resonant Raman scattering signal of ZnO nanoparticles.
8497 A probe for the target protein was constructed by
8498 binding the ZnO/Au nanoparticles to secondary protein
8499 by eletrostatic interaction. The detection of proteins
8500 was achieved by an antibody-based sandwich assay. A
8501 first antibody, which could be specifically recognized
8502 by target protein, was attached to a solid silicon
8503 surface. The ZnO/Au protein probe could specifically
8504 recognize and bind to the complex of the target protein
8505 and first antibody. This method on the resonant Raman
8506 scattering signal of ZnO nanoparticles showed good
8507 selectivity and sensitivity for the target protein.",
8509 doi = "10.1021/jp8046032",
8510 URL = "http://www.ncbi.nlm.nih.gov/pubmed/19138135",
8515 author = JMYuan #" and "# CLChyan #" and "# HXZhou #" and "#
8516 TYChung #" and "# HPeng #" and "# GPing #" and "#
8518 title = "The effects of macromolecular crowding on the
8519 mechanical stability of protein molecules.",
8524 address = "Department of Physics, Drexel University,
8525 Philadelphia, Pennsylvania 19104, USA.",
8528 pages = "2156--2166",
8529 keywords = "Circular Dichroism",
8530 keywords = "Dextrans",
8531 keywords = "Kinetics",
8532 keywords = "Microscopy, Atomic Force",
8533 keywords = "Microscopy, Scanning Probe",
8534 keywords = "Protein Folding",
8535 keywords = "Protein Stability",
8536 keywords = "Protein Structure, Secondary",
8537 keywords = "Thermodynamics",
8538 keywords = "Ubiquitin",
8539 abstract = "Macromolecular crowding, a common phenomenon in the
8540 cellular environments, can significantly affect the
8541 thermodynamic and kinetic properties of proteins. A
8542 single-molecule method based on atomic force microscopy
8543 (AFM) was used to investigate the effects of
8544 macromolecular crowding on the forces required to
8545 unfold individual protein molecules. It was found that
8546 the mechanical stability of ubiquitin molecules was
8547 enhanced by macromolecular crowding from added dextran
8548 molecules. The average unfolding force increased from
8549 210 pN in the absence of dextran to 234 pN in the
8550 presence of 300 g/L dextran at a pulling speed of 0.25
8551 microm/sec. A theoretical model, accounting for the
8552 effects of macromolecular crowding on the native and
8553 transition states of the protein molecule by applying
8554 the scaled-particle theory, was used to quantitatively
8555 explain the crowding-induced increase in the unfolding
8556 force. The experimental results and interpretation
8557 presented could have wide implications for the many
8558 proteins that experience mechanical stresses and
8559 perform mechanical functions in the crowded environment
8562 doi = "10.1110/ps.037325.108",
8563 URL = "http://www.ncbi.nlm.nih.gov/pubmed/18780817",
8568 author = YLiu #" and "# MZhong #" and "# GShan #" and "# YLi
8569 #" and "# BHuang #" and "# GYang,
8570 title = "Biocompatible Zn{O}/Au nanocomposites for
8571 ultrasensitive {DNA} detection using resonance Raman
8577 address = "Centre for Advanced Optoelectronic Functional
8578 Materials Research, Institute of Genetics and Cytology,
8579 Northeast Normal University, Changchun, People's
8580 Republic of China. ycliu@nenu.edu.cn",
8583 pages = "6484--6489",
8584 keywords = "Base Sequence",
8587 keywords = "Microscopy, Electron, Transmission",
8588 keywords = "Nanocomposites",
8589 keywords = "Sensitivity and Specificity",
8590 keywords = "Spectrum Analysis, Raman",
8591 keywords = "Zinc Oxide",
8592 abstract = "A novel method for identifying DNA microarrays based
8593 on ZnO/Au nanocomposites functionalized with
8594 thiol-oligonucleotide as probes is descried here. DNA
8595 labeled with ZnO/Au nanocomposites has a strong Raman
8596 signal even without silver acting as a surface-enhanced
8597 Raman scattering promoter. X-ray photoelectron spectra
8598 confirmed the formation of a three-component sandwich
8599 assay, i.e., constituted DNA and ZnO/Au nanocomposites.
8600 The resonance multiple-phonon Raman signal of the
8601 ZnO/Au nanocomposites as a spectroscopic fingerprint is
8602 used to detect a target sequence of oligonucleotide.
8603 This method exhibits extraordinary sensitivity and the
8604 detection limit is at least 1 fM.",
8606 doi = "10.1021/jp710399d",
8607 URL = "http://www.ncbi.nlm.nih.gov/pubmed/18444675",
8612 author = YGuo #" and "# AMylonakis #" and "# ZZhang #" and "#
8613 GYang #" and "# PLelkes #" and "# SChe #" and "#
8615 title = "Templated synthesis of electroactive periodic
8616 mesoporous organosilica bridged with oligoaniline.",
8619 address = "Department of Chemistry, Drexel University,
8620 Philadelphia, Pennsylvania 19104, USA.",
8623 pages = "2909--2917",
8624 keywords = "Aniline Compounds",
8625 keywords = "Cetrimonium Compounds",
8626 keywords = "Electrochemistry",
8627 keywords = "Hydrolysis",
8628 keywords = "Microscopy, Electron, Transmission",
8629 keywords = "Molecular Structure",
8630 keywords = "Organosilicon Compounds",
8631 keywords = "Particle Size",
8632 keywords = "Porosity",
8633 keywords = "Spectroscopy, Fourier Transform Infrared",
8634 keywords = "Surface Properties",
8635 keywords = "Thermogravimetry",
8636 keywords = "X-Ray Diffraction",
8637 abstract = "The synthesis and characterization of novel
8638 electroactive periodic mesoporous organosilica (PMO)
8639 are reported. The silsesquioxane precursor,
8640 N,N'-bis(4'-(3-triethoxysilylpropylureido)phenyl)-1,4-quinonene-diimine
8641 (TSUPQD), was prepared from the emeraldine base of
8642 amino-capped aniline trimer (EBAT) using a one-step
8643 coupling reaction and was used as an organic silicon
8644 source in the co-condensation with tetraethyl
8645 orthosilicate (TEOS) in proper ratios. By means of a
8646 hydrothermal sol-gel approach with the cationic
8647 surfactant cetyltrimethyl-ammonium bromide (CTAB) as
8648 the structure-directing template and acetone as the
8649 co-solvent for the dissolution of TSUPQD, a series of
8650 novel MCM-41 type siliceous materials (TSU-PMOs) were
8651 successfully prepared under mild alkaline conditions.
8652 The resultant mesoporous organosilica were
8653 characterized by Fourier transform infrared (FT-IR)
8654 spectroscopy, thermogravimetry, X-ray diffraction,
8655 nitrogen sorption, and transmission electron microscopy
8656 (TEM) and showed that this series of TSU-PMOs exhibited
8657 hexagonally patterned mesostructures with pore
8658 diameters of 2.1-2.8 nm. Although the structural
8659 regularity and pore parameters gradually deteriorated
8660 with increasing loading of organic bridges, the
8661 electrochemical behavior of TSU-PMOs monitored by
8662 cyclic voltammetry demonstrated greater
8663 electroactivities for samples with higher concentration
8664 of the incorporated TSU units.",
8666 doi = "10.1002/chem.200701605",
8667 URL = "http://www.ncbi.nlm.nih.gov/pubmed/18224650",
8672 author = LiLi #" and "# BLi #" and "# GYang #" and "# CYLi,
8673 title = "Polymer decoration on carbon nanotubes via physical
8679 address = "A. J. Drexel Nanotechnology Institute and Department
8680 of Materials Science and Engineering, Drexel
8681 University, Philadelphia, Pennsylvania 19104, USA.",
8684 pages = "8522--8525",
8685 keywords = "Microscopy, Atomic Force",
8686 keywords = "Microscopy, Electron, Transmission",
8687 keywords = "Nanotubes, Carbon",
8688 keywords = "Polymers",
8689 keywords = "Surface Properties",
8690 keywords = "Volatilization",
8691 abstract = "The polymer decoration technique has been widely used
8692 to study the chain folding behavior of polymer single
8693 crystals. In this article, we demonstrate that this
8694 method can be successfully adopted to pattern a variety
8695 of polymers on carbon nanotubes (CNTs). The resulting
8696 structure is a two-dimensional nanohybrid shish kebab
8697 (2D NHSK), wherein the CNT forms the shish and the
8698 polymer crystals form the kebabs. 2D NHSKs consisting
8699 of CNTs and polymers such as polyethylene, nylon 66,
8700 polyvinylidene fluoride and poly(L-lysine) have been
8701 achieved. Transmission electron microscopy and atomic
8702 force microscopy were used to study the nanoscale
8703 morphology of these hybrid materials. Relatively
8704 periodic decoration of polymers on both single-walled
8705 and multi-walled CNTs was observed. It is envisaged
8706 that this unique method offers a facile means to
8707 achieve patterned CNTs for nanodevice applications.",
8709 doi = "10.1021/la700480z",
8710 URL = "http://www.ncbi.nlm.nih.gov/pubmed/17602575",
8715 author = MSu #" and "# YYang #" and "# GYang,
8716 title = "Quantitative measurement of hydroxyl radical induced
8717 {DNA} double-strand breaks and the effect of
8718 {N}-acetyl-{L}-cysteine.",
8723 address = "Department of Physics, Drexel University,
8724 Philadelphia, PA 19104, USA.",
8727 pages = "4136--4142",
8728 keywords = "Acetylcysteine",
8729 keywords = "Animals",
8730 keywords = "DNA Damage",
8731 keywords = "Humans",
8732 keywords = "Hydroxyl Radical",
8733 keywords = "Microscopy, Atomic Force",
8734 keywords = "Nucleic Acid Conformation",
8735 keywords = "Plasmids",
8736 abstract = "Reactive oxygen species, such as hydroxyl or
8737 superoxide radicals, can be generated by exogenous
8738 agents as well as from normal cellular metabolism.
