@string{AW = "Addison-Wesley Longman Publishing Co., Inc."}
@string{AdvExpMedBiol = "Advances in Experimental Medicine and Biology"}
@string{SAinavarapu = "Ainavarapu, Sri Rama Koti"}
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@string{TRAlbrecht = "Albreacht, T.~R."}
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@string{FAli = "Ali, F."}
@string{JFAllemand = "Allemand, Jean-Fran\c{c}ois"}
@string{DAllen = "Allen, D."}
@string{HAn = "An, H."}
@string{KNAn = "An, Kai-Nan"}
@string{ABioChem = "Analytical biochemistry"}
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@string{IAndricioaei = "Andricioaei, Ioan"}
@string{ACIEE = "Angew. Chem. Int. Ed. Engl."}
@string{ARBBS = "Annu Rev Biophys Biomol Struct"}
@string{DAnselmetti = "Anselmetti, Dario"}
@string{AAntoniadis = "Antoniadis, Anestis"}
@string{AMC = "Applied Mathematics and Computation"}
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@string{SArcidiacono = "Arcidiacono, S"}
@string{CArciola = "Arciola, Carla Renata"}
@string{ABArtyukhin = "Artyukhin, Alexander B."}
@string{FWBartels = "Bartels, Frank Wilco"}
@string{BBarz = "Barz, Bogdan"}
@string{TBasche = "Basche, Th."}
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@string{ABasu = "Basu, A."}
@string{LBaugh = "Baugh, Loren"}
@string{BBaumgarth = "Baumgarth, Birgit"}
@string{EABayer = "Bayer, Edward A."}
@string{EBeasley = "Beasley, E."}
@string{JBechhoefer = "Bechhoefer, John"}
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@string{ABecker = "Becker, Anke"}
@string{GSBeddard = "Beddard, Godfrey S."}
@string{TBeebe = "Beebe, Thomas P."}
@string{DBensimon = "Bensimon, David"}
@string{DRBentley = "Bentley, D. R."}
@string{HJCBerendsen = "Berendsen, Herman J. C."}
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+@string{KBergSorensen = "Berg-S{\o}rensen, Kirstine"}
+@string{EBergantino = "Bergantino, Elisabetta"}
@string{DBerk = "Berk, D."}
@string{FBerkemeier = "Berkemeier, Felix"}
@string{BBerne = "Berne, Bruce J."}
@string{Biochem = "Biochemistry"}
@string{BBABE = "Biochimica et Biophysica Acta (BBA) - Bioenergetics"}
@string{BIOINFO = "Bioinformatics (Oxford, England)"}
+@string{Biomet = "Biometrika"}
@string{BPJ = "Biophysical Journal"}
%string{BPJ = "Biophys. J."}
@string{BIOSENSE = "Biosensors and Bioelectronics"}
@string{TBruls = "Bruls, T."}
@string{VBrumfeld = "Brumfeld, Vlad"}
@string{JDBryngelson = "Bryngelson, J. D."}
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@string{JBuckheit = "Buckheit, Jonathan B."}
@string{ABuguin = "Buguin, A."}
@string{ABulhassan = "Bulhassan, Ahmed"}
@string{BBullard = "Bullard, Belinda"}
@string{RBunk = "Bunk, Richard"}
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@string{DBusam = "Busam, D."}
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@string{CBustamante = "Bustamante, Carlos"}
@string{YBustanji = "Bustanji, Yasser"}
@string{HJButt = {Butt, Hans-J\"urgen}}
@string{EChapman = "Chapman, Edwin R."}
@string{RCharlab = "Charlab, R."}
@string{KChaturvedi = "Chaturvedi, K."}
+@string{AChauhan = "Chauhan, A."}
+@string{VPChauhan = "Chauhan, V.~P."}
@string{CChauzy = "Chauzy, C."}
@string{SChe = "Che, Shunai"}
@string{CEC = "Chemical Engineering Communications"}
@string{HCChen = "Chen, H. C."}
@string{LChen = "Chen, L."}
@string{XNChen = "Chen, X. N."}
-@string{XChen = "Chen, Xuming"}
+@string{XiChen = "Chen, Xinyong"}
+@string{XuChen = "Chen, Xuming"}
@string{JFCheng = "Cheng, J. F."}
@string{MLCheng = "Cheng, M. L."}
@string{VGCheung = "Cheung, V. G."}
@string{JClarkson = "Clarkson, John"}
@string{HClausen-Schaumann = "Clausen-Schaumann, H."}
@string{JMClaverie = "Claverie, J. M."}
+@string{WWCleland = "Cleland, W.~W."}
@string{KClerc-Blankenburg = "Clerc-Blankenburg, K."}
@string{NJCobb = "Cobb, Nathan J."}
@string{GHCohen = "Cohen, G.~H."}
@string{MCoyne = "Coyne, M."}
@string{DCraig = "Craig, David"}
@string{ACravchik = "Cravchik, A."}
+@string{PSCremer = "Cremer, Paul S."}
+@string{CCroarkin = "Croarkin, Carroll"}
@string{VCroquette = "Croquette, Vincent"}
+@string{LCCruz = "Cruz, Luis Cruz"}
@string{YCui = "Cui, Y."}
@string{COSB = "Current Opinion in Structural Biology"}
+@string{COCB = "Current Opinion in Chemical Biology"}
@string{LCurry = "Curry, L."}
@string{CDahlke = "Dahlke, C."}
@string{FDahlquist = "Dahlquist, Frederick W."}
+@string{PDalhaimer = "Dalhaimer, Paul"}
@string{SDanaher = "Danaher, S."}
@string{LDavenport = "Davenport, L."}
+@string{MCDavies = "Davies, M.~C."}
@string{MDavis = "Davis, Matt"}
@string{SDecatur = "Decatur, Sean M."}
@string{WDeGrado = "DeGrado, William F."}
@string{CDewhurst = "Dewhurst, Charles"}
@string{VDiFrancesco = "Di Francesco, V."}
@string{KDiemer = "Diemer, K."}
+@string{GDietler = "Dietler, Giovanni"}
@string{HDietz = "Dietz, Hendrik"}
@string{SDietz = "Dietz, S."}
@string{EDijkstra = "Dijkstra, Edsger Wybe"}
@string{MDors = "Dors, M."}
@string{LDougan = "Dougan, Lorna"}
@string{LDoup = "Doup, L."}
-@string{BDrake = "Drake, B."