8739 Those radicals are known to induce various lesions in
8740 DNA, including strand breaks and base modifications.
8741 These lesions have been implicated in a variety of
8742 diseases such as cancer, arteriosclerosis, arthritis,
8743 neurodegenerative disorders and others. To assess these
8744 oxidative DNA damages and to evaluate the effects of
8745 the antioxidant N-acetyl-L-cysteine (NAC), atomic force
8746 microscopy (AFM) was used to image DNA molecules
8747 exposed to hydroxyl radicals generated via Fenton
8748 chemistry. AFM images showed that the circular DNA
8749 molecules became linear after incubation with hydroxyl
8750 radicals, indicating the development of double-strand
8751 breaks. The occurrence of the double-strand breaks was
8752 found to depend on the concentration of the hydroxyl
8753 radicals and the duration of the reaction. Under the
8754 conditions of the experiments, NAC was found to
8755 exacerbate the free radical-induced DNA damage.",
8757 doi = "10.1016/j.febslet.2006.06.060",
8758 URL = "http://www.ncbi.nlm.nih.gov/pubmed/16828758",
8763 author = LiLi #" and "# YYang #" and "# GYang #" and "# XuChen
8764 #" and "# BHsiao #" and "# BChu #" and "#
8765 JSpanier #" and "# CYLi,
8766 title = "Patterning polyethylene oligomers on carbon nanotubes
8767 using physical vapor deposition.",
8771 address = "A. J. Drexel Nanotechnology Institute and Department
8772 of Materials Science and Engineering, Drexel
8773 University, Philadelphia, Pennsylvania 19104, USA.",
8776 pages = "1007--1012",
8777 keywords = "Microscopy, Atomic Force",
8778 keywords = "Nanotechnology",
8779 keywords = "Nanotubes, Carbon",
8780 keywords = "Polyethylenes",
8781 keywords = "Volatilization",
8782 abstract = "Periodic patterning on one-dimensional (1D) carbon
8783 nanotubes (CNTs) is of great interest from both
8784 scientific and technological points of view. In this
8785 letter, we report using a facile physical vapor
8786 deposition method to achieve periodic polyethylene (PE)
8787 oligomer patterning on individual CNTs. Upon heating
8788 under vacuum, PE degraded into oligomers and
8789 crystallized into rod-shaped single crystals. These PE
8790 rods periodically decorate on CNTs with their long axes
8791 perpendicular to the CNT axes. The formation mechanism
8792 was attributed to ``soft epitaxy'' growth of PE
8793 oligomer crystals on CNTs. Both SWNTs and MWNTs were
8794 decorated successfully with PE rods. The intermediate
8795 state of this hybrid structure, MWNTs absorbed with a
8796 thin layer of PE, was captured successfully by
8797 depositing PE vapor on MWNTs detached from the solid
8798 substrate, and was observed using high-resolution
8799 transmission electron microscopy. Furthermore, this
8800 hybrid structure formation depends critically on CNT
8801 surface chemistry: alkane-modification of the MWNT
8802 surface prohibited the PE single-crystal growth on the
8803 CNTs. We anticipate that this work could open a gateway
8804 for creating complex CNT-based nanoarchitectures for
8805 nanodevice applications.",
8807 doi = "10.1021/nl060276q",
8808 URL = "http://www.ncbi.nlm.nih.gov/pubmed/16683841",
8813 author = MKuhn #" and "# HJanovjak #" and "# MHubain #" and "# DJMuller,
8814 title = {Automated alignment and pattern recognition of
8815 single-molecule force spectroscopy data.},
8818 address = {Division of Computer Science, California Institute of
8819 Technology, Pasadena, California 91125, USA.},
8825 doi = {10.1111/j.1365-2818.2005.01478.x},
8826 URL = {http://www.ncbi.nlm.nih.gov/pubmed/15857374},
8828 keywords = {Algorithms},
8829 keywords = {Bacteriorhodopsins},
8830 keywords = {Data Interpretation, Statistical},
8831 keywords = {Escherichia coli Proteins},
8832 keywords = {Microscopy, Atomic Force},
8833 keywords = {Protein Folding},
8834 keywords = {Sodium-Hydrogen Antiporter},
8835 keywords = {Software},
8836 abstract = {Recently, direct measurements of forces stabilizing
8837 single proteins or individual receptor-ligand bonds became
8838 possible with ultra-sensitive force probe methods like the atomic
8839 force microscope (AFM). In force spectroscopy experiments using
8840 AFM, a single molecule or receptor-ligand pair is tethered between
8841 the tip of a micromachined cantilever and a supporting
8842 surface. While the molecule is stretched, forces are measured by
8843 the deflection of the cantilever and plotted against extension,
8844 yielding a force spectrum characteristic for each biomolecular
8845 system. In order to obtain statistically relevant results, several
8846 hundred to thousand single-molecule experiments have to be
8847 performed, each resulting in a unique force spectrum. We developed
8848 software and algorithms to analyse large numbers of force
8849 spectra. Our algorithms include the fitting polymer extension
8850 models to force peaks as well as the automatic alignment of
8851 spectra. The aligned spectra allowed recognition of patterns of
8852 peaks across different spectra. We demonstrate the capabilities of
8853 our software by analysing force spectra that were recorded by
8854 unfolding single transmembrane proteins such as bacteriorhodopsin
8855 and NhaA. Different unfolding pathways were detected by
8856 classifying peak patterns. Deviant spectra, e.g. those with no
8857 attachment or erratic peaks, can be easily identified. The
8858 software is based on the programming language C++, the GNU
8859 Scientific Library (GSL), the software WaveMetrics IGOR Pro and
8860 available open-source at http://bioinformatics.org/fskit/.},
8861 note = {Development stalled in 2005 after Michael graduated.},
8864 @article{ janovjak05,
8865 author = HJanovjak #" and "# JStruckmeier #" and "# DJMuller,
8866 title = {Hydrodynamic effects in fast {AFM} single-molecule
8867 force measurements.},
8871 address = {BioTechnological Center, University of Technology
8872 Dresden, 01307 Dresden, Germany.},
8878 doi = {10.1007/s00249-004-0430-3},
8879 url = {http://www.ncbi.nlm.nih.gov/pubmed/15257425},
8881 keywords = {Algorithms},
8882 keywords = {Computer Simulation},
8883 keywords = {Elasticity},
8884 keywords = {Microfluidics},
8885 keywords = {Microscopy, Atomic Force},
8886 keywords = {Models, Chemical},
8887 keywords = {Models, Molecular},
8888 keywords = {Physical Stimulation},
8889 keywords = {Protein Binding},
8890 keywords = {Proteins},
8891 keywords = {Stress, Mechanical},
8892 keywords = {Viscosity},
8893 abstract = {Atomic force microscopy (AFM) allows the critical forces
8894 that unfold single proteins and rupture individual receptor-ligand
8895 bonds to be measured. To derive the shape of the energy landscape,
8896 the dynamic strength of the system is probed at different force
8897 loading rates. This is usually achieved by varying the pulling
8898 speed between a few nm/s and a few $\mu$m/s, although for a more
8899 complete investigation of the kinetic properties higher speeds are
8900 desirable. Above 10 $\mu$m/s, the hydrodynamic drag force acting
8901 on the AFM cantilever reaches the same order of magnitude as the
8902 molecular forces. This has limited the maximum pulling speed in
8903 AFM single-molecule force spectroscopy experiments. Here, we
8904 present an approach for considering these hydrodynamic effects,
8905 thereby allowing a correct evaluation of AFM force measurements
8906 recorded over an extended range of pulling speeds (and thus
8907 loading rates). To support and illustrate our theoretical
8908 considerations, we experimentally evaluated the mechanical
8909 unfolding of a multi-domain protein recorded at $30\U{$mu$m/s}$
8914 author = MSandal #" and "# FValle #" and "# ITessari #" and "#
8915 SMammi #" and "# EBergantino #" and "# FMusiani #" and "#
8916 MBrucale #" and "# LBubacco #" and "# BSamori,
8917 title = {Conformational Equilibria in Monomeric $\alpha$-Synuclein
8918 at the Single-Molecule Level},
8921 address = {Department of Biochemistry G. Moruzzi,
8922 University of Bologna, Bologna, Italy.},
8928 doi = {10.1371/journal.pbio.0060006},
8929 url = {http://www.ncbi.nlm.nih.gov/pubmed/18198943},
8931 keywords = {Buffers},
8932 keywords = {Circular Dichroism},
8933 keywords = {Copper},
8934 keywords = {Entropy},
8935 keywords = {Models, Molecular},
8936 keywords = {Molecular Sequence Data},
8937 keywords = {Mutation},
8938 keywords = {Protein Structure, Secondary},
8939 keywords = {Protein Structure, Tertiary},
8940 keywords = {alpha-Synuclein},
8941 abstract = {Human $\alpha$-Synuclein ($\alpha$Syn) is a natively
8942 unfolded protein whose aggregation into amyloid fibrils is
8943 involved in the pathology of Parkinson disease. A full
8944 comprehension of the structure and dynamics of early intermediates
8945 leading to the aggregated states is an unsolved problem of
8946 essential importance to researchers attempting to decipher the
8947 molecular mechanisms of $\alpha$Syn aggregation and formation of
8948 fibrils. Traditional bulk techniques used so far to solve this
8949 problem point to a direct correlation between $\alpha$Syn's unique
8950 conformational properties and its propensity to aggregate, but
8951 these techniques can only provide ensemble-averaged information
8952 for monomers and oligomers alike. They therefore cannot
8953 characterize the full complexity of the conformational equilibria
8954 that trigger the aggregation process. We applied atomic force
8955 microscopy-based single-molecule mechanical unfolding methodology
8956 to study the conformational equilibrium of human wild-type and
8957 mutant $\alpha$Syn. The conformational heterogeneity of monomeric
8958 $\alpha$Syn was characterized at the single-molecule level. Three
8959 main classes of conformations, including disordered and
8960 ``$\beta$-like'' structures, were directly observed and quantified
8961 without any interference from oligomeric soluble forms. The
8962 relative abundance of the ``$\beta$-like'' structures
8963 significantly increased in different conditions promoting the
8964 aggregation of $\alpha$Syn: the presence of \Cu, the pathogenic
8965 A30P mutation, and high ionic strength. This methodology can
8966 explore the full conformational space of a protein at the
8967 single-molecule level, detecting even poorly populated conformers
8968 and measuring their distribution in a variety of biologically
8969 important conditions. To the best of our knowledge, we present
8970 for the first time evidence of a conformational equilibrium that
8971 controls the population of a specific class of monomeric
8972 $\alpha$Syn conformers, positively correlated with conditions
8973 known to promote the formation of aggregates. A new tool is thus
8974 made available to test directly the influence of mutations and
8975 pharmacological strategies on the conformational equilibrium of
8976 monomeric $\alpha$Syn.},
8980 author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
8981 AGomezCasado #" and "# BSamori,
8982 title = "Hooke: An open software platform for force spectroscopy.",
8987 address = "Department of Biochemistry, University of Bologna,
8988 Bologna, Italy. massimo.sandal@unibo.it",
8991 pages = "1428--1430",
8992 keywords = "Algorithms",
8993 keywords = "Computational Biology",
8994 keywords = "Internet",
8995 keywords = "Microscopy, Atomic Force",
8996 keywords = "Proteome",
8997 keywords = "Proteomics",
8998 keywords = "Software",
8999 abstract = "SUMMARY: Hooke is an open source, extensible software
9000 intended for analysis of atomic force microscope (AFM)-based
9001 single molecule force spectroscopy (SMFS) data. We propose it as a
9002 platform on which published and new algorithms for SMFS analysis
9003 can be integrated in a standard, open fashion, as a general
9004 solution to the current lack of a standard software for SMFS data
9005 analysis. Specific features and support for file formats are coded
9006 as independent plugins. Any user can code new plugins, extending
9007 the software capabilities. Basic automated dataset filtering and
9008 semi-automatic analysis facilities are included. AVAILABILITY:
9009 Software and documentation are available at
9010 (http://code.google.com/p/hooke). Hooke is a free software under
9011 the GNU Lesser General Public License.",
9013 doi = "10.1093/bioinformatics/btp180",
9014 URL = "http://www.ncbi.nlm.nih.gov/pubmed/19336443",
9018 @article{ materassi09,
9019 author = DMaterassi #" and "# PBaschieri #" and "# BTiribilli #" and "#
9020 GZuccheri #" and "# BSamori,
9021 title = {An open source/real-time atomic force microscope
9022 architecture to perform customizable force spectroscopy
9026 address = {Department of Electrical and Computer Engineering,
9027 University of Minnesota, 200 Union St. SE, Minneapolis,
9028 Minnesota 55455, USA. mater013@umn.edu},
9034 doi = "10.1063/1.3194046",
9035 url = "http://www.ncbi.nlm.nih.gov/pubmed/19725671",
9037 keywords = {Algorithms},
9038 keywords = {Animals},
9039 keywords = {Calibration},
9041 keywords = {Microscopy, Atomic Force},
9042 keywords = {Muscle Proteins},
9043 keywords = {Myocardium},
9044 keywords = {Optics and Photonics},
9045 keywords = {Ownership},
9046 keywords = {Protein Kinases},
9047 keywords = {Software},
9048 keywords = {Spectrum Analysis},
9049 keywords = {Time Factors},
9050 abstract = {We describe the realization of an atomic force
9051 microscope architecture designed to perform customizable
9052 experiments in a flexible and automatic way. Novel technological
9053 contributions are given by the software implementation platform
9054 (RTAI-LINUX), which is free and open source, and from a functional
9055 point of view, by the implementation of hard real-time control
9056 algorithms. Some other technical solutions such as a new way to
9057 estimate the optical lever constant are described as well. The
9058 adoption of this architecture provides many degrees of freedom in
9059 the device behavior and, furthermore, allows one to obtain a
9060 flexible experimental instrument at a relatively low cost. In
9061 particular, we show how such a system has been employed to obtain
9062 measures in sophisticated single-molecule force spectroscopy
9063 experiments\citep{fernandez04}. Experimental results on proteins
9064 already studied using the same methodologies are provided in order
9065 to show the reliability of the measure system.},
9066 note = {Although this paper claims to present an open source
9067 experiment control framework (on Linux!), it doesn't actually link
9068 to any source code. This is puzzling and frusterating.},
9071 @article{ aioanei11,
9072 author = DAioanei #" and "# MBrucale #" and "# BSamori,
9073 title = {Open source platform for the execution and analysis of
9074 mechanical refolding experiments.},
9078 address = {Department of Biochemistry G.~Moruzzi,
9079 University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
9080 aioaneid@gmail.com},
9086 doi = {10.1093/bioinformatics/btq663},
9087 url = {http://www.ncbi.nlm.nih.gov/pubmed/21123222},
9089 keywords = {Computational Biology},
9090 keywords = {Kinetics},
9091 keywords = {Protein Denaturation},
9092 keywords = {Protein Refolding},
9093 keywords = {Software},
9094 abstract = {Single-molecule force spectroscopy has facilitated the
9095 experimental investigation of biomolecular force-coupled kinetics,
9096 from which the kinetics at zero force can be extrapolated via
9097 explicit theoretical models. The atomic force microscope (AFM) in
9098 particular is routinely used to study protein unfolding kinetics,
9099 but only rarely protein folding kinetics. The discrepancy arises
9100 because mechanical protein refolding studies are more technically
9102 note = {\href{http://code.google.com/p/refolding/}{Refolding} is a
9103 suite for performing and analyzing double-pulse refolding
9104 experiments. The experiment-driver is mostly written in Java with
9105 the analysis code in Python. The driver is curious; it uses the
9106 NanoScope scripting interface to drive the experiment through the
9107 NanoScope software by impersonating a mouse-wielding user (like
9108 Selenium does for web browsers). See the
9109 \imint{sh}|RobotNanoDriver.java| code for details. There is also
9110 support for automatic velocity clamp analysis.},
9113 @article{ benedetti11,
9114 author = FBenedetti #" and "# CMicheletti #" and "# GBussi #" and "#
9115 SKSekatskii #" and "# GDietler,
9116 title = {Nonkinetic modeling of the mechanical unfolding of
9117 multimodular proteins: theory and experiments.},
9121 address = {Laboratory of Physics of Living Matter,
9122 Ecole Polytechnique F{\'e}d{\'e}rale de Lausanne,
9123 Lausanne, Switzerland.},
9127 pages = {1504--1512},
9129 doi = {10.1016/j.bpj.2011.07.047},
9130 url = {http://www.ncbi.nlm.nih.gov/pubmed/21943432},
9132 keywords = {Kinetics},
9133 keywords = {Microscopy, Atomic Force},
9134 keywords = {Models, Molecular},
9135 keywords = {Monte Carlo Method},
9136 keywords = {Protein Unfolding},
9137 keywords = {Stochastic Processes},
9138 abstract = {We introduce and discuss a novel approach called
9139 back-calculation for analyzing force spectroscopy experiments on
9140 multimodular proteins. The relationship between the histograms of
9141 the unfolding forces for different peaks, corresponding to a
9142 different number of not-yet-unfolded protein modules, is exploited
9143 in such a manner that the sole distribution of the forces for one
9144 unfolding peak can be used to predict the unfolding forces for
9145 other peaks. The scheme is based on a bootstrap prediction method
9146 and does not rely on any specific kinetic model for multimodular
9147 unfolding. It is tested and validated in both
9148 theoretical/computational contexts (based on stochastic
9149 simulations) and atomic force microscopy experiments on (GB1)(8)
9150 multimodular protein constructs. The prediction accuracy is so
9151 high that the predicted average unfolding forces corresponding to
9152 each peak for the GB1 construct are within only 5 pN of the
9153 averaged directly-measured values. Experimental data are also used
9154 to illustrate how the limitations of standard kinetic models can
9155 be aptly circumvented by the proposed approach.},
9158 @phdthesis{ benedetti12,
9159 author = FBenedetti,
9160 title = {Statistical Study of the Unfolding of Multimodular Proteins
9161 and their Energy Landscape by Atomic Force Microscopy},
9163 address = {Lausanne},
9164 affiliation = {EPFL},
9167 doi = {10.5075/epfl-thesis-5440},
9168 url = {http://infoscience.epfl.ch/record/181215},
9169 eprint = {http://infoscience.epfl.ch/record/181215/files/EPFL_TH5440.pdf},
9170 keywords = {atomic force microscope (AFM); single molecule force
9171 spectrosopy; velocity clamp AFM; Monte carlo simulations; force
9172 modulation spectroscopy; energy barrier model; non kinetic methods
9173 for force spectroscopy},
9174 abstract = {The aim of the present thesis is to investigate several
9175 aspects of: the proteins mechanics, interprotein interactions and
9176 to study also new techniques, theoretical and technical, to obtain
9177 and analyze the force spectroscopy experiments. The first section
9178 is dedicated to the statistical properties of the unfolding forces
9179 in a chain of homomeric multimodular proteins. The basic idea of
9180 this kind of statistic is to divide the peaks observed in a force
9181 extension curve in separate groups and then analyze these groups
9182 considering their position in the force curves. In fact in a
9183 multimodular homomeric protein the unfolding force is related to
9184 the number of not yet unfolded modules (we call it "N"). Such
9185 effect yields to a linear dependence of the most probable
9186 unfolding force of a peak on ln(N). We demonstrate how such
9187 dependence can be used to extract the kinetic parameters and how,
9188 ignoring it, could lead to significant errors. Following this
9189 topic we continue with non kinetic methods that, using the
9190 resampling from the rupture forces of any peak, could reconstruct
9191 the rupture forces for all the other peaks in a chain. Then a
9192 discussion about the Monte Carlo simulation for protein pulling is
9193 present. In fact a theoretical framework for such methodology has
9194 to be introduced to understand the various simulations done. In
9195 this chapter we also introduce a methodology to study the ligand
9196 receptor interactions when we directly functionalize the AFM tip
9197 and the substrate. In fact, in many of our experiments, we see a
9198 "cloud of points" in the force vs loading rate graph. We have
9199 modeled a system composed by "N" parallel springs, and studying
9200 the distribution of forces obtained in the force vs loading rate
9201 graph we have establish a procedure to restore the kinetic
9202 parameters used. Such procedure has then been used to discuss real
9203 experiments similar to biotin-avidin interaction. In the following
9204 chapter we discuss a first order approximation of the Bell-Evans
9205 model where a more explicit form of the potential is
9206 considered. In particular the dependence of the curvature of the
9207 potential on the applied force at the minimum and at the
9208 metastable state is considered. In the well known Bell-Evans model
9209 the prefactors of the transition rate are fixed at any force,
9210 however this is not what happen in nature, where the prefactors
9211 (that are the second local derivative of the interacting energy
9212 with respect to the reaction coordinate in its minimum and
9213 maximum) depend on the force applied. The results obtained with
9214 the force spectroscopy of the Laminin-binding-protein are
9215 discussed, in particular this protein showed a phase transition
9216 when the pH was changed. The behavior of this protein changes,
9217 from a normal WLC behavior to a plateau behavior. The analysis of
9218 the force spectroscopy curves shows a distribution of length where
9219 the maximum of the first prominent peak correspond to the full
9220 length of the protein. However, length that could be associated
9221 with dimers and trymers are also present in this
9222 distribution. Later a new approach to study the lock and key
9223 mechanism, using "handles" with a specific force extension
9224 pattern, is introduced. In particular handles of (I27)3 and
9225 (I27–SNase)3 were biochemically attached to: strept-actin
9226 molecules, biotin molecules, RNase and Angiogenin. The main idea
9227 is to have a system composed by "handle-(molecule A)-(molecule
9228 B)-handle" where the handles are covalently attached to the
9229 respective molecules and the two molecules "A and B" are attached
9230 by secondary bonds. This approach allows a better recognition of
9231 the protein-protein interaction enabling us to filter out spurious
9232 events. Doing a statistic on the rupture forces and comparing this
9233 with the statistic of the detachments of the system of the bare
9234 handles, we are able to extract the information of the interaction
9235 between the molecule A and B. The two last chapters are of more
9236 preliminary character that the previous part of the thesis. A
9237 section is dedicated to the estimation of effective mass and
9238 viscous drag of the cantilevers studied by autocorrelation and
9239 noise power spectrum. Usually the noise power spectrum method is
9240 the most used, however the autocorrelation should give
9241 approximately the same information. The parameters obtained are
9242 important in high frequency modulation techniques. In fact, they
9243 are needed to interpret the results. The results of these two
9244 methods show a good agreement in the estimation of the mass and
9245 the viscous drag of the various cantilever used. Afterwards a
9246 chapter is dedicated to the discussion of the force spectroscopy
9247 experiments using a low frequency modulation of the cantilever
9248 base. Such experiments allow us to record the phase and the
9249 amplitude shift of the modulation signal used. Using the amplitude
9250 channel we managed to restore the static force signal with a lower
9251 level of noise. Moreover these signals give us direct information
9252 about the dynamic stiffness and the lose of energy in the system,
9253 information that, using the standard technique would be difficult
9254 (or even impossible) to obtain.},
9258 author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson
9259 #" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht
9260 #" and "# DPlunkett #" and "# WDeLorbe,
9261 title = "Multiple-copy genes: Production and modification of
9262 monomeric peptides from large multimeric fusion proteins.",
9268 keywords = "Cloning, Molecular",
9269 keywords = "Cyanogen Bromide",
9270 keywords = "DNA, Recombinant",
9271 keywords = "Escherichia coli",
9272 keywords = "Gene Expression Regulation",
9273 keywords = "Genetic Vectors",
9274 keywords = "Humans",
9275 keywords = "Molecular Weight",
9276 keywords = "Peptide Fragments",
9277 keywords = "Plasmids",
9278 keywords = "Substance P",
9279 keywords = "beta-Galactosidase",
9280 abstract = "A vector system has been designed for obtaining high
9281 yields of polypeptides synthesized in Escherichia coli. Multiple
9282 copies of a synthetic gene encoding the neuropeptide substance P
9283 (SP) (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2) have been
9284 linked and fused to the lacZ gene. Each copy of the SP gene was
9285 flanked by codons for methionine to create sites for cleavage by
9286 cyanogen bromide (CNBr). The isolated multimeric SP fusion
9287 protein was converted to monomers of SP analog, each containing a
9288 carboxyl-terminal homoserine lactone (Hse-lactone) residue
9289 (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Hse-lactone), upon
9290 treatment with CNBr in formic acid. The Hse-lactone moiety was
9291 subjected to chemical modifications to produce an SP Hse
9292 amide. This method permits synthesis of peptide amide analogs and
9293 other peptide derivatives by combining recombinant DNA techniques
9294 and chemical methods.",
9296 URL = "http://www.ncbi.nlm.nih.gov/pubmed/2419204",
9301 author = MHonda #" and "# YBaba #" and "# NHiaro #" and "# TSekiguchi,
9302 title = "Metal-molecular interface of sulfur-containing amino acid
9303 and thiophene on gold surface",
9308 url = "http://dx.doi.org/10.1088/1742-6596/100/5/052071",
9310 abstract = "Chemical-bonding states of metal-molecular interface
9311 have been investigated for L-cysteine and thiophene on gold by
9312 x-ray photoelectron spectroscopy (XPS) and near edge x-ray
9313 adsorption fine structure (NEXAFS). A remarkable difference in
9314 Au-S bonding states was found between L-cysteine and
9315 thiophene. For mono-layered L-cysteine on gold, the binding energy
9316 of S 1s in XPS and the resonance energy at the S K-edge in NEXAFS
9317 are higher by 8–9 eV than those for multi-layered film (molecular
9318 L-cysteine). In contrast, the S K-edge resonance energy for
9319 mono-layered thiophene on gold was 2475.0 eV, which is the same as
9320 that for molecular L-cysteine. In S 1s XPS for mono-layered
9321 thiophene, two peaks were observed. The higher binging-energy and
9322 more intense peak at 2473.4 eV are identified as gold sulfide. The
9323 binding energy of smaller peak, whose intensity is less than 1/3
9324 of the higher binding energy peak, is 2472.2 eV, which is the same
9325 as that for molecular thiophene. These observations indicate that
9326 Au-S interface behavior shows characteristic chemical bond only
9327 for the Au-S interface of L-cysteine monolayer on gold
9333 title = "Formation and Structure of Self-Assembled Monolayers.",
9338 address = "Department of Chemical Engineering, Chemistry and
9339 Materials Science, and the Herman F. Mark Polymer Research
9340 Institute, Polytechnic University, Six MetroTech Center, Brooklyn,
9344 pages = "1533--1554",
9346 URL = "http://www.ncbi.nlm.nih.gov/pubmed/11848802",
9351 author = GHager #" and "# ABrolo,
9352 title = "Adsorption/desorption behaviour of cysteine and cystine in
9353 neutral and basic media: electrochemical evidence for differing
9354 thiol and disulfide adsorption to a {Au(111)} single crystal
9357 volume = "550--551",
9362 doi = "10.1016/S0022-0728(03)00052-4",
9363 url = "http://dx.doi.org/10.1016/S0022-0728(03)00052-4",
9365 keywords = "Disulfide",
9366 keywords = "Thiol adsorption",
9367 keywords = "Self-assembled monolayers",
9368 keywords = "Au(111) single crystal electrode",
9369 keywords = "Cysteine",
9370 keywords = "Cystine",
9371 abstract = "The adsorption/desorption behaviour of the
9372 thiol/disulfide redox couple, cysteine/cystine, was monitored at a
9373 Au(111) single crystal electrode. The monolayers were formed
9374 electrochemically from 0.1 M KClO4 and 0.1 M NaOH solutions
9375 containing either the thiol or the disulfide. Distinct features in
9376 the adsorption potential were noted. An adsorption peak was
9377 observed in the cyclic voltammograms (CVs) from Au(111) in 0.1 M
9378 KClO4 solutions containing cystine at $-0.57$ V vs. saturated
9379 calomel electrode. Under the same conditions, the CVs from
9380 solutions containing cysteine showed an adsorption peak at $-0.43$
9381 V (0.14 V more positive than the corresponding peak from disulfide
9382 solutions). This showed that the thiol and disulfide species have
9383 different adsorption properties. Similar behaviour was observed in
9384 0.1 M NaOH. Cyclic voltammetric and chronocoulometric data were
9385 employed to determine the surface coverage of the different
9386 monolayers. Cysteine solutions prepared in 0.1 M KClO4 provided
9387 coverages of $3.0\times10^{-10}$ and $2.5\times10^{-10}$
9388 mol~cm$^{-2}$ for the L and the D--L species, respectively as
9389 evaluated from the desorption peaks. Desorption of cystine in the
9390 same medium yielded coverages of $1.2\times10^{-10}$ mol~cm$^{-2}$
9391 for both L and D--L solutions (or $2.4\times10^{-10}$
9392 mol~cm$^{-2}$ in cysteine equivalents). Surface coverages obtained
9393 from Au(111) in 0.1 M NaOH corresponded to $3.9\times10^{10}$
9394 mol~cm$^{-2}$ for L-cysteine, and $1.2\times10^{-10}$
9395 mol~cm$^{-2}$ (or $2.4\times10^{-10}$ mol~cm$^{-2}$ cysteine
9396 equivalents) for L and D--L cystine.",
9401 title = "The Nanomechanics of Polycystin-1: A Kidney Mechanosensor",
9405 url = "http://etd.utmb.edu/theses/available/etd-07072010-132038/",
9407 keywords = "Polycystin-1",
9408 keywords = "Missense mutations",
9409 keywords = "Atomic Force Microscopy",
9410 keywords = "Osmolyte",
9411 keywords = "Mechanosensor",
9412 abstract = "Mutations in polycystin-1 (PC1) can cause Autosomal
9413 Dominant Polycystic Kidney Disease (ADPKD), which is a leading
9414 cause of renal failure. The available evidence suggests that PC1
9415 acts as a mechanosensor, receiving signals from the primary cilia,
9416 neighboring cells, and extracellular matrix. PC1 is a large
9417 membrane protein that has a long N-terminal extracellular region
9418 (about 3000 aa) with a multimodular structure including sixteen
9419 Ig-like PKD domains, which are targeted by many naturally
9420 occurring missense mutations. Nothing is known about the effects
9421 of these mutations on the biophysical properties of PKD
9422 domains. In addition, PC1 is expressed along the renal tubule,
9423 where it is exposed to a wide range of concentration of urea. Urea
9424 is known to destabilize proteins. Other osmolytes found in the
9425 kidney such as sorbitol, betaine and TMAO are known to counteract
9426 urea's negative effects on proteins. Nothing is known about how
9427 the mechanical properties of PC1 are affected by these
9428 osmolytes. Here I use nano-mechanical techniques to study the
9429 effects of missense mutations and effects of denaturants and
9430 various osmolytes on the mechanical properties of PKD
9431 domains. Several missense mutations were found to alter the
9432 mechanical stability of PKD domains resulting in distinct
9433 mechanical phenotypes. Based on these findings, I hypothesize that