+@string{BDrake = "Drake, B."}
@string{TDrobek = "Drobek, T."}
@string{Drexel = "Drexel University"}
@string{OKDudko = "Dudko, Olga K."}
+@string{YFDufrene = "Dufr{\^e}ne, Yves F."}
@string{ADunham = "Dunham, A."}
@string{DDunlap = "Dunlap, D."}
@string{PDunn = "Dunn, P."}
+@string{VDupres = "Dupres, Vincent"}
+@string{HJDyson = "Dyson, H.~Jane"}
@string{EMBORep = "EMBO Rep"}
@string{EMBO = "EMBO Rep."}
@string{REckel = "Eckel, R."}
@string{HErickson = "Erickson, Harold P."}
@string{MEsaki = "Esaki, Masatoshi"}
@string{SEsparham = "Esparham, S."}
+@string{EBJ = "European Biophysics Journal"}
@string{EJP = "European Journal of Physics"}
@string{EPL = "Europhysics Letters"}
@string{CEvangelista = "Evangelista, C."}
@string{BFlannery = "Flannery, B."}
@string{LFlorea = "Florea, L."}
@string{ELFlorin = "Florin, Ernst-Ludwig"}
+@string{HFlyvbjerg = "Flyvbjerg, Henrik"}
@string{FoldDes = "Fold Des"}
@string{NRForde = "Forde, Nancy R."}
@string{CFosler = "Fosler, C."}
@string{LFrench = "French, L."}
@string{RWFriddle = "Friddle, Raymond W."}
@string{CFriedman = "Friedman, C."}
+@string{RFriedman = "Friedman, Ran"}
@string{MFritz = "Fritz, M."}
@string{HFuchs = "Fuchs, Harald"}
@string{TFujii = "Fujii, Tadashi"}
@string{LAGavrilov = "Gavrilov, L. A."}
@string{NSGavrilova = "Gavrilova, N. S."}
@string{WGe = "Ge, W."}
+@string{UGeisler = "Geisler, Ulrich"}
@string{GENE = "Gene"}
@string{CGerber = "Gerber, Christoph"}
@string{CGergely = "Gergely, C."}
@string{DGilbert = "Gilbert, D."}
@string{HGire = "Gire, H."}
@string{MGiuntini = "Giuntini, M."}
+@string{FGittes = "Gittes, Frederick"}
@string{SGlanowski = "Glanowski, S."}
@string{JGlaser = "Glaser, Jens"}
@string{KGlasser = "Glasser, K."}
@string{HJGuntherodt = "Guntherodt, Hans-Joachim"}
@string{NGuo = "Guo, N."}
@string{YGuo = "Guo, Yi"}
+@string{MGutman = "Gutman, Menachem"}
@string{RTGuy = "Guy, Richard T."}
@string{PHanggi = {H\"anggi, Peter}}
@string{THa = "Ha, Taekjip"}
@string{SHladun = "Hladun, S."}
@string{WKHo = "Ho, W.~K."}
@string{RHochstrasser = "Hochstrasser, Robin M."}
+@string{CSHodges = "Hodges, C.~S."}
@string{CHoff = "Hoff, C."}
@string{WHoff = "Hoff, Wouter D."}
@string{JLHolden = "Holden, J. L."}
@string{RAHolt = "Holt, R. A."}
+@string{GHofmann = "Hofmann, Gerd"}
+@string{FHofmeister = "Hofmeister, Franz"}
@string{MHonda = "Honda, M."}
@string{NPCHong = "Hong, Neil P. Chue"}
@string{XHong = "Hong, Xia"}
@string{THowland = "Howland, T."}
@string{BHsiao = "Hsiao, Benjamin S."}
@string{CKHu = "Hu, Chin-Kun"}
+@string{DLHu = "Hu, David L."}
@string{BHuang = "Huang, Baiqu"}
@string{HHuang = "Huang, Hector Han-Li"}
-@string{HJHudspeth = "Hudspeth, H.~J."}
+@string{MHubain = "Hubain, Maurice"}
+@string{AJHudspeth = "Hudspeth, A.~J."}
@string{KHuff = "Huff, Katy"}
@string{JHughes = "Hughes, John"}
@string{GHummer = "Hummer, Gerhard"}
@string{TInoue = "Inoue, Tadashi"}
@string{IJBMM = "International Journal of Biological Macromolecules"}
@string{IJCIS = "International Journal of Computer \& Information Sciences"}
+@string{AItkin = "Itkin, Anna"}
@string{HItoh = "Itoh, Hiroyasu"}
@string{AIrback = "Irback, Anders"}
+@string{AMIsaacs = "Isaacs, Adrian M."}
@string{BIsralewitz = "Isralewitz, B."}
@string{SIstrail = "Istrail, S."}
@string{MIvemeyer = "Ivemeyer, M."}
@string{DIzhaky = "Izhaky, David"}
@string{SIzrailev = "Izrailev, S."}
-%string{JACS = "J Am Chem Soc"}
-@string{JACS = "Journal of the American Chemical Society"}
-@string{JAP = "Journal of Applied Physics"}
-@string{JBM = "J Biomech"}
-@string{JBT = "J Biotechnol"}
-@string{JEChem = "Journal of Electroanalytical Chemistry"}
-@string{JMathBiol = "J Math Biol"}
-@string{JPhysio = "Journal of physiology"}
-@string{JStructBiol = "Journal of structural biology"}
-@string{JTB = "J Theor Biol"}
+@string{TJahnke = "J{\"a}hnke, Torsten"}
@string{WJang = "Jang, W."}
+@string{HJanovjak = "Janovjak, Harald"}
@string{LJanosi = "Janosi, Lorant"}
@string{AJanshoff = "Janshoff, Andreas"}
@string{JJAP = "Japanese Journal of Applied Physics"}
@string{SJones = "Jones, S."}
@string{CJordan = "Jordan, C."}
@string{JJordan = "Jordan, J."}
+%string{JACS = "J Am Chem Soc"}
+@string{JACS = "Journal of the American Chemical Society"}
+@string{JASA = "Journal of the American Statistical Association"}
+@string{JAP = "Journal of Applied Physics"}
+@string{JBM = "J Biomech"}
+@string{JBT = "J Biotechnol"}
@string{JCPPCB = "Journal de Chimie Physique et de Physico-Chimie Biologique"}
@string{JCS = "Journal of Cell Science"}
@string{JCompP = "Journal of Computational Physics"}
+@string{JEChem = "Journal of Electroanalytical Chemistry"}
+@string{JMathBiol = "J Math Biol"}
+@string{JMicro = "Journal of Microscopy"}
+@string{JPhysio = "Journal of Physiology"}
+@string{JStructBiol = "Journal of Structural Biology"}
+@string{JTB = "J Theor Biol"}
@string{JMB = "Journal of Molecular Biology"}
@string{JP:CM = "Journal of Physics: Condensed Matter"}
@string{JP:CON = "Journal of Physics: Conference Series"}
@string{JRNBS:C = "Journal of Research of the National Bureau of Standards. Section C: Engineering and Instrumentation"}
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@string{WSJuang = "Juang, F.~S."}
@string{DAJuckett = "Juckett, D. A."}
@string{SRJun = "Jun, Se-Ran"}
@string{KAPPP = "Kluwer Academic Publishers--Plenum Publishers"}
@string{CDKodira = "Kodira, C. D."}
@string{SKoduru = "Koduru, S."}
+@string{PKoehl = "Koehl, Patrice"}
@string{BKolmerer = "Kolmerer, B."}
@string{JKorenberg = "Korenberg, J."}
@string{IKosztin = "Kosztin, Ioan"}
@string{TAKucaba = "Kucaba, T. A."}
@string{Kucherlapati = "Kucherlapati"}
@string{JKudoh = "Kudoh, J."}
+@string{MKuhn = "Kuhn, Michael"}
@string{MKulke = "Kulke, Michael"}
@string{CKwok = "Kwok, Carol H."}
@string{RLevy = "L\'evy, R"}
@string{DLabeit = "Labeit, Dietmar"}
@string{SLabeit = "Labeit, Siegfried"}
+@string{DLabudde = "Labudde, Dirk"}
@string{SLahmers = "Lahmers, Sunshine"}
@string{ZLai = "Lai, Z."}
@string{CLam = "Lam, Canaan"}
@string{CLethias = "Lethias, Claire"}
@string{SLeuba = "Leuba, Sanford H."}
@string{ALeung = "Leung, A."}
+@string{MLeuschner = "Leuschner, Mirko"}
@string{AJLevine = "Levine, A. J."}
@string{CLevinthal = "Levinthal, Cyrus"}
@string{ALevitsky = "Levitsky, A."}
@string{WLiu = "Liu, W."}
@string{XLiu = "Liu, X."}
@string{YLiu = "Liu, Yichun"}
+@string{LLivadaru = "Livadaru, L."}
@string{YSLo = "Lo, Yu-Shiu"}
@string{GLois = "Lois, Gregg"}
@string{JLopez = "Lopez, J."}
@string{WMajoros = "Majoros, W."}
@string{DEMakarov = "Makarov, Dmitrii E."}
@string{RMamdani = "Mamdani, Reneeta"}
+@string{SMammi = "Mammi, Stefano"}
@string{EMandello = "Mandello, Enrico"}
@string{GManderson = "Manderson, Gavin"}
@string{FMann = "Mann, F."}
@string{MMarra = "Marra, M."}
@string{PMarszalek = "Marszalek, Piotr E."}
@string{MMartin = "Martin, M. J."}
+@string{YMartin = "Martin, Y."}
@string{HMassa = "Massa, H."}