9434 missense mutations may cause ADPKD by altering the stability of
9435 the PC1 ectodomain, thereby perturbing its ability to sense
9436 mechanical signals. I also found that urea has a significant
9437 impact on both the mechanical stability and refolding rate of PKD
9438 domains. It not only lowers their mechanical stability, but also
9439 slows down their refolding rate. Moreover, several osmolytes were
9440 found to effectively counteract the effects of urea. Our data
9441 provide the evidence that naturally occurring osmolytes can help
9442 to maintain Polycystin-1 mechanical stability and folding
9443 kinetics. This study has the potential to provide new therapeutic
9444 approaches (e.g. through the use of osmolytes or chemical
9445 chaperones) for rescuing destabilized and misfolded PKD domains.",
9449 @article{ sundberg03,
9450 author = MSundberg #" and "# JRosengren #" and "# RBunk
9451 #" and "# JLindahl #" and "# INicholls #" and "# STagerud
9452 #" and "# POmling #" and "# LMontelius #" and "# AMansson,
9453 title = "Silanized surfaces for in vitro studies of actomyosin
9454 function and nanotechnology applications.",
9459 address = "Department of Chemistry and Biomedical Sciences,
9460 University of Kalmar, SE-391 82 Kalmar, Sweden.",
9464 keywords = "Actomyosin",
9465 keywords = "Adsorption",
9466 keywords = "Animals",
9467 keywords = "Collodion",
9468 keywords = "Kinetics",
9469 keywords = "Methods",
9470 keywords = "Movement",
9471 keywords = "Nanotechnology",
9472 keywords = "Rabbits",
9473 keywords = "Silicon",
9474 keywords = "Surface Properties",
9475 keywords = "Trimethylsilyl Compounds",
9476 abstract = "We have previously shown that selective heavy meromyosin
9477 (HMM) adsorption to predefined regions of nanostructured polymer
9478 resist surfaces may be used to produce a nanostructured in vitro
9479 motility assay. However, actomyosin function was of lower quality
9480 than on conventional nitrocellulose films. We have therefore
9481 studied actomyosin function on differently derivatized glass
9482 surfaces with the aim to find a substitute for the polymer
9483 resists. We have found that surfaces derivatized with
9484 trimethylchlorosilane (TMCS) were superior to all other surfaces
9485 tested, including nitrocellulose. High-quality actin filament
9486 motility was observed up to 6 days after incubation with HMM and
9487 the fraction of motile actin filaments and the velocity of smooth
9488 sliding were generally higher on TMCS than on nitrocellulose. The
9489 actomyosin function on TMCS-derivatized glass and nitrocellulose
9490 is considered in relation to roughness and hydrophobicity of these
9491 surfaces. The results suggest that TMCS is an ideal substitute for
9492 polymer resists in the nanostructured in vitro motility
9493 assay. Furthermore, TMCS derivatized glass also seems to offer
9494 several advantages over nitrocellulose for HMM adsorption in the
9495 ordinary in /vitro motility assay.",
9497 URL = "http://www.ncbi.nlm.nih.gov/pubmed/14622967",
9498 doi = "10.1016/j.ab.2003.07.022",
9503 author = HItoh #" and "# ATakahashi #" and "# KAdachi #" and "#
9504 HNoji #" and "# RYasuda #" and "# MYoshida #" and "#
9506 title = "Mechanically driven {ATP} synthesis by {F1}-{ATP}ase.",
9511 address = "Tsukuba Research Laboratory, Hamamatsu Photonics KK,
9512 Joko, Hamamatsu 431-3103, Japan.
9513 hiritoh@hpk.trc-net.co.jp",
9517 keywords = "Adenosine Diphosphate",
9518 keywords = "Adenosine Triphosphate",
9519 keywords = "Bacillus",
9520 keywords = "Catalysis",
9522 keywords = "Magnetics",
9523 keywords = "Microchemistry",
9524 keywords = "Microspheres",
9525 keywords = "Molecular Motor Proteins",
9526 keywords = "Proton-Translocating ATPases",
9527 keywords = "Rotation",
9528 keywords = "Torque",
9529 abstract = "ATP, the main biological energy currency, is synthesized
9530 from ADP and inorganic phosphate by ATP synthase in an
9531 energy-requiring reaction. The F1 portion of ATP synthase, also
9532 known as F1-ATPase, functions as a rotary molecular motor: in
9533 vitro its gamma-subunit rotates against the surrounding
9534 alpha3beta3 subunits, hydrolysing ATP in three separate catalytic
9535 sites on the beta-subunits. It is widely believed that reverse
9536 rotation of the gamma-subunit, driven by proton flow through the
9537 associated F(o) portion of ATP synthase, leads to ATP synthesis in
9538 biological systems. Here we present direct evidence for the
9539 chemical synthesis of ATP driven by mechanical energy. We attached
9540 a magnetic bead to the gamma-subunit of isolated F1 on a glass
9541 surface, and rotated the bead using electrical magnets. Rotation
9542 in the appropriate direction resulted in the appearance of ATP in
9543 the medium as detected by the luciferase-luciferin reaction. This
9544 shows that a vectorial force (torque) working at one particular
9545 point on a protein machine can influence a chemical reaction
9546 occurring in physically remote catalytic sites, driving the
9547 reaction far from equilibrium.",
9549 doi = "10.1038/nature02212",
9550 URL = "http://www.ncbi.nlm.nih.gov/pubmed/14749837",
9555 author = NSakaki #" and "# RShimoKon #" and "# KAdachi
9556 #" and "# HItoh #" and "# SFuruike #" and "# EMuneyuki
9557 #" and "# MYoshida #" and "# KKinosita,
9558 title = "One rotary mechanism for {F1}-{ATP}ase over {ATP}
9559 concentrations from millimolar down to nanomolar.",
9564 address = "Department of Functional Molecular Science, The Graduate
9565 University for Advanced Studies, Nishigonaka 38, Myodaiji, Okazaki
9569 pages = "2047--2056",
9570 keywords = "Adenosine Triphosphate",
9571 keywords = "Hydrolysis",
9572 keywords = "Kinetics",
9573 keywords = "Microchemistry",
9574 keywords = "Molecular Motor Proteins",
9575 keywords = "Nanostructures",
9576 keywords = "Protein Binding",
9577 keywords = "Protein Conformation",
9578 keywords = "Proton-Translocating ATPases",
9579 keywords = "Rotation",
9580 keywords = "Torque",
9581 abstract = "F(1)-ATPase is a rotary molecular motor in which the
9582 central gamma-subunit rotates inside a cylinder made of
9583 alpha(3)beta(3)-subunits. The rotation is driven by ATP hydrolysis
9584 in three catalytic sites on the beta-subunits. How many of the
9585 three catalytic sites are filled with a nucleotide during the
9586 course of rotation is an important yet unsettled question. Here we
9587 inquire whether F(1) rotates at extremely low ATP concentrations
9588 where the site occupancy is expected to be low. We observed under
9589 an optical microscope rotation of individual F(1) molecules that
9590 carried a bead duplex on the gamma-subunit. Time-averaged rotation
9591 rate was proportional to the ATP concentration down to 200 pM,
9592 giving an apparent rate constant for ATP binding of 2 x 10(7)
9593 M(-1)s(-1). A similar rate constant characterized bulk ATP
9594 hydrolysis in solution, which obeyed a simple Michaelis-Menten
9595 scheme between 6 mM and 60 nM ATP. F(1) produced the same torque
9596 of approximately 40 pN.nm at 2 mM, 60 nM, and 2 nM ATP. These
9597 results point to one rotary mechanism governing the entire range
9598 of nanomolar to millimolar ATP, although a switchover between two
9599 mechanisms cannot be dismissed. Below 1 nM ATP, we observed less
9600 regular rotations, indicative of the appearance of another
9603 doi = "10.1529/biophysj.104.054668",
9604 URL = "http://www.ncbi.nlm.nih.gov/pubmed/15626703",
9608 @article{ schmidt02,
9609 author = JSchmidt #" and "# XJiang #" and "# CMontemagno,
9610 title = "Force Tolerances of Hybrid Nanodevices",
9614 pages = "1229--1233",
9616 doi = "10.1021/nl025773v",
9617 URL = "http://pubs.acs.org/doi/abs/10.1021/nl025773v",
9618 eprint = "http://pubs.acs.org/doi/pdf/10.1021/nl025773v",
9619 abstract = "We have created hybrid devices consisting of nanoscale
9620 fabricated inorganic components integrated with and powered by a
9621 genetically engineered motor protein. We wish to increase the
9622 assembly yield and lifetime of these devices through
9623 identification, measurement, and improvement of weak internal
9624 bonds. Using dynamic force spectroscopy, we have measured the bond
9625 rupture force of (histidine)\textsubscript{6} on a number of
9626 different surfaces as a function of loading rate. The bond sizes,
9627 lifetimes, and energy barrier heights were derived from these
9628 measurements. We compare the (His)\textsubscript{6}--nickel bonds
9629 to other bonds composing the hybrid device and describe
9630 preliminary measurements of the force tolerances of the protein
9631 itself. Pathways for improvement of device longevity and
9632 robustness are discussed.",
9636 author = YSLo #" and "# YJZhu #" and "# TBeebe,
9637 title = "Loading-Rate Dependence of Individual Ligand−Receptor
9638 Bond-Rupture Forces Studied by Atomic Force Microscopy",
9642 pages = "3741--3748",
9644 doi = "10.1021/la001569g",
9645 URL = "http://pubs.acs.org/doi/abs/10.1021/la001569g",
9646 eprint = "http://pubs.acs.org/doi/pdf/10.1021/la001569g",
9647 abstract = "It is known that bond strength is a dynamic property
9648 that is dependent upon the force loading rate applied during the
9649 rupturing of a bond. For biotin--avidin and biotin--streptavidin
9650 systems, dynamic force spectra, which are plots of bond strength
9651 vs loge(loading rate), have been acquired in a recent biomembrane
9652 force probe (BFP) study at force loading rates in the range
9653 0.05--60 000 pN/s. In the present study, the dynamic force spectrum
9654 of the biotin--streptavidin bond strength in solution was extended
9655 from loading rates of ∼104 to ∼107 pN/s with the atomic force
9656 microscope (AFM). A Poisson statistical analysis method was
9657 applied to extract the magnitude of individual bond-rupture forces
9658 and nonspecific interactions from the AFM force--distance curve
9659 measurements. The bond strengths were found to scale linearly with
9660 the logarithm of the loading rate. The nonspecific interactions
9661 also exhibited a linear dependence on the logarithm of loading
9662 rate, although not increasing as rapidly as the specific
9663 interactions. The dynamic force spectra acquired here with the AFM
9664 combined well with BFP measurements by Merkel et al. The combined
9665 spectrum exhibited two linear regimes, consistent with the view
9666 that multiple energy barriers are present along the unbinding
9667 coordinate of the biotin--streptavidin complex. This study
9668 demonstrated that unbinding forces measured by different
9669 techniques are in agreement and can be used together to obtain a
9670 dynamic force spectrum covering 9 orders of magnitude in loading
9672 note = "These guys seem to be pretty thorough, give this one another read.",
9676 author = ABaljon #" and "# MRobbins,
9677 title = "Energy Dissipation During Rupture of Adhesive Bonds",
9684 doi = "10.1126/science.271.5248.482",
9685 URL = "http://www.sciencemag.org/content/271/5248/482.abstract",
9686 eprint = "http://www.sciencemag.org/content/271/5248/482.full.pdf",
9687 abstract = "Molecular dynamics simulations were used to study
9688 energy-dissipation mechanisms during the rupture of a thin
9689 adhesive bond formed by short chain molecules. The degree of
9690 dissipation and its velocity dependence varied with the state of
9691 the film. When the adhesive was in a liquid phase, dissipation was
9692 caused by viscous loss. In glassy films, dissipation occurred
9693 during a sequence of rapid structural rearrangements. Roughly
9694 equal amounts of energy were dissipated in each of three types of
9695 rapid motion: cavitation, plastic yield, and bridge rupture. These
9696 mechanisms have similarities to nucleation, plastic flow, and
9697 crazing in commercial polymeric adhesives.",
9700 @article{ fisher99a,
9701 author = TEFisher #" and "# PMarszalek #" and "# AOberhauser
9702 #" and "# MCarrionVazquez #" and "# JFernandez,
9703 title = "The micro-mechanics of single molecules studied with
9704 atomic force microscopy.",
9709 address = "Department of Physiology and Biophysics, Mayo Foundation,
9710 1-117 Medical Sciences Building, Rochester, MN 55905, USA.",
9711 volume = "520 Pt 1",
9713 keywords = "Animals",
9714 keywords = "Extracellular Matrix",
9715 keywords = "Extracellular Matrix Proteins",
9716 keywords = "Humans",
9717 keywords = "Microscopy, Atomic Force",
9718 keywords = "Polysaccharides",
9719 abstract = "The atomic force microscope (AFM) in its force-measuring
9720 mode is capable of effecting displacements on an angstrom scale
9721 (10 A = 1 nm) and measuring forces of a few piconewtons. Recent
9722 experiments have applied AFM techniques to study the mechanical
9723 properties of single biological polymers. These properties
9724 contribute to the function of many proteins exposed to mechanical
9725 strain, including components of the extracellular matrix
9726 (ECM). The force-bearing proteins of the ECM typically contain
9727 multiple tandem repeats of independently folded domains, a common
9728 feature of proteins with structural and mechanical
9729 roles. Polysaccharide moieties of adhesion glycoproteins such as
9730 the selectins are also subject to strain. Force-induced extension
9731 of both types of molecules with the AFM results in conformational
9732 changes that could contribute to their mechanical function. The
9733 force-extension curve for amylose exhibits a transition in
9734 elasticity caused by the conversion of its glucopyranose rings
9735 from the chair to the boat conformation. Extension of multi-domain
9736 proteins causes sequential unraveling of domains, resulting in a
9737 force-extension curve displaying a saw tooth pattern of peaks. The
9738 engineering of multimeric proteins consisting of repeats of
9739 identical domains has allowed detailed analysis of the mechanical
9740 properties of single protein domains. Repetitive extension and
9741 relaxation has enabled direct measurement of rates of domain
9742 unfolding and refolding. The combination of site-directed
9743 mutagenesis with AFM can be used to elucidate the amino acid
9744 sequences that determine mechanical stability. The AFM thus offers
9745 a novel way to explore the mechanical functions of proteins and
9746 will be a useful tool for studying the micro-mechanics of
9749 URL = "http://www.ncbi.nlm.nih.gov/pubmed/10517795",
9753 @article{ fisher99b,
9754 author = TEFisher #" and "# AOberhauser #" and "# MCarrionVazquez
9755 #" and "# PMarszalek #" and "# JFernandez,
9756 title = "The study of protein mechanics with the atomic force microscope.",
9757 journal = "Trends in biochemical sciences",
9760 address = "Dept of Physiology and Biophysics, Mayo Foundation, 1-117
9761 Medical Sciences Building, Rochester, MN 55905, USA.",
9765 keywords = "Entropy",
9766 keywords = "Kinetics",
9767 keywords = "Microscopy, Atomic Force",
9768 keywords = "Protein Binding",
9769 keywords = "Protein Folding",
9770 keywords = "Proteins",
9771 abstract = "The unfolding and folding of single protein molecules
9772 can be studied with an atomic force microscope (AFM). Many
9773 proteins with mechanical functions contain multiple, individually
9774 folded domains with similar structures. Protein engineering
9775 techniques have enabled the construction and expression of
9776 recombinant proteins that contain multiple copies of identical
9777 domains. Thus, the AFM in combination with protein engineering
9778 has enabled the kinetic analysis of the force-induced unfolding
9779 and refolding of individual domains as well as the study of the
9780 determinants of mechanical stability.",
9782 URL = "http://www.ncbi.nlm.nih.gov/pubmed/10500301",
9786 @article{ zlatanova00,
9787 author = JZlatanova #" and "# SLindsay #" and "# SLeuba,
9788 title = "Single molecule force spectroscopy in biology using the
9789 atomic force microscope.",
9792 address = "Biochip Technology Center, Argonne National Laboratory,
9793 9700 South Cass Avenue, Bldg. 202-A253, Argonne, IL 60439,
9794 USA. jzlatano@duke.poly.edu",
9798 keywords = "Biophysics",
9799 keywords = "Cell Adhesion",
9801 keywords = "Elasticity",
9802 keywords = "Microscopy, Atomic Force",
9803 keywords = "Polysaccharides",
9804 keywords = "Proteins",
9805 keywords = "Signal Processing, Computer-Assisted",
9806 keywords = "Viscosity",
9807 abstract = "The importance of forces in biology has been recognized
9808 for quite a while but only in the past decade have we acquired
9809 instrumentation and methodology to directly measure interactive
9810 forces at the level of single biological macromolecules and/or
9811 their complexes. This review focuses on force measurements
9812 performed with the atomic force microscope. A general introduction
9813 to the principle of action is followed by review of the types of
9814 interactions being studied, describing the main results and
9815 discussing the biological implications.",
9817 URL = "http://www.ncbi.nlm.nih.gov/pubmed/11106806",
9819 note = "Lots of great force-clamp cartoons explaining different
9820 approach/retract features.",
9824 author = MViani #" and "# TESchafer #" and "# AChand #" and "# MRief
9825 #" and "# HEGaub #" and "# HHansma,
9826 title = "Small cantilevers for force spectroscopy of single molecules",
9831 pages = "2258--2262",
9832 abstract = "We have used a simple process to fabricate small
9833 rectangular cantilevers out of silicon nitride. They have lengths
9834 of 9--50 $\mu$m, widths of 3--5 $\mu$m, and thicknesses of 86 and
9835 102 nm. We have added metallic reflector pads to some of the
9836 cantilever ends to maximize reflectivity while minimizing
9837 sensitivity to temperature changes. We have characterized small
9838 cantilevers through their thermal spectra and show that they can
9839 measure smaller forces than larger cantilevers with the same
9840 spring constant because they have lower coefficients of viscous
9841 damping. Finally, we show that small cantilevers can be used for
9842 experiments requiring large measurement bandwidths, and have used
9843 them to unfold single titin molecules over an order of magnitude
9844 faster than previously reported with conventional cantilevers.",
9846 issn_online = "1089-7550",
9847 doi = "10.1063/1.371039",
9848 URL = "http://jap.aip.org/resource/1/japiau/v86/i4/p2258_s1",
9852 @article{ capitanio02,
9853 author = MCapitanio #" and "# GRomano #" and "# RBallerini #" and "#
9854 MGiuntini #" and "# FPavone #" and "# DDunlap #" and "# LFinzi,
9855 title = "Calibration of optical tweezers with differential
9856 interference contrast signals",
9861 pages = "1687--1696",
9862 abstract = "A comparison of different calibration methods for
9863 optical tweezers with the differential interference contrast (DIC)
9864 technique was performed to establish the uses and the advantages
9865 of each method. A detailed experimental and theoretical analysis
9866 of each method was performed with emphasis on the anisotropy
9867 involved in the DIC technique and the noise components in the
9868 detection. Finally, a time of flight method that permits the
9869 reconstruction of the optical potential well was demonstrated.",
9871 issn_online = "1089-7623",
9872 doi = "10.1063/1.1460929",
9873 URL = "http://rsi.aip.org/resource/1/rsinak/v73/i4/p1687_s1",
9878 author = GBinnig #" and "# CQuate #" and "# CGerber,
9879 title = "Atomic force microscope",
9887 abstract = "The scanning tunneling microscope is proposed as a
9888 method to measure forces as small as $10^{-18}$ N. As one
9889 application for this concept, we introduce a new type of
9890 microscope capable of investigating surfaces of insulators on an
9891 atomic scale. The atomic force microscope is a combination of the
9892 principles of the scanning tunneling microscope and the stylus
9893 profilometer. It incorporates a probe that does not damage the
9894 surface. Our preliminary results in air demonstrate a lateral
9895 resolution of 30 \AA and a vertical resolution less than 1 \AA.",
9897 doi = "10.1103/PhysRevLett.56.930",
9898 URL = "http://www.ncbi.nlm.nih.gov/pubmed/10033323",
9899 eprint = {http://prl.aps.org/pdf/PRL/v56/i9/p930_1},
9901 note = "Original AFM paper.",
9905 author = BDrake #" and "# CBPrater #" and "# ALWeisenhorn #" and "#
9906 SAGould #" and "# TRAlbrecht #" and "# CQuate #" and "#
9907 DSCannell #" and "# HHansma #" and "# PHansma,
9908 title = {Imaging crystals, polymers, and processes in water with the
9909 atomic force microscope},
9916 pages = {1586--1589},
9917 doi = {10.1126/science.2928794},
9918 url = {http://www.sciencemag.org/content/243/4898/1586.abstract},
9919 eprint = {http://www.sciencemag.org/content/243/4898/1586.full.pdf},
9920 abstract ={The atomic force microscope (AFM) can be used to image
9921 the surface of both conductors and nonconductors even if they are
9922 covered with water or aqueous solutions. An AFM was used that
9923 combines microfabricated cantilevers with a previously described
9924 optical lever system to monitor deflection. Images of mica
9925 demonstrate that atomic resolution is possible on rigid materials,
9926 thus opening the possibility of atomic-scale corrosion experiments
9927 on nonconductors. Images of polyalanine, an amino acid polymer,
9928 show the potential of the AFM for revealing the structure of
9929 molecules important in biology and medicine. Finally, a series of
9930 ten images of the polymerization of fibrin, the basic component of
9931 blood clots, illustrate the potential of the AFM for revealing
9932 subtle details of biological processes as they occur in real
9936 @article{ radmacher92,
9937 author = MRadmacher #" and "# RWTillmann #" and "# MFritz #" and "# HEGaub,
9938 title = {From molecules to cells: imaging soft samples with the
9939 atomic force microscope},
9946 pages = {1900--1905},
9947 doi = {10.1126/science.1411505},
9948 url = {http://www.sciencemag.org/content/257/5078/1900.abstract},
9949 eprint = {http://www.sciencemag.org/content/257/5078/1900.full.pdf},
9950 abstract ={Since its invention a few years ago, the atomic force microscope has become one of the most widely used near-field microscopes. Surfaces of hard sample are imaged routinely with atomic resolution. Soft samples, however, remain challenging. An overview is presented on the application of atomic force microscopy to organic samples ranging from thin ordered films at molecular resolution to living cells. Fundamental mechanisms of the image formation are discussed, and novel imaging modes are introduced that exploit different aspects of the tip-sample interaction for local measurements of the micromechanical properties of the sample. As examples, images of Langmuir-Blodgett films, which map the local viscoelasticity as well as the friction coefficient, are presented.},
9953 @article{ williams86,
9954 author = CCWilliams #" and "# HKWickramasinghe,
9955 title = "Scanning thermal profiler",
9962 pages = "1587--1589",
9963 abstract = "A new high-resolution profilometer has been demonstrated
9964 based upon a noncontacting near-field thermal probe. The thermal
9965 probe consists of a thermocouple sensor with dimensions
9966 approaching 100 nm. Profiling is achieved by scanning the heated
9967 sensor above but close to the surface of a solid. The conduction
9968 of heat between tip and sample via the air provides a means for
9969 maintaining the sample spacing constant during the lateral
9970 scan. The large difference in thermal properties between air and
9971 solids makes the profiling technique essentially independent of
9972 the material properties of the solid. Noncontact profiling of
9973 resist and metal films has shown a lateral resolution of 100 nm
9974 and a depth solution of 3 nm. The basic theory of the new probe is
9975 described and the results presented.",
9977 issn_online = "1077-3118",
9978 doi = "10.1063/1.97288",
9979 URL = "http://apl.aip.org/resource/1/applab/v49/i23/p1587_s1",
9984 author = GMeyer #" and "# NMAmer,
9985 title = "Novel optical approach to atomic force microscopy",
9992 pages = "1045--1047",
9993 abstract = "A sensitive and simple optical method for detecting the
9994 cantilever deflection in atomic force microscopy is described. The
9995 method was incorporated in an atomic force microscope, and imaging
9996 and force measurements, in ultrahigh vacuum, were successfully
9999 issn_online = "1077-3118",
10000 doi = "10.1063/1.100061",
10001 URL = "http://apl.aip.org/resource/1/applab/v53/i12/p1045_s1",
10006 author = EDijkstra,
10007 title = {Notes on Structured Programming},
10010 url = {http://www.cs.utexas.edu/users/EWD/ewd02xx/EWD249.PDF},
10011 publisher = THEMath,
10012 note = {T.H. Report 70-WSK-03},
10017 title = {On the Composition of Well-Structured Programs},
10018 journal = ACM:CSur,
10023 pages = {247--259},
10025 issn = {0360-0300},
10026 doi = {10.1145/356635.356639},
10027 url = {http://doi.acm.org/10.1145/356635.356639},
10029 address = {New York, NY, USA},
10032 @article{ shneiderman79,
10033 author = BShneiderman #" and "# RMayer,
10034 title = {Syntactic/semantic interactions in programmer behavior: A
10035 model and experimental results},
10040 pages = {219--238},
10041 issn = {0091-7036},
10042 doi = {10.1007/BF00977789},
10043 url = {http://dx.doi.org/10.1007/BF00977789},
10045 keywords = {Programming; programming languages; cognitive models;
10046 program composition; program comprehension; debugging;
10047 modification; learning; education; information processing},
10048 language = {English},
10051 @article{ hughes89,
10053 title = {Why Functional Programming Matters},
10059 doi = {10.1093/comjnl/32.2.98},
10060 URL = {http://comjnl.oxfordjournals.org/content/32/2/98.abstract},
10061 eprint = {http://comjnl.oxfordjournals.org/content/32/2/98.full.pdf+html},
10062 abstract ={As software becomes more and more complex, it is more and
10063 more important to structure it well. Well-structured software is
10064 easy to write, easy to debug, and provides a collection of modules
10065 that can be re-used to reduce future programming
10066 costs. Conventional languages place conceptual limits on the way
10067 problems can be modularised. Functional languages push those
10068 limits back. In this paper we show that two features of functional
10069 languages in particular, higher-order functions and lazy
10070 evaluation, can contribute greatly to modularity. As examples, we
10071 manipulate lists and trees, program several numerical algorithms,
10072 and implement the alpha-beta heuristics (an Artificial
10073 Intelligence algorithm used in game-playing programs). Since
10074 modularity is the key to successful programming, functional
10075 languages are vitally important to the real world.},
10078 @article{ hilburn93,
10080 title = {A top-down approach to teaching an introductory computer science course},
10081 journal = ACM:SIGCSE,
10086 issn = {0097-8418},
10089 doi = {10.1145/169073.169349},
10090 url = {http://doi.acm.org/10.1145/169073.169349},
10093 address = {New York, NY, USA},
10098 title = {The mythical man-month},
10099 edition = {20$^\text{th}$ anniversary},
10101 isbn = {0-201-83595-9},
10103 address = {Boston, MA, USA},
10104 url = {http://dl.acm.org/citation.cfm?id=207583},
10105 note = {First published in 1975},
10108 @inproceedings{ claerbout92,
10109 author = JClaerbout #" and "# MKarrenbach,
10110 title = {Electronic documents give reproducible research a new meaning},
10111 booktitle = {SEG Technical Program Expanded Abstracts 1992},
10114 pages = {601--604},
10115 doi = {10.1190/1.1822162},
10116 issn = {1052-3812},
10118 url = {http://library.seg.org/doi/abs/10.1190/1.1822162},
10119 eprint = {http://sepwww.stanford.edu/doku.php?id=sep:research:reproducible:seg92},
10122 @incollection{ buckheit95,
10123 author = JBuckheit #" and "# DDonoho,
10124 title = {WaveLab and Reproducible Research},
10125 booktitle = {Wavelets and Statistics},
10126 series = {Lecture Notes in Statistics},
10127 editor = AAntoniadis #" and "# GOppenheim,
10131 isbn = {978-0-387-94564-4},
10132 doi = {10.1007/978-1-4612-2544-7_5},
10133 url = {http://dx.doi.org/10.1007/978-1-4612-2544-7_5},
10134 eprint = {http://www-stat.stanford.edu/~wavelab/Wavelab_850/wavelab.pdf},
10135 publisher = SPRINGER,
10136 language = {English},
10139 @article{ schwab00,
10140 author = MSchwab #" and "# MKarrenbach #" and "# JClaerbout,
10141 title = {Making scientific computations reproducible},
10144 month = {November--December},
10148 doi = {10.1109/5992.881708},
10149 ISSN = {1521-9615},