+@string{MIT = "Massachusetts Institute of Technology"}
+@string{GAMatei = "Matei, G.~A."}
+@string{DMaterassi = "Materassi, Donatello"}
@string{JMathe = "Math\'e, J\'er\^ome"}
@string{AMatouschek = "Matouschek, Andreas"}
@string{BMatthews = "Matthews, Brian W."}
@string{CCMello = "Mello, Cecilia C."}
@string{RMerkel = "Merkel, R."}
@string{GVMerkulov = "Merkulov, G. V."}
+@string{FMerzel = "Merzel, Franci"}
@string{HMetiu = "Metiu, Horia"}
@string{NMetropolis = "Metropolis, Nicholas"}
@string{GMeyer = "Meyer, Gerhard"}
@string{HMi = "Mi, H."}
+@string{LMiao = "Miao, Linlin"}
+@string{CMicheletti = "Micheletti, Cristian"}
@string{MMickler = "Mickler, Moritz"}
@string{AMiller = "Miller, A."}
@string{NMilshina = "Milshina, N."}
@string{SMinoshima = "Minoshima, S."}
@string{IMitchell = "Mitchell, Ian"}
@string{SMitternacht = "Mitternacht, Simon"}
+@string{NJMlot = "Mlot, Nathan J."}
@string{CMobarry = "Mobarry, C."}
@string{NMohandas = "Mohandas, N."}
@string{SMohanty = "Mohanty, Sandipan"}
@string{MMoy = "Moy, M."}
@string{VMoy = "Moy, Vincent T."}
@string{SMukamel = "Mukamel, Shaul"}
-@string{PMundel = "Mundel, P."}
+@string{DJMuller = "M{\"u}ller, Daniel J."}
+@string{PMundel = "Mundeol, P."}
@string{EMuneyuki = "Muneyuki, Eiro"}
@string{RJMural = "Mural, R. J."}
@string{BMurphy = "Murphy, B."}
@string{SMurphy = "Murphy, S."}
@string{AMuruganujan = "Muruganujan, A."}
+@string{FMusiani = "Musiani, Francesco"}
@string{EWMyers = "Myers, E. W."}
@string{RMMyers = "Myers, R. M."}
@string{AMylonakis = "Mylonakis, Andreas"}
+@string{ENachliel = "Nachliel, Esther"}
@string{JNadeau = "Nadeau, J."}
@string{AKNaik = "Naik, A. K."}
@string{NANO = "Nano letters"}
@string{NAT = "Nature"}
@string{NSB = "Nature Structural Biology"}
@string{NSMB = "Nature Structural Molecular Biology"}
+@string{NRMCB = "Nature Reviews Molecular Cell Biology"}
@string{SNaylor = "Naylor, S."}
@string{CNeagoe = "Neagoe, Ciprian"}
@string{BNeelam = "Neelam, B."}
@string{MNeitzert = "Neitzert, Marcus"}
@string{CNelson = "Nelson, C."}
@string{KNelson = "Nelson, K."}
+@string{RRNetz = "Netz, R.~R."}
+@string{NR = "Neurochemical research"}
@string{NEURON = "Neuron"}
@string{RNevo = "Nevo, Reinat"}
@string{NJP = "New Journal of Physics"}
@string{DBNewell = "Newell, David B."}
@string{MNewman = "Newman, M."}
+@string{INewton = "Newton, Isaac"}
@string{SNg = "Ng, Sean P."}
@string{NNguyen = "Nguyen, N."}
@string{TNguyen = "Nguyen, T."}
@string{ANoy = "Noy, Aleksandr"}
@string{NAR = "Nucleic Acids Research"}
@string{JNummela = "Nummela, Jeremiah"}
+@string{JNunes = "Nunes, Joao"}
@string{DNusskern = "Nusskern, D."}
@string{GNyakatura = "Nyakatura, G."}
@string{CSOHern = "O'Hern, Corey S."}
@string{MPeterson = "Peterson, M."}
@string{SMPeterson = "Peterson, Susan M."}
@string{CPfannkoch = "Pfannkoch, C."}
-@string{PA = "Pflugers Arch"}
+@string{PA = "Pfl{\"u}gers Archiv: European journal of physiology"}
@string{PTRSL = "Philosophical Transactions of the Royal Society of London"}
@string{PR:E = "Phys Rev E Stat Nonlin Soft Matter Phys"}
-@string{PRL = "Physical review letters"}
+@string{PRL = "Physical Review Letters"}
%string{PRL = "Phys Rev Lett"}
@string{Physica = "Physica"}
@string{GPing = "Ping, Guanghui"}
@string{NPinotsis = "Pinotsis, Nikos"}
@string{MPlumbley = "Plumbley, Mark"}
+@string{PLOS:ONE = "PLOS ONE"}
+%string{PLOS:ONE = "Public Library of Science ONE"}
+@string{PLOS:BIO = "PLOS Biology"}
@string{DPlunkett = "Plunkett, David"}
@string{PPodsiadlo = "Podsiadlo, Paul"}
@string{ASPolitou = "Politou, A. S."}
@string{PBPMB = "Progress in Biophysics and Molecular Biology"}
@string{PS = "Protein Science"}
@string{PROT = "Proteins"}
+@string{RSUP = "Published for the Royal Society at the University Press"}
@string{EPuchner = "Puchner, Elias M."}
@string{VPuri = "Puri, V."}
@string{WPyckhout-Hintzen = "Pyckhout-Hintzen, Wim"}
+@string{HQin = "Qin, Haina"}
@string{SQin = "Qin, S."}
@string{SRQuake = "Quake, Stephen R."}
@string{CQuate = "Quate, Calvin F."}
@string{LRamirez = "Ramirez, L."}
@string{JRamser = "Ramser, J."}
@string{LRandles = "Randles, Lucy G."}
+@string{VRaussens = "Raussens, Vincent"}
+@string{IRay = "Ray, I."}
@string{MReardon = "Reardon, M."}
@string{ALCReddin = "Reddin, Andrew L. C."}
@string{SRedick = "Redick, Sambra D."}
@string{MRief = "Rief, Matthias"}
@string{KRitchie = "Ritchie, K."}
@string{MRobbins = "Robbins, Mark O."}
+@string{CJRoberts = "Roberts, C.~J."}
@string{RJRoberts = "Roberts, R. J."}
@string{RRobertson = "Robertson, Ragan B."}
@string{HRoder = "Roder, Heinrich"}
@string{LRowen = "Rowen, L."}
@string{BRuhfel = "Ruhfel, B."}
@string{DBRusch = "Rusch, D. B."}
+@string{JMRuysschaert = "Ruysschaert, Jean-Marie"}
@string{JPRyckaert = "Ryckaert, Jean-Paul"}
@string{NSakaki = "Sakaki, Naoyoshi"}
@string{YSakaki = "Sakaki, Y."}
@string{NScherer = "Scherer, Norbert F."}
@string{SScherer = "Scherer, S."}
@string{MSchilhabel = "Schilhabel, M."}
+@string{HSchillers = "Schillers, Hermann"}
@string{BSchlegelberger = "Schlegelberger, B."}
@string{MSchleicher = "Schleicher, Michael"}
@string{MSchlierf = "Schlierf, Michael"}
+@string{CFSchmidt = "Schmidt, Christoph F."}
@string{JSchmidt = "Schmidt, Jacob J."}
@string{LSchmitt = "Schmitt, Lutz"}
@string{JSchmutz = "Schmutz, J."}
@string{JScott = "Scott, J."}
@string{RScott = "Scott, R."}
@string{USeifert = "Seifert, Udo"}
+@string{SKSekatskii = "Sekatskii, Sergey K."}
@string{MSekhon = "Sekhon, M."}
@string{TSekiguchi = "Sekiguchi, T."}
@string{BSenger = "Senger, B."}
+@string{DBSenn = "Senn, David B."}
@string{PSeranski = "Seranski, P."}
@string{RSesboue = {Sesbo\"u\'e, R.}}
@string{EShakhnovich = "Shakhnovich, Eugene"}
@string{AShimizu = "Shimizu, A."}
@string{NShimizu = "Shimizu, N."}
@string{RShimoKon = "Shimo-Kon, Rieko"}
+@string{JPShine = "Shine, James P."}
@string{AShintani = "Shintani, A."}
@string{BShneiderman = "Shneiderman, Ben"}
@string{BShue = "Shue, B."}
@string{DASmith = "Smith, D. Alastair"}
@string{HOSmith = "Smith, H. O."}
@string{KBSmith = "Smith, Kathryn B."}
+@string{MDSmith = "Smith, Micholas Dean"}
@string{SSmith = "Smith, S."}
@string{SBSmith = "Smith, S. B."}
@string{TSmith = "Smith, T."}
@string{SEG = "Society of Exploration Geophysicists"}
@string{ESodergren = "Sodergren, E."}
@string{CSoderlund = "Soderlund, C."}
+@string{JSong = "Song, Jianxing"}
@string{JSpanier = "Spanier, Jonathan E."}
@string{DSpeicher = "Speicher, David W."}
@string{GSpier = "Spier, G."}
@string{ASprague = "Sprague, A."}
@string{SPRINGER = "Springer Science + Business Media, LLC"}
+@string{SPRINGER:V = "Springer-Verlag"}
@string{DBStaple = "Staple, Douglas B."}
@string{RStark = "Stark, R. W."}
@string{PSStayton = "Stayton, P. S."}
@string{TRStrick = "Strick, T. R."}
@string{CStroh = "Stroh, Cordula"}
@string{RStrong = "Strong, R."}
+@string{JStruckmeier = "Struckmeier, Jens"}
@string{STR = "Structure"}
@string{TStrunz = "Strunz, Torsten"}
@string{MSu = "Su, Meihong"}
@string{PTalkner = "Talkner, Peter"}
@string{RTampe = "Tamp{\'e}, Robert"}
@string{JTang = "Tang, Jianyong"}
+@string{PTavan = "Tavan, P."}
@string{BNTaylor = "Taylor, Barry N."}
@string{THEMath = "Technische Hogeschool Eindhoven, Nederland,
Onderafdeling der Wiskunde"}
+@string{SJBTendler = "Tendler, S.~J.~B."}
+@string{ITessari = "Tessari, Isabella"}
@string{STeukolsky = "Teukolsky, S."}
@string{CJ = "The Computer Journal"}
+@string{JBC = "The Journal of Biological Chemistry"}
@string{JCP = "The Journal of Chemical Physics"}
@string{JPC:B = "The Journal of Physical Chemistry B"}
@string{JPC:C = "The Journal of Physical Chemistry C"}
@string{PDThomas = "Thomas, P. D."}
@string{RThomas = "Thomas, R."}
@string{JThompson = "Thompson, J. B."}
+@string{EJThoreson = "Thoreson, E.~J."}
@string{SThornton = "Thornton, S."}
@string{RWTillmann = "Tillmann, R.~W."}
@string{NNTint = "Tint, N. N."}
+@string{BTiribilli = "Tiribilli, Bruno"}
@string{TTlusty = "Tlusty, Tsvi"}
+@string{PTobias = "Tobias, Paul"}
@string{JTocaHerrera = "Toca-Herrera, Jose L."}
+@string{CATovey = "Tovey, Craig A."}
@string{AToyoda = "Toyoda, A."}
@string{TASME = "Transactions of the American Society of Mechanical Engineers"}
@string{BTrask = "Trask, B."}
@string{ZTshiprut = "Tshiprut, Z."}
@string{JCMTsibris = "Tsibris, J.C.M."}
@string{LTskhovrebova = "Tskhovrebova, Larissa"}
+@string{HWTurnbull = "Turnbull, Herbert Westren"}
@string{RTurner = "Turner, R."}
@string{AUlman = "Ulman, Abraham"}
@string{UltraMic = "Ultramicroscopy"}
@string{UIP:Urbana = "University of Illinois Press, Urbana"}
@string{UTMB = "University of Texas Medical Branch"}
@string{MUrbakh = "Urbakh, M."}
+@string{FValle = "Valle, Francesco"}
@string{KJVanVliet = "Van Vliet, Krystyn J."}
@string{PVandewalle = "Vandewalle, Patrick"}
@string{CVech = "Vech, C."}
@string{JCVoegel = "Voegel, J.-C."}
@string{VVogel = "Vogel, Viola"}
@string{CWagner-McPherson = "Wagner-McPherson, C."}
+@string{RWahl = "Wahl, Reiner"}
@string{TAWaigh = "Waigh, Thomas A."}
@string{BWalenz = "Walenz, B."}
@string{JWallis = "Wallis, J."}
@string{KWatanabe = "Watanabe, Kaori"}
@string{RHWaterston = "Waterston, R. H."}
@string{BWaugh = "Waugh, Ben"}
+@string{JWegiel = "Wegiel, J."}
@string{MWei = "Wei, M."}
@string{YWei = "Wei, Yen"}
@string{ALWeisenhorn = "Weisenhorn, A.~L."}
@string{JWeissenbach = "Weissenbach, J."}
+@string{BLWelch = "Welch, Bernard Lewis"}
@string{GWen = "Wen, G."}
@string{MWen = "Wen, M."}
@string{JWetter = "Wetter, J."}
@string{EPWhite = "White, Ethan P."}
+@string{ANWhitehead = "Whitehead, Alfred North"}
@string{AWhittaker = "Whittaker, A."}
-@string{YWickramasinghe = "Wickramasinghe, H. K."}
+@string{HKWickramasinghe = "Wickramasinghe, H. K."}
@string{RWides = "Wides, R."}
@string{AWiita = "Wiita, Arun P."}
@string{MWilchek = "Wilchek, Meir"}
@string{CCWilliams = "Williams, C. C."}
@string{MWilliams = "Williams, M."}
@string{SWilliams = "Williams, S."}
+@string{WN = "Williams \& Norgate"}
@string{MWilmanns = "Wilmanns, Matthias"}
@string{GWilson = "Wilson, Greg"}
@string{PWilson = "Wilson, Paul"}
@string{SWindsor = "Windsor, S."}
@string{EWinn-Deen = "Winn-Deen, E."}
@string{NWirth = "Wirth, Niklaus"}
+@string{HMWisniewski = "Wisniewski, H.~M."}
@string{CWitt = "Witt, Christian"}
@string{KWolfe = "Wolfe, K."}
@string{TGWolfsberg = "Wolfsberg, T. G."}
@string{TWoodage = "Woodage, T."}
@string{GRWoodcock = "Woodcock, Glenna R."}
@string{JRWortman = "Wortman, J. R."}
+@string{PEWright = "Wright, Peter E."}
@string{DWu = "Wu, D."}
@string{GAWu = "Wu, Guohong A."}
@string{JWWu = "Wu, Jong-Wuu"}
@string{MYandell = "Yandell, M."}
@string{GYang = "Yang, Guoliang"}
@string{YYang = "Yang, Yao"}
+@string{BAYankner = "Yankner, Bruce A."}
@string{AYao = "Yao, A."}
@string{RYasuda = "Yaduso, Ryohei"}
@string{JYe = "Ye, J."}
@string{MYoshida = "Yoshida, Masasuke"}
@string{WYu = "Yu, Weichang"}
@string{JMYuan = "Yuan, Jian-Min"}
+@string{MYuan = "Yuan, Menglan"}
@string{AZandieh = "Zandieh, A."}
@string{JZaveri = "Zaveri, J."}
@string{KZaveri = "Zaveri, K."}
@string{JZhang = "Zhang, J."}
@string{QZhang = "Zhang, Q."}
@string{WZhang = "Zhang, W."}
+@string{YZhang = "Zhang, Yanjie"}
@string{ZZhang = "Zhang, Zongtao"}
@string{JZhao = "Zhao, Jason Ming"}
@string{LZhao = "Zhao, Liming"}
@string{XZhu = "Zhu, X."}
@string{YJZhu = "Zhu, Ying-Jie"}
@string{WZhuang = "Zhuang, Wei"}
+@string{JZidar = "Zidar, Jernej"}
@string{JZiegler = "Ziegler, J.G."}
@string{NZinder = "Zinder, N."}
@string{RCZinober = "Zinober, Rebecca C."}
@string{JZlatanova = "Zlatanova, Jordanka"}
@string{PZou = "Zou, Peng"}
+@string{GZuccheri = "Zuccheri, Giampaolo"}
@string{RZwanzig = "Zwanzig, R."}
@string{arXiv = "arXiv"}
@string{PGdeGennes = "de Gennes, P. G."}
@string{PJdeJong = "de Jong, P. J."}
@string{NGvanKampen = "van Kampen, N.G."}
-@string{NISTSEMATECH = "{NIST/SEMATECH}"}
+@string{NIST:SEMATECH = "{NIST/SEMATECH}"}
@string{EDCola = "{\uppercase{d}}i Cola, Emanuela"}
-@misc { NIST:gumbel,
- author = NISTSEMATECH,
- key = "NIST:gumbel",
- title = "e-Handbook of Statistical Methods: Extreme Value Type {I}
- Distribution",
- year = 2009,
- month = oct,
- day = 9,
- url = "http://www.itl.nist.gov/div898/handbook/eda/section3/eda366g.htm"
+@inbook{ NIST:chi-square,
+ crossref = {NIST:ESH},
+ chapter = {1.3.5.15: Chi-Square Goodness-of-Fit Test},
+ year = 2013,
+ month = may,
+ day = 15,
+ url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda35f.htm},
+}
+
+@inbook{ NIST:gumbel,
+ crossref = {NIST:ESH},
+ chapter = {1.3.6.6.16: Extreme Value Type {I} Distribution},
+ year = 2009,
+ month = oct,
+ day = 9,
+ url = {http://www.itl.nist.gov/div898/handbook/eda/section3/eda366g.htm},
+}
+
+@book{ NIST:ESH,
+ editor = CCroarkin #" and "# PTobias,
+ author = NIST:SEMATECH,
+ title = {e-{H}andbook of Statistical Methods},
+ year = 2013,
+ month = may,
+ publisher = NIST:SEMATECH,
+ address = {Boulder, Colorado},
+ url = {http://www.itl.nist.gov/div898/handbook/},
+ note = {This manual was developed from seed material produced by
+ Mary Natrella.},
}
@misc{ wikipedia:gumbel,
year = 1958,
publisher = CUP,
address = "New York",
- note = "TODO: read",
+ wtk_note = "Find and read",
}
@misc{ wikipedia:GEV,
number = 3,
pages = "1236--1241",
issn = "0006-291X",
- doi = "DOI: 10.1016/0006-291X(90)90526-S",
- url = "http://www.sciencedirect.com/science/article/B6WBK-
- 4F5M7K3-3C/2/c94b612e06efc8534ee24bb1da889811",
+ doi = "10.1016/0006-291X(90)90526-S",
+ url = "http://dx.doi.org/10.1016/0006-291X(90)90526-S",
keywords = "Amino Acid Sequence;Animals;Bacterial Proteins;Binding
Sites;Cell Line;Cell Membrane;Cricetinae;Fibronectins;Molecular
Sequence Data;Streptavidin",
url = "http://link.aip.org/link/?AJP/70/393/1",
keywords = "student experiments; safety; radiation pressure; laser beam
applications",
- note = "Good discussion of the effect of correlation time on calibration.