10150 keywords = {document handling;file organisation;natural sciences
10151 computing;research and development
10152 management;ReDoc;authors;computational results;reproducible
10153 scientific computations;research paper;software filing
10154 system;standardized rules;Computer
10155 interfaces;Documentation;Electronic
10156 publishing;Laboratories;Organizing;Reproducibility of
10157 results;Software maintenance;Software systems;Software
10158 testing;Technological innovation},
10159 abstract = {To verify a research paper's computational results,
10160 readers typically have to recreate them from scratch. ReDoc is a
10161 simple software filing system for authors that lets readers easily
10162 reproduce computational results using standardized rules and
10166 @article{ wilson06a,
10168 title = {Where's the Real Bottleneck in Scientific Computing?},
10171 month = {January--February},
10174 @article{ wilson06b,
10176 title = {Software Carpentry: Getting Scientists to Write Better
10177 Code by Making Them More Productive},
10180 month = {November--December},
10183 @article{ vandewalle09,
10184 author = PVandewalle #" and "# JKovacevic #" and "# MVetterli ,
10185 title = {Reproducible Research in Signal Processing - What, why, and how},
10186 journal = IEEE:SPM,
10192 doi = {10.1109/MSP.2009.932122},
10193 issn = {1053-5888},
10194 url = {http://rr.epfl.ch/17/},
10195 eprint = {http://rr.epfl.ch/17/1/VandewalleKV09.pdf},
10196 keywords={research and development;signal processing;high-quality
10197 reviewing process;large data set;reproducible research;signal
10198 processing;win-win situation;Advertising;Digital signal
10199 processing;Education;Programming;Reproducibility of
10200 results;Scholarships;Signal processing;Signal processing
10201 algorithms;Testing;Wikipedia},
10202 abstract = {Have you ever tried to reproduce the results presented
10203 in a research paper? For many of our current publications, this
10204 would unfortunately be a challenging task. For a computational
10205 algorithm, details such as the exact data set, initialization or
10206 termination procedures, and precise parameter values are often
10207 omitted in the publication for various reasons, such as a lack of
10208 space, a lack of self-discipline, or an apparent lack of interest
10209 to the readers, to name a few. This makes it difficult, if not
10210 impossible, for someone else to obtain the same results. In our
10211 experience, it is often even worse as even we are not always able
10212 to reproduce our own experiments, making it difficult to answer
10213 questions from colleagues about details. Following are some
10214 examples of e-mails we have received: ``I just read your paper
10215 X. It is very completely described, however I am confused by
10216 Y. Could you provide the implementation code to me for reference
10217 if possible?'' ``Hi! I am also working on a project related to
10218 X. I have implemented your algorithm but cannot get the same
10219 results as described in your paper. Which values should I use for
10220 parameters Y and Z?''},
10223 @article{ aruliah12,
10224 author = DAruliah #" and "# CTBrown #" and "# NPCHong #" and "#
10225 MDavis #" and "# RTGuy #" and "# SHaddock #" and "# KHuff #" and "#
10226 IMitchell #" and "# MPlumbley #" and "# BWaugh #" and "#
10227 EPWhite #" and "# GWilson #" and "# PWilson,
10228 title = {Best Practices for Scientific Computing},
10230 volume = {abs/1210.0530},
10235 url = {http://arxiv.org/abs/1210.0530},
10236 eprint = {http://arxiv.org/pdf/1210.0530v3},
10237 note = {v3: Thu, 29 Nov 2012 19:28:27 GMT},
10240 @article{ ziegler42,
10241 author = JZiegler #" and "# NNichols,
10242 title = {Optimum Settings for Automatic Controllers},
10247 pages = {759--765},
10248 url = {http://www.driedger.ca/Z-N/Z-N.html},
10249 eprint = {http://www.driedger.ca/Z-N/Z-n.pdf},
10253 author = GHCohen #" and "# GACoon,
10254 title = {Theoretical considerations of retarded control},
10258 pages = {827--834},
10262 author = FSWang #" and "# WSJuang #" and "# CTChan,
10263 title = {Optimal tuning of {PID} controllers for single and
10264 cascade control loops},
10270 publisher = GordonBreach,
10271 issn = {0098-6445},
10272 doi = {10.1080/00986449508936294},
10273 url = {http://www.tandfonline.com/doi/abs/10.1080/00986449508936294},
10274 keywords = {process control; cascade control; controller tuning},
10275 abstract = {Design of one parameter tuning of three-mode PID
10276 controller was developed in this present study. The integral time
10277 and the derivative time of the controller were expressed in terms
10278 of the time constant and dead time of the process. Only the
10279 proportional gain was observed to be dependent on the implemented
10280 tunable parameter in which the stable region could be
10281 predetermined by the Routh test. Extension of the concept towards
10282 designing cascade PID controllers was straightforward such that
10283 only two parameters for the inner and outer PID controllers
10284 required to be tuned, respectively. The optimal tuning correlative
10285 formulas of the proportional gain for single and cascade control
10286 systems were obtained by the least square regression method.},
10289 @article{ astrom93,
10290 author = KAstrom #" and "# THagglund #" and "# CCHang #" and "# WKHo,
10291 title = {Automatic tuning and adaptation for {PID} controllers---a survey},
10296 pages = {699--714},
10297 issn = "0967-0661",
10298 doi = "10.1016/0967-0661(93)91394-C",
10299 url = "http://dx.doi.org/10.1016/0967-0661(93)91394-C",
10300 keywords = {Adaptive control},
10301 keywords = {automatic tuning},
10302 keywords = {gain scheduling},
10303 keywords = {{PID} control},
10304 abstract = {Adaptive techniques such as gain scheduling, automatic
10305 tuning and continuous adaptation have been used in industrial
10306 single-loop controllers for about ten years. This paper gives a
10307 survey of the different adaptive techniques, the underlying
10308 process models and control designs. An overview of industrial
10309 products is also presented, which includes a fairly detailed
10310 investigation of four different adaptive single-loop
10316 title = {Notes on the use of propagation of error formulas},
10322 pages = {263--273},
10324 issn = {0022-4316},
10325 url = {http://nistdigitalarchives.contentdm.oclc.org/cdm/compoundobject/collection/p13011coll6/id/78003/rec/5},
10326 eprint = {http://nistdigitalarchives.contentdm.oclc.org/utils/getfile/collection/p13011coll6/id/78003/filename/print/page/download},
10327 keywords = {Approximation; error; formula; imprecision; law of
10328 error; products; propagation of error; random; ratio; systematic;
10330 abstract = {The ``law of propagation of error'' is a tool that
10331 physical scientists have conveniently and frequently used in their
10332 work for many years, yet an adequate reference is difficult to
10333 find. In this paper an expository review of this topic is
10334 presented, particularly in the light of current practices and
10335 interpretations. Examples on the accuracy of the approximations
10336 are given. The reporting of the uncertainties of final results is
10340 @article{ livadaru03,
10341 author = LLivadaru #" and "# RRNetz #" and "# HJKreuzer,
10342 title = {Stretching Response of Discrete Semiflexible Polymers},
10346 journal = Macromol,
10349 pages = {3732--3744},
10350 doi = {10.1021/ma020751g},
10351 URL = {http://pubs.acs.org/doi/abs/10.1021/ma020751g},
10352 eprint = {http://pubs.acs.org/doi/pdf/10.1021/ma020751g},
10353 abstract = {We demonstrate that semiflexible polymer chains
10354 (characterized by a persistence length $l$) made up of discrete
10355 segments or bonds of length $b$ show at large stretching forces a
10356 crossover from the standard wormlike chain (WLC) behavior to a
10357 discrete-chain (DC) behavior. In the DC regime, the stretching
10358 response is independent of the persistence length and shows a
10359 different force dependence than in the WLC regime. We perform
10360 extensive transfer-matrix calculations for the force-response of a
10361 freely rotating chain (FRC) model as a function of varying bond
10362 angle $\gamma$ (and thus varying persistence length) and chain
10363 length. The FRC model is a first step toward the understanding of
10364 the stretching behavior of synthetic polymers, denatured proteins,
10365 and single-stranded DNA under large tensile forces. We also
10366 present scaling results for the force response of the elastically
10367 jointed chain (EJC) model, that is, a chain made up of freely
10368 jointed bonds that are connected by joints with some bending
10369 stiffness; this is the discretized version of the continuum WLC
10370 model. The EJC model might be applicable to stiff biopolymers such
10371 as double-stranded DNA or Actin. Both models show a similar
10372 crossover from the WLC to the DC behavior, which occurs at a force
10373 $f/k_BT\sim l/b^2$ and is thus (for polymers with a moderately
10374 large persistence length) in the piconewton range probed in many
10375 AFM experiments. We also give a heuristic simple function for the
10376 force--distance relation of a FRC, valid in the global force
10377 range, which can be used to fit experimental data. Our findings
10378 might help to resolve the discrepancies encountered when trying to
10379 fit experimental data for the stretching response of polymers in a
10380 broad force range with a single effective persistence length.},
10381 note = {There are two typos in \fref{equation}{46}.
10382 \citet{livadaru03} have
10384 \frac{R_z}{L} = \begin{cases}
10385 \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
10386 1 - \p({\frac{fl}{4k_BT}})^{-0.5}
10387 & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
10388 1 - \p({\frac{fb}{ck_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
10391 but the correct formula is
10393 \frac{R_z}{L} = \begin{cases}
10394 \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
10395 1 - \p({\frac{4fl}{k_BT}})^{-0.5}
10396 & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
10397 1 - \p({\frac{cfb}{k_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
10400 with both the $4$ and the $c$ moved into their respective
10401 numerators. I pointed these errors out to Roland Netz in 2012,
10402 along with the fact that even with the corrected formula there is
10403 a discontinuity between the low- and moderate-force regimes. Netz
10404 confirmed the errors, and pointed out that the discontinuity is
10405 because \fref{equation}{46} only accounts for the scaling (without
10406 prefactors). Unfortunately, there does not seem to be a published
10407 erratum pointing out the error and at least \citet{puchner08} have
10408 quoted the incorrect form.},
10412 author = PCarl #" and "# PDalhaimer,
10413 title = {{PUNIAS}: Protein Unfolding and Nano-indentation Analysis
10418 note = {4 Int. Workshop, Scanning Probe Microscopy in Life Sciences},
10419 address = {Berlin},
10420 url = {http://punias.voila.net/},
10424 author = PCarl #" and "# HSchillers,
10425 title = {Elasticity measurement of living cells with an atomic force
10426 microscope: data acquisition and processing.},
10430 address = {Institute of Physiology II, University of M{\"u}nster,
10431 Robert-Koch-Str. 27b, 48149, M{\"u}nster, Germany.},
10435 pages = {551--559},
10436 issn = {0031-6768},
10437 doi = {10.1007/s00424-008-0524-3},
10438 url = {http://www.ncbi.nlm.nih.gov/pubmed/18481081},
10440 keywords = {Animals},
10441 keywords = {Biomechanics},
10442 keywords = {CHO Cells},
10443 keywords = {Cricetinae},
10444 keywords = {Cricetulus},
10445 keywords = {Cystic Fibrosis Transmembrane Conductance Regulator},
10446 keywords = {Elastic Modulus},
10447 keywords = {Equipment Design},
10448 keywords = {Microscopy, Atomic Force},
10449 keywords = {Models, Biological},
10450 keywords = {Reproducibility of Results},
10451 keywords = {Signal Processing, Computer-Assisted},
10452 keywords = {Transfection},
10453 abstract = {Elasticity of living cells is a parameter of increasing
10454 importance in cellular physiology, and the atomic force microscope
10455 is a suitable instrument to quantitatively measure it. The
10456 principle of an elasticity measurement is to physically indent a
10457 cell with a probe, to measure the applied force, and to process
10458 this force-indentation data using an appropriate model. It is
10459 crucial to know what extent the geometry of the indenting probe
10460 influences the result. Therefore, we indented living Chinese
10461 hamster ovary cells at 37 degrees C with sharp tips and colloidal
10462 probes (spherical particle tips) of different sizes and
10463 materials. We furthermore developed an implementation of the Hertz
10464 model, which simplifies the data processing. Our results show (a)
10465 that the size of the colloidal probe does not influence the result
10466 over a wide range (radii $0.5$-$26\U{$\mu$m}$) and (b) indenting
10467 cells with sharp tips results in higher Young's moduli
10468 (approximately $1,300\U{Pa}$) than using colloidal probes
10469 (approximately $400\U{Pa}$).},
10470 note = {Mentions \citetalias{punias} as if it was in-house software,
10471 which makes sense because Philippe Carl seems to be a major author.},
10474 @article{ struckmeier08,
10475 author = JStruckmeier #" and "# RWahl #" and "# MLeuschner #" and "#
10476 JNunes #" and "# HJanovjak #" and "# UGeisler #" and "#
10477 GHofmann #" and "# TJahnke #" and "# DJMuller,
10478 title = {Fully automated single-molecule force spectroscopy for
10479 screening applications},
10483 address = {Cellular Machines, Biotechnology Center,
10484 Technische Universit{\"a}t Dresden, Tatzberg 47, D-01307
10490 issn = {0957-4484},
10491 doi = {10.1088/0957-4484/19/38/384020},
10492 url = {http://www.ncbi.nlm.nih.gov/pubmed/21832579},
10494 abstract = {With the introduction of single-molecule force
10495 spectroscopy (SMFS) it has become possible to directly access the
10496 interactions of various molecular systems. A bottleneck in
10497 conventional SMFS is collecting the large amount of data required
10498 for statistically meaningful analysis. Currently, atomic force
10499 microscopy (AFM)-based SMFS requires the user to tediously `fish'