- Excellent detail on power spectrum derivation and thermal noise for
- extremely overdamped oscillators in Appendix A (references
- \citet{rief65}). References work on deconvolving thermal noise from
- other noise\citep{cowan98}",
+ note = {Good discussion of the effect of correlation time on
+ calibration. References work on deconvolving thermal noise from
+ other noise\citep{cowan98}. Excellent detail on power spectrum
+ derivation and thermal noise for extremely overdamped
+ oscillators in Appendix A (references \citet{rief65}), except
+ that their equation A12 is missing a factor of $1/\pi$. I
+ pointed this out to John Bechhoefer and he confirmed the
+ error.},
project = "Cantilever Calibration"
}
+@article{ berg-sorensen04,
+ author = KBergSorensen #" and "# HFlyvbjerg,
+ title = {Power spectrum analysis for optical tweezers},
+ journal = RSI,
+ year = 2004,
+ volume = 75,
+ number = 3,
+ pages = {594--612},
+ publisher = AIP,
+ url = {http://rsi.aip.org/resource/1/rsinak/v75/i3/p594_s1},
+ doi = {10.1063/1.1645654},
+ issn = {0034-6748},
+ keywords = {radiation pressure, Brownian motion, spectral analysis,
+ dielectric bodies, measurement by laser beam, flow measurement},
+ abstract = {The force exerted by an optical trap on a dielectric
+ bead in a fluid is often found by fitting a Lorentzian to the
+ power spectrum of Brownian motion of the bead in the trap. We
+ present explicit functions of the experimental power spectrum that
+ give the values of the parameters fitted, including error bars and
+ correlations, for the best such $\chi^2$ fit in a given frequency
+ range. We use these functions to determine the information
+ content of various parts of the power spectrum, and find, at odds
+ with lore, much information at relatively high frequencies.
+ Applying the method to real data, we obtain perfect fits and
+ calibrate tweezers with less than 1\% error when the trapping
+ force is not too strong. Relatively strong traps have power
+ spectra that cannot be fitted properly with any Lorentzian, we
+ find. This underscores the need for better understanding of the
+ power spectrum than the Lorentzian provides. This is achieved
+ using old and new theory for Brownian motion in an incompressible
+ fluid, and new results for a popular photodetection system. The
+ trap and photodetection system are then calibrated simultaneously
+ in a manner that makes optical tweezers a tool of precision for
+ force spectroscopy, local viscometry, and probably other
+ applications.},
+}
+
@article{ berg-sorensen05,
author = KBergSorensen #" and "# HFlyvbjerg,
title = {The colour of thermal noise in classical Brownian motion: a
@article { bedard08,
author = SBedard #" and "# MMGKrishna #" and "# LMayne #" and "#
SWEnglander,
- title = "Protein folding: independent unrelated pathways or predetermined
+ title = "Protein folding: Independent unrelated pathways or predetermined
pathway with optional errors.",
year = 2008,
month = may,
mechanical resistance of a protein is not dictated solely by amino acid
sequence, topology or unfolding rate constant, but depends critically
on the direction of the applied extension.",
- note = "Another scaffold effect paper. TODO: details"
+ note = "Another scaffold effect paper.",
}
@article { brower-toland02,
rationalized at the molecular level."
}
-@article{ martin87
- author = YMartin #" and "# CCWilliams #" and "# HKWickamasinghe,
+@article{ martin87,
+ author = YMartin #" and "# CCWilliams #" and "# HKWickramasinghe,
title = {Atomic force microscope---force mapping and profiling on a
sub 100-\AA scale},
year = 1987,
volume = 61,
number = 10,
pages = {4723--4729},
+ issn = "0021-8979",
+ issn_online = "1089-7550",
doi = {10.1063/1.338807},
- url = {http://jap.aip.org/resource/1/japiau/v61/i10/p4723_s1}
+ url = {http://jap.aip.org/resource/1/japiau/v61/i10/p4723_s1},
+ language = "eng",
abstract = {A modified version of the atomic force microscope is
introduced that enables a precise measurement of the force between
a tip and a sample over a tip-sample distance range of 30--150
project = "Cantilever Calibration"
}
+@article{ jaschke95,
+ author = MJaschke #" and "# HJButt,
+ title = {Height calibration of optical lever atomic force
+ microscopes by simple laser interferometry},
+ journal = RSI,
+ year = 1995,
+ volume = 66,
+ number = 2,
+ pages = {1258--1259},
+ publisher = AIP,
+ url = {http://rsi.aip.org/resource/1/rsinak/v66/i2/p1258_s1},
+ doi = {10.1063/1.1146018},
+ issn = {0034-6748},
+ keywords = {atomic force microscopy;calibration;interferometry;laser
+ beam applications;mirrors;spatial resolution},
+ abstract = {A new and simple interferometric method for height
+ calibration of AFM piezo scanners is presented. Except for a small
+ mirror no additional equipment is required since the fixed
+ wavelength of the laser diode is used as a calibration
+ standard. The calibration is appliable in the range between
+ several ten nm and several $\mu$m. Besides vertical calibration
+ many problems of piezo elements like hysteresis, nonlinearity,
+ creep, derating, etc. and their dependence on scan parameters or
+ temperature can be investigated.},
+}
+
@article { cao07,
author = YCao #" and "# MBalamurali #" and "# DSharma #" and "# HLi,
title = "A functional single-molecule binding assay via force spectroscopy",
volume = 74,
number = "1-2",
pages = "63--91",
+ doi = "10.1016/S0079-6107(00)00017-1",
issn = "0079-6107",
eprint = "http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1302160&blo
btype=pdf",
elucidate the dynamic mechanical properties of a wide variety of
proteins at the single molecule level and provide an important
complement to other structural and dynamic techniques (e.g., X-ray
- crystallography, NMR spectroscopy, patch-clamp)."
+ crystallography, NMR spectroscopy, patch-clamp).",
+ note = {Surface contact \fref{figure}{2} is a modified version of
+ \xref{baljon96}{figure}{1}. They are both good pictures for
+ explaining that the tip's radius of curvature ($\sim 20\U{nm}$) is
+ larger than the I27 domains\citet{improta96} ($\sim 2\U{nm}$).},
}
@article { carrion-vazquez03,
@article { collins03,
author = FSCollins #" and "# MMorgan #" and "# APatrinos,
- title = "The Human Genome Project: lessons from large-scale biology.",
+ title = "The Human Genome Project: Lessons from large-scale biology.",
year = 2003,
month = apr,
day = 11,
doi = "10.1073/pnas.0404549101",
eprint = "http://www.pnas.org/cgi/reprint/101/46/16192.pdf",
url = "http://www.pnas.org/cgi/content/abstract/101/46/16192",
- abstract = "We use single-molecule force spectroscopy to drive single GFP
- molecules from the native state through their complex energy landscape
- into the completely unfolded state. Unlike many smaller proteins,
- mechanical GFP unfolding proceeds by means of two subsequent
- intermediate states. The transition from the native state to the first
- intermediate state occurs near thermal equilibrium at {approx}35 pN and
+ abstract = "We use single-molecule force spectroscopy to drive
+ single GFP molecules from the native state through their
+ complex energy landscape into the completely unfolded
+ state. Unlike many smaller proteins, mechanical GFP unfolding
+ proceeds by means of two subsequent intermediate states. The
+ transition from the native state to the first intermediate
+ state occurs near thermal equilibrium at $\approx35\U{pN}$ and
is characterized by detachment of a seven-residue N-terminal
- {alpha}-helix from the beta barrel. We measure the equilibrium free
- energy cost associated with this transition as 22 kBT. Detachment of
- this small {alpha}-helix completely destabilizes GFP thermodynamically
- even though the {beta}-barrel is still intact and can bear load.
- Mechanical stability of the protein on the millisecond timescale,
- however, is determined by the activation barrier of unfolding the
- {beta}-barrel out of this thermodynamically unstable intermediate
- state. High bandwidth, time-resolved measurements of the cantilever
- relaxation phase upon unfolding of the {beta}-barrel revealed a second
- metastable mechanical intermediate with one complete {beta}-strand
- detached from the barrel. Quantitative analysis of force distributions
- and lifetimes lead to a detailed picture of the complex mechanical
+ $\alpha$-helix from the beta barrel. We measure the
+ equilibrium free energy cost associated with this transition
+ as 22 kBT. Detachment of this small $\alpha$-helix completely
+ destabilizes GFP thermodynamically even though the
+ $\beta$-barrel is still intact and can bear load. Mechanical
+ stability of the protein on the millisecond timescale,
+ however, is determined by the activation barrier of unfolding
+ the $\beta$-barrel out of this thermodynamically unstable
+ intermediate state. High bandwidth, time-resolved measurements
+ of the cantilever relaxation phase upon unfolding of the
+ $\beta$-barrel revealed a second metastable mechanical
+ intermediate with one complete $\beta$-strand detached from
+ the barrel. Quantitative analysis of force distributions and
+ lifetimes lead to a detailed picture of the complex mechanical
unfolding pathway through a rough energy landscape.",
- note = "Nice energy-landscape-to-one-dimension compression graphic.