10500 for single molecules. In addition, most experimental and
10501 environmental conditions must be manually adjusted. Here, we
10502 developed a fully automated single-molecule force
10503 spectroscope. The instrument is able to perform SMFS while
10504 monitoring and regulating experimental conditions such as buffer
10505 composition and temperature. Cantilever alignment and calibration
10506 can also be automatically performed during experiments. This,
10507 combined with in-line data analysis, enables the instrument, once
10508 set up, to perform complete SMFS experiments autonomously.},
10509 note = {An advertisement for JPK's \citetalias{force-robot}.},
10512 @article{ andreopoulos11,
10513 author = BAndreopoulos #" and "# DLabudde,
10514 title = {Efficient unfolding pattern recognition in single molecule
10515 force spectroscopy data},
10519 address = {Department of Bioinformatics, Biotechnological Center,
10520 University of Technology Dresden, Dresden, Germany.
10521 williama@biotec.tu-dresden.de},
10526 issn = {1748-7188},
10527 doi = {10.1186/1748-7188-6-16},
10528 url = {http://www.ncbi.nlm.nih.gov/pubmed/21645400},
10530 abstract = {Single-molecule force spectroscopy (SMFS) is a technique
10531 that measures the force necessary to unfold a protein. SMFS
10532 experiments generate Force-Distance (F-D) curves. A statistical
10533 analysis of a set of F-D curves reveals different unfolding
10534 pathways. Information on protein structure, conformation,
10535 functional states, and inter- and intra-molecular interactions can
10540 editor = HWTurnbull,
10542 title = {The correspondence of Isaac Newton},
10547 url = {http://books.google.com/books?id=pr8WAQAAMAAJ},
10548 note = {The ``Giants'' quote is on page 416, in a letter to Robert
10549 Hooke dated February 5, 1676.},
10552 @book{ whitehead11,
10553 author = ANWhitehead,
10554 title = {An introduction to mathematics},
10558 address = {London},
10559 url = {http://archive.org/details/introductiontoma00whitiala},
10560 note = {The ``civilization'' quote is on page 61.},
10564 author = NJMlot #" and "# CATovey #" and "# DLHu,
10565 title = {Fire ants self-assemble into waterproof rafts to survive floods},
10569 address = {Schools of Mechanical Engineering, Industrial and
10570 Systems Engineering, and Biology,
10571 Georgia Institute of Technology, Atlanta, GA 30318, USA.},
10575 pages = {7669--7673},
10576 issn = {1091-6490},
10577 doi = {10.1073/pnas.1016658108},
10578 url = {http://www.ncbi.nlm.nih.gov/pubmed/21518911},
10580 keywords = {Animals},
10582 keywords = {Behavior, Animal},
10583 keywords = {Biophysical Phenomena},
10584 keywords = {Floods},
10585 keywords = {Hydrophobic and Hydrophilic Interactions},
10586 keywords = {Microscopy, Electron, Scanning},
10587 keywords = {Models, Biological},
10588 keywords = {Social Behavior},
10589 keywords = {Surface Properties},
10590 keywords = {Time-Lapse Imaging},
10591 keywords = {Video Recording},
10592 keywords = {Water},
10593 abstract = {Why does a single fire ant \species{Solenopsis invicta}
10594 struggle in water, whereas a group can float effortlessly for
10595 days? We use time-lapse photography to investigate how fire ants
10596 \species{S.~invicta} link their bodies together to build
10597 waterproof rafts. Although water repellency in nature has been
10598 previously viewed as a static material property of plant leaves
10599 and insect cuticles, we here demonstrate a self-assembled
10600 hydrophobic surface. We find that ants can considerably enhance
10601 their water repellency by linking their bodies together, a process
10602 analogous to the weaving of a waterproof fabric. We present a
10603 model for the rate of raft construction based on observations of
10604 ant trajectories atop the raft. Central to the construction
10605 process is the trapping of ants at the raft edge by their
10606 neighbors, suggesting that some ``cooperative'' behaviors may rely
10608 note = {Higher resolution pictures are available at
10609 \url{http://antlab.gatech.edu/antlab/The_Ant_Raft.html}.},
10612 @article{ chauhan97,
10613 author = VPChauhan #" and "# IRay #" and "# AChauhan #" and "#
10614 JWegiel #" and "# HMWisniewski,
10615 title = {Metal cations defibrillize the amyloid beta-protein fibrils.},
10618 address = {New York State Institute for Basic Research in
10619 Developmental Disabilities, Staten Island 10314-6399,
10624 pages = {805--809},
10625 issn = {0364-3190},
10626 url = {http://www.ncbi.nlm.nih.gov/pubmed/9232632},
10627 doi = {10.1023/A:1022079709085},
10629 keywords = {Alzheimer Disease},
10630 keywords = {Amyloid beta-Peptides},
10631 keywords = {Drug Evaluation, Preclinical},
10632 keywords = {Humans},
10633 keywords = {Metals},
10634 keywords = {Peptide Fragments},
10635 keywords = {Solubility},
10636 abstract = {Amyloid beta-protein (A beta) is the major constituent
10637 of amyloid fibrils composing beta-amyloid plaques and
10638 cerebrovascular amyloid in Alzheimer's disease (AD). We studied
10639 the effect of metal cations on preformed fibrils of synthetic A
10640 beta by Thioflavin T (ThT) fluorescence spectroscopy and
10641 electronmicroscopy (EM) in negative staining. The amount of cross
10642 beta-pleated sheet structure of A beta 1-40 fibrils was found to
10643 decrease by metal cations in a concentration-dependent manner as
10644 measured by ThT fluorescence spectroscopy. The order of
10645 defibrillization of A beta 1-40 fibrils by metal cations was: Ca2+
10646 and Zn2+ (IC50 = 100 microM) > Mg3+ (IC50 = 300 microM) > Al3+
10647 (IC50 = 1.1 mM). EM analysis in negative staining showed that A
10648 beta 1-40 fibrils in the absence of cations were organized in a
10649 fine network with a little or no amorphous material. The addition
10650 of Ca2+, Mg2+, and Zn2+ to preformed A beta 1-40 fibrils
10651 defibrillized the fibrils or converted them into short rods or to
10652 amorphous material. Al3+ was less effective, and reduced the
10653 fibril network by about 80\% of that in the absence of any metal
10654 cation. Studies with A beta 1-42 showed that this peptide forms
10655 more dense network of fibrils as compared to A beta 1-40. Both ThT
10656 fluorescence spectroscopy and EM showed that similar to A beta
10657 1-40, A beta 1-42 fibrils are also defibrillized in the presence
10658 of millimolar concentrations of Ca2+. These studies suggest that
10659 metal cations can defibrillize the fibrils of synthetic A beta.},
10660 note = {From page 806, ``The exact mechanism by which these metal
10661 ions affect the fibrillization of A$\beta$ is not known.''},
10664 @article{ friedman05,
10665 author = RFriedman #" and "# ENachliel #" and "# MGutman,
10666 title = {Molecular dynamics of a protein surface: ion-residues
10671 address = {Laser Laboratory for Fast Reactions in Biology,
10672 Department of Biochemistry, The George S. Wise Faculty
10673 for Life Sciences, Tel Aviv University, Israel.},
10677 pages = {768--781},
10678 issn = {0006-3495},
10679 doi = {10.1529/biophysj.105.058917},
10680 url = {http://www.ncbi.nlm.nih.gov/pubmed/15894639},
10682 keywords = {Amino Acids},
10683 keywords = {Binding Sites},
10684 keywords = {Chlorine},
10685 keywords = {Computer Simulation},
10687 keywords = {Models, Chemical},
10688 keywords = {Models, Molecular},
10689 keywords = {Motion},
10690 keywords = {Protein Binding},
10691 keywords = {Protein Conformation},
10692 keywords = {Ribosomal Protein S6},
10693 keywords = {Sodium},
10694 keywords = {Solutions},
10695 keywords = {Static Electricity},
10696 keywords = {Surface Properties},
10697 keywords = {Water},
10698 abstract = {Time-resolved measurements indicated that protons could
10699 propagate on the surface of a protein or a membrane by a special
10700 mechanism that enhanced the shuttle of the proton toward a
10701 specific site. It was proposed that a suitable location of
10702 residues on the surface contributes to the proton shuttling
10703 function. In this study, this notion was further investigated by
10704 the use of molecular dynamics simulations, where Na(+) and Cl(-)
10705 are the ions under study, thus avoiding the necessity for quantum
10706 mechanical calculations. Molecular dynamics simulations were
10707 carried out using as a model a few Na(+) and Cl(-) ions enclosed
10708 in a fully hydrated simulation box with a small globular protein
10709 (the S6 of the bacterial ribosome). Three independent 10-ns-long
10710 simulations indicated that the ions and the protein's surface were
10711 in equilibrium, with rapid passage of the ions between the
10712 protein's surface and the bulk. However, it was noted that close
10713 to some domains the ions extended their duration near the surface,
10714 thus suggesting that the local electrostatic potential hindered
10715 their diffusion to the bulk. During the time frame in which the
10716 ions were detained next to the surface, they could rapidly shuttle
10717 between various attractor sites located under the electrostatic
10718 umbrella. Statistical analysis of the molecular dynamics and
10719 electrostatic potential/entropy consideration indicated that the
10720 detainment state is an energetic compromise between attractive
10721 forces and entropy of dilution. The similarity between the motion
10722 of free ions next to a protein and the proton transfer on the
10723 protein's surface are discussed.},
10726 @article{ friedman11,
10727 author = RFriedman,
10728 title = {Ions and the protein surface revisited: extensive molecular
10729 dynamics simulations and analysis of protein structures in
10730 alkali-chloride solutions.},
10734 address = {School of Natural Sciences, Linn{\ae}us University,
10735 391 82 Kalmar, Sweden. ran.friedman@lnu.se},
10739 pages = {9213--9223},
10740 issn = {1520-5207},
10741 doi = {10.1021/jp112155m},
10742 URL = {http://www.ncbi.nlm.nih.gov/pubmed/21688775},
10744 keywords = {Alkalies},
10745 keywords = {Amyloid},
10746 keywords = {Chlorides},
10747 keywords = {Databases, Protein},
10748 keywords = {Fungal Proteins},
10749 keywords = {HIV Protease},
10750 keywords = {Humans},
10751 keywords = {Molecular Dynamics Simulation},
10752 keywords = {Protein Multimerization},
10753 keywords = {Protein Structure, Secondary},
10754 keywords = {Proteins},
10755 keywords = {Ribosomal Protein S6},
10756 keywords = {Solutions},
10757 keywords = {Solvents},
10758 keywords = {Surface Properties},
10759 abstract = {Proteins interact with ions in various ways. The surface
10760 of proteins has an innate capability to bind ions, and it is also
10761 influenced by the screening of the electrostatic potential owing
10762 to the presence of salts in the bulk solution. Alkali metal ions
10763 and chlorides interact with the protein surface, but such
10764 interactions are relatively weak and often transient. In this
10765 paper, computer simulations and analysis of protein structures are
10766 used to characterize the interactions between ions and the protein
10767 surface. The results show that the ion-binding properties of
10768 protein residues are highly variable. For example, alkali metal
10769 ions are more often associated with aspartate residues than with
10770 glutamates, whereas chlorides are most likely to be located near
10771 arginines. When comparing NaCl and KCl solutions, it was found
10772 that certain surface residues attract the anion more strongly in
10773 NaCl. This study demonstrates that protein-salt interactions
10774 should be accounted for in the planning and execution of
10775 experiments and simulations involving proteins, particularly if
10776 subtle structural details are sought after.},
10780 author = YZhang #" and "# PSCremer,
10781 title = {Interactions between macromolecules and ions: The
10782 {H}ofmeister series.},
10786 address = {Department of Chemistry, Texas A\&M University,
10787 College Station, TX 77843, USA.},
10791 pages = {658--663},
10792 issn = {1367-5931},
10793 doi = {10.1016/j.cbpa.2006.09.020},
10794 url = {http://www.ncbi.nlm.nih.gov/pubmed/17035073},
10796 keywords = {Acrylamides},
10797 keywords = {Biopolymers},
10798 keywords = {Solubility},
10799 keywords = {Thermodynamics},
10800 keywords = {Water},
10801 abstract = {The Hofmeister series, first noted in 1888, ranks the
10802 relative influence of ions on the physical behavior of a wide
10803 variety of aqueous processes ranging from colloidal assembly to
10804 protein folding. Originally, it was thought that an ion's
10805 influence on macromolecular properties was caused at least in part
10806 by `making' or `breaking' bulk water structure. Recent
10807 time-resolved and thermodynamic studies of water molecules in salt
10808 solutions, however, demonstrate that bulk water structure is not
10809 central to the Hofmeister effect. Instead, models are being
10810 developed that depend upon direct ion-macromolecule interactions
10811 as well as interactions with water molecules in the first
10812 hydration shell of the macromolecule.},
10813 note = {A quick pass through Hofmeister history, but no discussion
10814 of cations (``A complete picture will inevitably involve an
10815 integrated understanding of the role of cations (including
10816 guanidinium ions) and osmolytes (such as urea and tri-methylamine
10817 N-oxide) as well. There has been some progress in these fields,
10818 although such subjects are generally beyond the scope of this
10819 short review.'').},
10822 @article{ isaacs06,
10823 author = AMIsaacs #" and "# DBSenn #" and "# MYuan #" and "#
10824 JPShine #" and "# BAYankner,
10825 title = {Acceleration of Amyloid $\beta$-Peptide Aggregation by
10826 Physiological Concentrations of Calcium.},
10830 address = {Department of Neurology and Division of Neuroscience,
10831 The Children's Hospital, Harvard Medical School,
10832 Boston, Massachusetts 02115, USA.},
10836 pages = {27916--27923},
10837 issn = {0021-9258},
10838 doi = {10.1074/jbc.M602061200},
10839 url = {http://www.ncbi.nlm.nih.gov/pubmed/16870617},
10841 keywords = {Alzheimer Disease},
10842 keywords = {Amyloid},
10843 keywords = {Amyloid beta-Peptides},
10844 keywords = {Animals},
10845 keywords = {Calcium},
10846 keywords = {Cells, Cultured},
10847 keywords = {Copper},
10848 keywords = {Neurons},
10851 abstract = {Alzheimer disease is characterized by the accumulation
10852 of aggregated amyloid beta-peptide (Abeta) in the brain. The
10853 physiological mechanisms and factors that predispose to Abeta
10854 aggregation and deposition are not well understood. In this
10855 report, we show that calcium can predispose to Abeta aggregation
10856 and fibril formation. Calcium increased the aggregation of early
10857 forming protofibrillar structures and markedly increased
10858 conversion of protofibrils to mature amyloid fibrils. This
10859 occurred at levels 20-fold below the calcium concentration in the
10860 extracellular space of the brain, the site at which amyloid plaque
10861 deposition occurs. In the absence of calcium, protofibrils can
10862 remain stable in vitro for several days. Using this approach, we
10863 directly compared the neurotoxicity of protofibrils and mature
10864 amyloid fibrils and demonstrate that both species are inherently
10865 toxic to neurons in culture. Thus, calcium may be an important
10866 predisposing factor for Abeta aggregation and toxicity. The high
10867 extracellular concentration of calcium in the brain, together with
10868 impaired intraneuronal calcium regulation in the aging brain and
10869 Alzheimer disease, may play an important role in the onset of
10870 amyloid-related pathology.},
10871 note = {Physiological levels of \NaCl\ are $\sim 150\U{mM}$. \Ca\
10872 is $\sim 2\U{mM}$.},
10876 author = AItkin #" and "# VDupres #" and "# YFDufrene #" and "#
10877 BBechinger #" and "# JMRuysschaert #" and "# VRaussens,
10878 title = {Calcium ions promote formation of amyloid $\beta$-peptide
10879 (1-40) oligomers causally implicated in neuronal toxicity of
10880 {A}lzheimer's disease.},
10884 address = {Laboratory of Structure and Function of Biological
10885 Membranes, Center for Structural Biology and
10886 Bioinformatics, Universit{\'e} Libre de Bruxelles,
10887 Brussels, Belgium.},
10888 journal = PLOS:ONE,
10892 keywords = {Alzheimer Disease},
10893 keywords = {Amyloid beta-Peptides},
10894 keywords = {Blotting, Western},
10895 keywords = {Calcium},
10896 keywords = {Fluorescence},
10897 keywords = {Humans},
10899 keywords = {Models, Biological},
10900 keywords = {Mutant Proteins},
10901 keywords = {Neurons},
10902 keywords = {Protein Structure, Quaternary},
10903 keywords = {Protein Structure, Secondary},
10904 keywords = {Spectroscopy, Fourier Transform Infrared},
10905 keywords = {Thiazoles},
10906 ISSN = {1932-6203},
10907 doi = {10.1371/journal.pone.0018250},
10908 URL = {http://www.ncbi.nlm.nih.gov/pubmed/21464905},
10910 abstract = {Amyloid $\beta$-peptide (A$\beta$) is directly linked to
10911 Alzheimer's disease (AD). In its monomeric form, A$\beta$
10912 aggregates to produce fibrils and a range of oligomers, the latter
10913 being the most neurotoxic. Dysregulation of Ca(2+) homeostasis in
10914 aging brains and in neurodegenerative disorders plays a crucial
10915 role in numerous processes and contributes to cell dysfunction and
10916 death. Here we postulated that calcium may enable or accelerate
10917 the aggregation of A$\beta$. We compared the aggregation pattern
10918 of A$\beta$(1-40) and that of A$\beta$(1-40)E22G, an amyloid
10919 peptide carrying the Arctic mutation that causes early onset of
10920 the disease. We found that in the presence of Ca(2+),
10921 A$\beta$(1-40) preferentially formed oligomers similar to those
10922 formed by A$\beta$(1-40)E22G with or without added Ca(2+), whereas
10923 in the absence of added Ca(2+) the A$\beta$(1-40) aggregated to
10924 form fibrils. Morphological similarities of the oligomers were
10925 confirmed by contact mode atomic force microscopy imaging. The
10926 distribution of oligomeric and fibrillar species in different
10927 samples was detected by gel electrophoresis and Western blot
10928 analysis, the results of which were further supported by
10929 thioflavin T fluorescence experiments. In the samples without
10930 Ca(2+), Fourier transform infrared spectroscopy revealed
10931 conversion of oligomers from an anti-parallel $\beta$-sheet to the
10932 parallel $\beta$-sheet conformation characteristic of
10933 fibrils. Overall, these results led us to conclude that calcium
10934 ions stimulate the formation of oligomers of A$\beta$(1-40), that
10935 have been implicated in the pathogenesis of AD.},
10936 note = {$2\U{mM}$ of \Ca\ is the \emph{extracellular} concentration.
10937 Cytosol concetrations are in the $\mu$M range.},
10941 author = JZidar #" and "# FMerzel,
10942 title = {Probing amyloid-beta fibril stability by increasing ionic
10947 address = {National Institute of Chemistry, Hajdrihova 19,
10948 SI-1000 Ljubljana, Slovenia.},
10952 pages = {2075--2081},
10953 issn = {1520-5207},
10954 doi = {10.1021/jp109025b},
10955 URL = {http://www.ncbi.nlm.nih.gov/pubmed/21329333},
10957 keywords = {Amyloid beta-Peptides},
10958 keywords = {Entropy},
10959 keywords = {Hydrogen Bonding},
10960 keywords = {Molecular Dynamics Simulation},
10961 keywords = {Osmolar Concentration},
10962 keywords = {Protein Multimerization},
10963 keywords = {Protein Stability},
10964 keywords = {Protein Structure, Secondary},
10965 keywords = {Solvents},
10966 keywords = {Vibration},
10967 abstract = {Previous experimental studies have demonstrated changing
10968 the ionic strength of the solvent to have a great impact on the
10969 mechanism of aggregation of amyloid-beta (A$\beta$) protein
10970 leading to distinct fibril morphology at high and low ionic
10971 strength. Here, we use molecular dynamics simulations to elucidate
10972 the ionic strength-dependent effects on the structure and dynamics
10973 of the model A$\beta$ fibril. The change in ionic strength was
10974 brought forth by varying the NaCl concentration in the environment
10975 surrounding the A$\beta$ fibril. Comparison of the calculated
10976 vibrational spectra of A$\beta$ derived from 40 ns all-atom
10977 molecular dynamics simulations at different ionic strength reveals
10978 the fibril structure to be stiffer with increasing ionic
10979 strength. This finding is further corroborated by the calculation
10980 of the stretching force constants. Decomposition of binding and
10981 dynamical properties into contributions from different structural
10982 segments indicates the elongation of the fibril at low ionic
10983 strength is most likely promoted by hydrogen bonding between
10984 N-terminal parts of the fibril, whereas aggregation at higher
10985 ionic strength is suggested to be driven by the hydrophobic
10987 note = {Only study \NaCl\ over the range to $308\U{mM}$, but show a
10988 general decreased hydrogen bonding as concentration increases.},
10992 author = LMiao #" and "# HQin #" and "# PKoehl #" and "# JSong,
10993 title = {Selective and specific ion binding on proteins at
10994 physiologically-relevant concentrations.},
10998 address = {Department of Biological Sciences, Faculty of Science,
10999 National University of Singapore, Singapore.},
11003 pages = {3126--3132},
11004 issn = {1873-3468},
11005 doi = {10.1016/j.febslet.2011.08.048},
11006 url = {http://www.ncbi.nlm.nih.gov/pubmed/21907714},
11008 keywords = {Amino Acid Sequence},
11009 keywords = {Ephrin-B2},
11011 keywords = {Models, Molecular},
11012 keywords = {Molecular Sequence Data},
11013 keywords = {Nuclear Magnetic Resonance, Biomolecular},
11014 keywords = {Protein Binding},
11015 keywords = {Protein Folding},
11016 keywords = {Protein Structure, Tertiary},
11017 keywords = {Salts},
11018 keywords = {Solutions},
11019 keywords = {Thermodynamics},
11020 keywords = {Water},
11021 abstract = {Insoluble proteins dissolved in unsalted water appear to
11022 have no well-folded tertiary structures. This raises a fundamental
11023 question as to whether being unstructured is due to the absence of
11024 salt ions. To address this issue, we solubilized the insoluble
11025 ephrin-B2 cytoplasmic domain in unsalted water and first confirmed
11026 using NMR spectroscopy that it is only partially folded. Using NMR
11027 HSQC titrations with 14 different salts, we further demonstrate
11028 that the addition of salt triggers no significant folding of the
11029 protein within physiologically relevant ion concentrations. We
11030 reveal however that their 8 anions bind to the ephrin-B2 protein
11031 with high affinity and specificity at biologically-relevant
11032 concentrations. Interestingly, the binding is found to be both
11033 salt- and residue-specific.},
11034 note = {They suggest that for low concentrations ($<100\U{mM}$),
11035 protein-ion interactions are mostly electrostatic. The Hofmeister
11036 effects only kick in at higher consentrations.},
11040 author = MDSmith #" and "# LCCruz,
11041 title = {Effect of Ionic Aqueous Environments on the Structure and
11042 Dynamics of the A$\beta_{21-30}$ Fragment: a Molecular-Dynamics
11047 address = {Department of Physics, 3141 Chestnut Street,
11048 Drexel University, Philadelphia, Pennsylvania 19104,
11053 pages = {6614--6624},
11054 issn = {1520-5207},
11055 doi = {10.1021/jp312653h},
11056 url = {http://www.ncbi.nlm.nih.gov/pubmed/23675877},
11058 abstract = {The amyloid $\beta$-protein (A$\beta$) has been
11059 implicated in the pathogenesis of Alzheimer's disease. The role
11060 of the structure and dynamics of the central A$\beta_{21-30}$
11061 decapeptide region of the full-length A$\beta$ is considered
11062 crucial in the aggregation pathway of A$\beta$. Here we report
11063 results of isobaric--isothermal (NPT) all-atom explicit water
11064 molecular dynamics simulations of the monomeric form of the
11065 wild-type A$\beta_{21-30}$ fragment in aqueous salt environments
11066 formed by neurobiologically important group IA (\NaCl, \KCl) and
11067 group IIA (\CaCl, \MgCl) salts. Our simulations reveal the
11068 existence of salt-specific changes to secondary structure
11069 propensities, lifetimes, hydrogen bonding, salt-bridge formation,
11070 and decapeptide--ion contacts of this decapeptide. These results
11071 suggest that aqueous environments with the \CaCl\ salt, and to a
11072 much lesser extent the \MgCl\ salt, have profound effects by
11073 increasing random coil structure propensities and lifetimes and
11074 diminishing intrapeptide hydrogen bonding. These effects are
11075 rationalized in terms of direct cation--decapeptide contacts and
11076 changes to the hydration-shell water molecules. On the other side
11077 of the spectrum, environments with the \NaCl\ and \KCl\ salts have
11078 little influence on the decapeptide's secondary structure despite
11079 increasing hydrogen bonding, salt-bridge formation, and lifetime
11080 of turn structures. The observed enhancement of open structures
11081 by group IIA may be of importance in the folding and aggregation
11082 pathway of the full-length A$\beta$.},
11086 author = HJDyson #" and "# PEWright,
11087 title = {Intrinsically unstructured proteins and their functions.},
11091 address = {Department of Molecular Biology and Skaggs Institute
11092 for Chemical Biology, The Scripps Research Institute,
11093 10550 North Torrey Pines Road, La Jolla, California
11094 92037, USA. dyson@scripps.edu},
11097 pages = {197--208},
11098 issn = {1471-0072},
11099 doi = {10.1038/nrm1589},
11100 url = {http://www.ncbi.nlm.nih.gov/pubmed/15738986},
11102 keywords = {CREB-Binding Protein},
11103 keywords = {Humans},
11104 keywords = {Nuclear Proteins},
11105 keywords = {Nucleic Acids},
11106 keywords = {Protein Binding},
11107 keywords = {Protein Processing, Post-Translational},
11108 keywords = {Protein Structure, Tertiary},
11109 keywords = {Proteins},
11110 keywords = {Trans-Activators},
11111 keywords = {Tumor Suppressor Protein p53},
11112 abstract = {Many gene sequences in eukaryotic genomes encode entire
11113 proteins or large segments of proteins that lack a well-structured
11114 three-dimensional fold. Disordered regions can be highly conserved
11115 between species in both composition and sequence and, contrary to
11116 the traditional view that protein function equates with a stable
11117 three-dimensional structure, disordered regions are often
11118 functional, in ways that we are only beginning to discover. Many
11119 disordered segments fold on binding to their biological targets
11120 (coupled folding and binding), whereas others constitute flexible
11121 linkers that have a role in the assembly of macromolecular
11125 @article{ cleland64,
11126 author = WWCleland,
11127 title = {Dithiothreitol, a New Protective Reagent for SH Groups},
11133 pages = {480--482},
11134 keywords = {Alcohols},
11135 keywords = {Chromatography},
11136 keywords = {Coenzyme A},
11137 keywords = {Oxidation-Reduction},
11138 keywords = {Research},
11139 keywords = {Sulfhydryl Compounds},
11140 keywords = {Sulfides},
11141 keywords = {Ultraviolet Rays},
11142 issn = {0006-2960},
11143 doi = {10.1021/bi00892a002},
11144 url = {http://www.ncbi.nlm.nih.gov/pubmed/14192894},
11145 eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi00892a002},