- Unfolding Green Flourescent Protein (GFP) towards using it as an
- embedded force probe.",
+ note = "Towards use of Green Flourescent Protein (GFP) as an
+ embedded force probe. Nice energy-landscape-to-one-dimension
+ compression graphic.",
project = "Energy landscape roughness"
}
author = OKDudko #" and "# JMathe #" and "# ASzabo #" and "# AMeller #" and
"# GHummer,
title = "Extracting kinetics from single-molecule force spectroscopy:
- nanopore unzipping of {DNA} hairpins",
+ Nanopore unzipping of {DNA} hairpins",
year = 2007,
month = jun,
day = 15,
pages = "105--128",
issn = "1056-8700",
doi = "10.1146/annurev.biophys.30.1.105",
- url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophy
- s.30.1.105",
+ url = "http://arjournals.annualreviews.org/doi/abs/10.1146%2Fannurev.biophys.30.1.105",
keywords = "Biophysics;Kinetics;Microscopy, Atomic Force;Models,
Chemical;Protein Binding;Spectrum Analysis;Time Factors",
abstract = "On laboratory time scales, the energy landscape of a weak bond
force techniques.",
note = "Develops Kramers improvement on Bell model for domain unfolding.
Presents unfolding under variable loading rates. Often cited as the
- ``Bell-Evans'' model? They derive a unitless treatment, scaling force
- by $f_\beta$, TODO; time by $\tau_f$, TODO; elasiticity by compliance
+ ``Bell--Evans'' model. They derive a unitless treatment, scaling force
+ by $f_\beta$, time by $\tau_f$, and elasiticity by compliance
$c(f)$. The appendix has relaxation time formulas for WLC and FJC
polymer models.",
project = "sawtooth simulation"
pages = "895--901",
issn = "0956-5663",
doi = "10.1016/0956-5663(95)99227-C",
- url = "http://www.sciencedirect.com/science/article/B6TFC-
- 3XY2HK9-G/2/6f4e9f67e9a1e14c8bbcc478e5360682",
+ url = "http://dx.doi.org/10.1016/0956-5663(95)99227-C",
abstract = "One of the unique features of the atomic force microscope (AFM)
is its capacity to measure interactions between tip and sample with
high sensitivity and unparal leled spatial resolution. Since the
project = "Cantilever Calibration"
}
+@article{ burnham03,
+ author = NABurnham #" and "# XiChen #" and "# CSHodges #" and "#
+ GAMatei #" and "# EJThoreson #" and "# CJRoberts #" and "#
+ MCDavies #" and "# SJBTendler,
+ title = {Comparison of calibration methods for atomic-force
+ microscopy cantilevers},
+ year = 2003,
+ month = jan,
+ journal = NT,
+ volume= 14,
+ number = 1,
+ pages = {1--6},
+ url = {http://stacks.iop.org/0957-4484/14/i=1/a=301},
+ abstract = {The scientific community needs a rapid and reliable way
+ of accurately determining the stiffness of atomic-force microscopy
+ cantilevers. We have compared the experimentally determined values
+ of stiffness for ten cantilever probes using four different
+ methods. For rectangular silicon cantilever beams of well defined
+ geometry, the approaches all yield values within 17\% of the
+ manufacturer's nominal stiffness. One of the methods is new, based
+ on the acquisition and analysis of thermal distribution functions
+ of the oscillator's amplitude fluctuations. We evaluate this
+ method in comparison to the three others and recommend it for its
+ ease of use and broad applicability.},
+ note = {Contains both the overdamped (\fref{equation}{6}) and
+ general (\fref{equation}{8}) power spectral densities used in
+ thermal cantilever calibration, but punts to textbooks for the
+ derivation.},
+}
+
@article { forde02,
author = NRForde #" and "# DIzhaky #" and "# GRWoodcock #" and "# GJLWuite
#" and "# CBustamante,
jstor_issuetitle = ""
}
+@article{ welch38,
+ author = BLWelch,
+ title = {The significance of the difference between two means when
+ the population variances are unequal},
+ year = 1938,
+ month = feb,
+ journal = Biomet,
+ volume = 29,
+ number = "3-4",
+ pages = {350--362},
+ keywords = "Population",
+ issn = "0006-3444",
+ url = "http://www.jstor.org/stable/2332010",
+ language = "eng",
+}
+
+@article{ welch47,
+ author = BLWelch,
+ title = {The generalization of {Student's} problems when several
+ different population variances are involved},
+ year = 1947,
+ month = jan,
+ journal = Biomet,
+ volume = 34,
+ number = "1-2",
+ pages = {28--35},
+ keywords = "Population",
+ issn = "0006-3444",
+ url = "http://www.ncbi.nlm.nih.gov/pubmed/20287819",
+ jstor_url = "http://www.jstor.org/stable/2332510",
+ language = "eng",
+}
+
@article { granzier97,
author = HLGranzier #" and "# MSKellermayer #" and "# MHelmes #" and "#
KTrombitas,
season = "Fall",
numpages = 12,
eprint = "http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf",
- note = "Fairly complete overdamped PSD derivation in section 4.3., cites
- \citet{tlusty98} and \citet{bechhoefer02} for further details. However,
- Tlusty (listed as reference 8) doesn't contain the thermal response
- fn.\ derivation it was cited for. Also, the single sided PSD definition
- credited to reference 9 (listed as Bechhoefer) looks more like Press
- (listed as reference 10). I imagine Grossman and Stout mixed up their
- references, and meant to refer to \citet{bechhoefer02} and
- \citet{press92} respectively instead.",
+ note = {Fairly complete overdamped PSD derivation in
+ \fref{section}{4.3}. Cites \citet{tlusty98} and
+ \citet{bechhoefer02} for further details. However, Tlusty
+ (listed as reference 8) doesn't contain the thermal response
+ fn.\ derivation it was cited for. Also, the single sided PSD
+ definition credited to reference 9 (listed as Bechhoefer)
+ looks more like Press (listed as reference 10). I imagine
+ Grossman and Stout mixed up their references, and meant to
+ refer to \citet{bechhoefer02} and \citet{press92} respectively
+ instead.},
project = "Cantilever Calibration"
}
@article { hanggi90,
author = PHanggi #" and "# PTalkner #" and "# MBorkovec,
- title = "Reaction-rate theory: fifty years after {K}ramers",
+ title = "Reaction-rate theory: Fifty years after {K}ramers",
year = 1990,
month = "Apr",
journal = RMP,
@article { hutter05,
author = JHutter,
- title = "Comment on tilt of atomic force microscope cantilevers: effect on
+ title = "Comment on tilt of atomic force microscope cantilevers: Effect on
spring constant and adhesion measurements.",
year = 2005,
month = mar,
mechanical unfolding experiments of proteins and RNA, the ruggedness
energy scale epsilon, can be directly measured.",
note = "Derives the major theory behind my thesis. The Kramers rate
- equation is \citet{hanggi90} Eq.~4.56c (page 275).",
+ equation is \xref{hanggi90}{equation}{4.56c} (page 275).",
project = "Energy Landscape Roughness"
}
@article { improta96,
author = SImprota #" and "# ASPolitou #" and "# APastore,
- title = "Immunoglobulin-like modules from titin {I}-band: extensible
+ title = "Immunoglobulin-like modules from titin {I}-band: Extensible
components of muscle elasticity.",
year = 1996,
month = mar,
verified experimentally but appears physically reasonable."
}
+@article{ grubmuller96,
+ author = HGrubmuller #" and "# BHeymann #" and "# PTavan,
+ title = {Ligand binding: molecular mechanics calculation of the
+ streptavidin-biotin rupture force.},
+ year = 1996,
+ month = feb,
+ day = 16,
+ address = {Theoretische Biophysik, Institut f{\"u}r Medizinische
+ Optik, Ludwig- Maximilians-Universit{\"a}t M{\"u}nchen,
+ Germany. Helmut.Grubmueller@ Physik.uni-muenchen.de},
+ journal = SCI,
+ volume = 271,
+ number = 5251,
+ pages = {997--999},
+ issn = {0036-8075},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/8584939},
+ eprint = {http://pubman.mpdl.mpg.de/pubman/item/escidoc:1690312:2/component/escidoc:1690313/1690312.pdf},
+ language = {eng},
+ keywords = {Bacterial Proteins},
+ keywords = {Biotin},
+ keywords = {Chemistry, Physical},
+ keywords = {Computer Simulation},
+ keywords = {Hydrogen Bonding},
+ keywords = {Ligands},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Chemical},
+ keywords = {Molecular Conformation},
+ keywords = {Physicochemical Phenomena},
+ keywords = {Protein Conformation},
+ keywords = {Streptavidin},
+ keywords = {Thermodynamics},
+ abstract = {The force required to rupture the streptavidin-biotin
+ complex was calculated here by computer simulations.
+ The computed force agrees well with that obtained by
+ recent single molecule atomic force microscope
+ experiments. These simulations suggest a detailed
+ multiple-pathway rupture mechanism involving five major
+ unbinding steps. Binding forces and specificity are
+ attributed to a hydrogen bond network between the
+ biotin ligand and residues within the binding pocket of
+ streptavidin. During rupture, additional water bridges
+ substantially enhance the stability of the complex and
+ even dominate the binding interactions. In contrast,
+ steric restraints do not appear to contribute to the
+ binding forces, although conformational motions were
+ observed.},
+}
+
+
@article { izrailev97,
author = SIzrailev #" and "# SStepaniants #" and "# MBalsera #" and "#
YOono #" and "# KSchulten,
number = 3,
pages = "355--361",
issn = "0301-679X",
- doi = "DOI: 10.1016/j.triboint.2004.08.016",
- url = "http://www.sciencedirect.com/science/article/B6V57-4DN9K7J-1/2/fef91
- ac022594c2c6a701376d83ecd31",
+ doi = "10.1016/j.triboint.2004.08.016",
+ url = "http://dx.doi.org/10.1016/j.triboint.2004.08.016",
keywords = "AFM;Liquid;Hydrodynamic;Lubrication",
abstract = "With the availability of equipment used in Scanning Probe
Microscopy (SPM), researchers have been able to probe the local fluid-
issn = "0141-8130",
alternative_issn = "1879-0003",
doi = "10.1016/j.ijbiomac.2009.12.001",
- url = "http://www.sciencedirect.com/science/article/B6T7J-
- 4XWMND2-1/2/7ef768562b4157fc201d450553e5de5e",
+ url = "http://dx.doi.org/10.1016/j.ijbiomac.2009.12.001",
language = "eng",
keywords = "Atomic force microscopy;Mechanical unfolding;Monte Carlo
simulation;Worm-like chain;Single molecule methods",
results fit experimental data. These findings will be helpful in
experimental design, artifact identification, and data analysis for
single molecule studies of various proteins using the mechanical
- unfolding method."
+ unfolding method.",
+ note = "Sawsim is available at \url{http://blog.tremily.us/posts/sawsim/}.",
}
@article { kleiner07,
protein) for all 20 structures deposited in the Protein Data Bank. Our
approach suggests a natural way to measure the phase diagram in the
(f,C) plane, where C is the concentration of denaturants.",
- note = "Simulated unfolding timescales for Ig27-like S1 and S2 domains"
+ note = {Simulated unfolding time scales for Ig27-like S1 and S2 domains.},
}
@article { klimov99,
author = DKlimov #" and "# DThirumalai,
- title = "Stretching single-domain proteins: phase diagram and kinetics of
+ title = "Stretching single-domain proteins: Phase diagram and kinetics of
force-induced unfolding",
year = 1999,
month = may,
@article{ labeit95,
author = SLabeit #" and "# BKolmerer,
- title = "Titins: giant proteins in charge of muscle ultrastructure
+ title = "Titins: Giant proteins in charge of muscle ultrastructure
and elasticity.",
journal = SCI,
year = 1995,
@article { levy02,
author = RLevy #" and "# MMaaloum,
title = "Measuring the spring constant of atomic force microscope
- cantilevers: thermal fluctuations and other methods",
+ cantilevers: Thermal fluctuations and other methods",
year = 2002,
journal = NT,
volume = 13,
volume = 481,
pages = "143--60",
issn = "0065-2598",
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/10987071},
keywords = "Amino Acid Sequence;Animals;Computer
Simulation;Elasticity;Fibronectins;Humans;Hydrogen
Bonding;Immunoglobulins;Models, Molecular;Muscle Proteins;Muscle,
number = 1,
pages = "51--65",
issn = "0006-3495",
+ doi = {10.1016/S0006-3495(00)76273-4},
+ url = {http://www.cell.com/biophysj/abstract/S0006-3495%2800%2976273-4},
+ eprint = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1300915/pdf/10866937.pdf},
keywords = "Amino Acid Sequence;Computer Simulation;Double Bind
Interaction;Hydrogen Bonding;Immunoglobulins;Microscopy, Atomic
Force;Models, Chemical;Models, Molecular;Molecular Sequence Data;Muscle
@article { metropolis87,
author = NMetropolis,
- title = "The Beginning of the Monte Carlo Method",
+ title = "The Beginning of the {M}onte {C}arlo Method",
year = 1987,
journal = LAS,
volume = 15,
allowed us to map the features of the complex energy landscape of GFP
including a characterization of the structures, albeit at a coarse-
grained level, of the three metastable intermediates.",
- note = "Hiccup in unfolding leg corresponds to unfolding intermediate (See
- Figure 2). The unfolding timescale in GFP is about 6 ms."
+ note = {Hiccup in unfolding leg corresponds to unfolding
+ intermediate (\fref{figure}{2}). The unfolding time scale in GFP
+ is about $6\U{ms}$.},
}
@article { nevo03,
day = 24,
issn = "0022-2836",
doi = "10.1016/j.jmb.2007.06.015",
- url = "http://www.sciencedirect.com/science/article/pii/S0022283607007966",
+ url = "http://dx.doi.org/10.1016/j.jmb.2007.06.015",
keywords = "AFM",
keywords = "MD simulations",
keywords = "titin",
publisher = CUP,
address = "New York",
eprint = "http://www.nrbook.com/a/bookcpdf.php",
- note = "See sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
+ note = "See Sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to
Fourier transforms and power spectrum estimation.",
project = "Cantilever Calibration"
}
force spectroscopy data and for novel automated screening techniques is
shown with bacteriorhodopsin and with protein constructs containing GFP
and titin kinase.",
- note = "Contour length space and barrier position fingerprinting.",
+ note = {Contour length space and barrier position fingerprinting.
+ There are errors in \fref{equation}{3}, propagated from
+ \citet{livadaru03}. I contacted Elias Puchner and pointed out the
+ typos, and he revised his FRC fit parameters from $\gamma=22\dg$
+ and $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The
+ combined effect on \fref{figure}{3} of fixing the equation typos
+ and adjusting the fit parameters was small, so their conclusions
+ are still sound.},
}
@article { raible04,
year = 1965,
publisher = McGraw-Hill,
address = "New York",
- note = "Thermal noise for SHOs, in Chapter 15, Sections 6 and 10.",
+ note = "Thermal noise for simple harmonic oscillators, in Chapter
+ 15, Sections 6 and 10.",
project = "Cantilever Calibration"
}
viscoelastic properties of the surface. For example, the viscous
coupling to the surface is strongly increased when the surface is
covered with a swollen `polymer brush'.",
- note = "They actually write down Lagrangian formula and give a decent
+ note = "They actually write down a Lagrangian formula and give a decent
derivation of PSD, but don't show or work out the integrals.",
project = "Cantilever Calibration"
}
+@article{ gittes98,
+ author = FGittes #" and "# CFSchmidt,
+ title = {Thermal noise limitations on micromechanical experiments},
+ year = 1998,
+ month = jan,
+ journal = EBJ,
+ volume = 27,
+ number = 1,
+ pages = {75--81},
+ doi = {10.1007/s002490050113},
+ url = {http://dx.doi.org/10.1007/s002490050113},
+ issn = {0175-7571},
+ publisher = SPRINGER:V,
+ keywords = {Key words Thermal noise; Optical tweezers; Atomic force
+ microscopy; Single molecules; Micromechanics},
+ language = {English},
+}
+
@article { ryckaert77,
author = JPRyckaert #" and "# GCiccotti #" and "# HJCBerendsen,
title = "Numerical integration of the cartesian equations of motion of a
resolved details of the unfolding energy landscape from mechanical
single-molecule protein unfolding experiments requires models that go
beyond the Bell model.",
- note = "The inspiration behind my sawtooth simulation. Bell model fit to
- $f_{unfold}(v)$, but Kramers model fit to unfolding distribution for a
- given $v$. Eqn.~3 in the supplement is \citet{evans99} 1999's Eqn.~2,
- but it is just ``[dying percent] * [surviving population] = [deaths]''
- (TODO, check). $\nu \equiv k$ is the force/time-dependent off rate...
- (TODO) The Kramers' rate equation (second equation in the paper) is
- \citet{hanggi90} Eq.~4.56b (page 275). It is important to extract $k_0$
- and $\Delta x$ using every available method."
+ note = {The inspiration behind my sawtooth simulation. Bell model
+ fit to $f_{unfold}(v)$, but Kramers model fit to unfolding
+ distribution for a given $v$. \fref{equation}{3} in the
+ supplement is \xref{evans99}{equation}{2}, but it is just
+ $[\text{dying percent}] \cdot [\text{surviving population}]
+ = [\text{deaths}]$.
+ $\nu \equiv k$ is the force/time-dependent off rate. The Kramers'
+ rate equation (on page L34, the second equation in the paper) is
+ \xref{hanggi90}{equation}{4.56b} (page 275) and
+ \xref{socci96}{equation}{2} but \citet{schlierf06} gets the minus
+ sign wrong in the exponent. $U_F(x=0)\gg 0$ and
+ $U_F(x_\text{max})\ll 0$ (\cf~\xref{schlierf06}{figure}{1}).
+ Schlierf's integral (as written) contains
+ $\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, which is huge, when
+ it should contain $\exp{U_F(x_\text{max})}\cdot\exp{-U_F(0)}$,
+ which is tiny. For more details and a picture of the peak that
+ forms the bulk of the integrand, see
+ \cref{eq:kramers,fig:kramers:integrand}. I pointed out this
+ problem to Michael Schlierf, but he was unconvinced.},
}
@article { schwaiger04,
the different driving forces in protein folding."
}
+@mastersthesis{ lee05,
+ author = SLee,
+ title = {Chemical Functionalization of AFM Cantilevers},
+ school = MIT,
+ year = 2005,
+ month = sep,
+ url = {http://dspace.mit.edu/handle/1721.1/34205},
+ abstract = {Atomic force microscopy (AFM) has been a powerful
+ instrument that provides nanoscale imaging of surface features,
+ mainly of rigid metal or ceramic surfaces that can be insulators
+ as well as conductors. Since it has been demonstrated that AFM
+ could be used in aqueous environment such as in water or various
+ buffers from which physiological condition can be maintained, the
+ scope of the application of this imaging technique has been
+ expanded to soft biological materials. In addition, the main usage
+ of AFM has been to image the material and provide the shape of
+ surface, which has also been diversified to molecular-recognition
+ imaging - functional force imaging through force spectroscopy and
+ modification of AFM cantilevers. By immobilizing of certain
+ molecules at the end of AFM cantilever, specific molecules or
+ functionalities can be detected by the combination of intrinsic
+ feature of AFM and chemical modification technique of AFM
+ cantilever. The surface molecule that is complementary to the
+ molecule at the end of AFM probe can be investigated via
+ specificity of molecule-molecule interaction.(cont.) Thus, this
+ AFM cantilever chemistry, or chemical functionalization of AFM
+ cantilever for the purpose of chemomechanical surface
+ characterization, can be considered as an infinite source of
+ applications important to understanding biological materials and
+ material interactions. This thesis is mainly focused on three
+ parts: (1) AFM cantilever chemistry that introduces specific
+ protocols in details such as adsorption method, gold chemistry,
+ and silicon nitride cantilever modification; (2) validation of
+ cantilever chemistry such as X-ray photoelectron spectroscopy
+ (XPS), AFM blocking experiment, and fluorescence microscopy,
+ through which various AFM cantilever chemistry is verified; and
+ (3) application of cantilever chemistry, especially toward the
+ potential of force spectroscopy and the imaging of biological
+ material surfaces.},
+ language = {eng},
+ note = {Binding proteins to gold-coated cantilevers via EDC (among
+ other things in this thesis.},
+}
+
@article { walton08,
author = EBWalton #" and "# SLee #" and "# KJVanVliet,
- title = "Extending {B}ell's model: how force transducer stiffness alters
+ title = "Extending {B}ell's model: How force transducer stiffness alters
measured unbinding forces and kinetics of molecular complexes",
year = 2008,
month = apr,
}
@article { lli06,
- author = LiLi #" and "# YYang #" and "# GYang #" and "# XChen
+ author = LiLi #" and "# YYang #" and "# GYang #" and "# XuChen
#" and "# BHsiao #" and "# BChu #" and "#
JSpanier #" and "# CYLi,
title = "Patterning polyethylene oligomers on carbon nanotubes
language = "eng",
}
+@article{ kuhn05,
+ author = MKuhn #" and "# HJanovjak #" and "# MHubain #" and "# DJMuller,
+ title = {Automated alignment and pattern recognition of
+ single-molecule force spectroscopy data.},
+ year = 2005,
+ month = may,
+ address = {Division of Computer Science, California Institute of
+ Technology, Pasadena, California 91125, USA.},
+ journal = JMicro,
+ volume = 218,
+ number = 2,
+ pages = {125--132},
+ ISSN = {0022-2720},
+ doi = {10.1111/j.1365-2818.2005.01478.x},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/15857374},
+ language = {eng},
+ keywords = {Algorithms},
+ keywords = {Bacteriorhodopsins},
+ keywords = {Data Interpretation, Statistical},
+ keywords = {Escherichia coli Proteins},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Protein Folding},
+ keywords = {Sodium-Hydrogen Antiporter},
+ keywords = {Software},
+ abstract = {Recently, direct measurements of forces stabilizing
+ single proteins or individual receptor-ligand bonds became
+ possible with ultra-sensitive force probe methods like the atomic
+ force microscope (AFM). In force spectroscopy experiments using
+ AFM, a single molecule or receptor-ligand pair is tethered between
+ the tip of a micromachined cantilever and a supporting
+ surface. While the molecule is stretched, forces are measured by
+ the deflection of the cantilever and plotted against extension,
+ yielding a force spectrum characteristic for each biomolecular
+ system. In order to obtain statistically relevant results, several
+ hundred to thousand single-molecule experiments have to be
+ performed, each resulting in a unique force spectrum. We developed
+ software and algorithms to analyse large numbers of force
+ spectra. Our algorithms include the fitting polymer extension
+ models to force peaks as well as the automatic alignment of
+ spectra. The aligned spectra allowed recognition of patterns of
+ peaks across different spectra. We demonstrate the capabilities of
+ our software by analysing force spectra that were recorded by
+ unfolding single transmembrane proteins such as bacteriorhodopsin
+ and NhaA. Different unfolding pathways were detected by
+ classifying peak patterns. Deviant spectra, e.g. those with no
+ attachment or erratic peaks, can be easily identified. The
+ software is based on the programming language C++, the GNU
+ Scientific Library (GSL), the software WaveMetrics IGOR Pro and
+ available open-source at http://bioinformatics.org/fskit/.},
+ note = {Development stalled in 2005 after Michael graduated.},
+}
+
+@article{ janovjak05,
+ author = HJanovjak #" and "# JStruckmeier #" and "# DJMuller,
+ title = {Hydrodynamic effects in fast {AFM} single-molecule
+ force measurements.},
+ year = 2005,
+ month = feb,
+ day = 15,
+ address = {BioTechnological Center, University of Technology
+ Dresden, 01307 Dresden, Germany.},
+ journal = EBJ,
+ volume = 34,
+ number = 1,
+ pages = {91--96},
+ issn = {0175-7571},
+ doi = {10.1007/s00249-004-0430-3},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/15257425},
+ language = {eng},
+ keywords = {Algorithms},
+ keywords = {Computer Simulation},
+ keywords = {Elasticity},
+ keywords = {Microfluidics},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Chemical},
+ keywords = {Models, Molecular},
+ keywords = {Physical Stimulation},
+ keywords = {Protein Binding},
+ keywords = {Proteins},
+ keywords = {Stress, Mechanical},
+ keywords = {Viscosity},
+ abstract = {Atomic force microscopy (AFM) allows the critical forces
+ that unfold single proteins and rupture individual receptor-ligand
+ bonds to be measured. To derive the shape of the energy landscape,
+ the dynamic strength of the system is probed at different force
+ loading rates. This is usually achieved by varying the pulling
+ speed between a few nm/s and a few $\mu$m/s, although for a more
+ complete investigation of the kinetic properties higher speeds are
+ desirable. Above 10 $\mu$m/s, the hydrodynamic drag force acting
+ on the AFM cantilever reaches the same order of magnitude as the
+ molecular forces. This has limited the maximum pulling speed in
+ AFM single-molecule force spectroscopy experiments. Here, we
+ present an approach for considering these hydrodynamic effects,
+ thereby allowing a correct evaluation of AFM force measurements
+ recorded over an extended range of pulling speeds (and thus
+ loading rates). To support and illustrate our theoretical
+ considerations, we experimentally evaluated the mechanical
+ unfolding of a multi-domain protein recorded at $30\U{$mu$m/s}$
+ pulling speed.},
+}
+
+@article{ sandal08,
+ author = MSandal #" and "# FValle #" and "# ITessari #" and "#
+ SMammi #" and "# EBergantino #" and "# FMusiani #" and "#
+ MBrucale #" and "# LBubacco #" and "# BSamori,
+ title = {Conformational Equilibria in Monomeric $\alpha$-Synuclein
+ at the Single-Molecule Level},
+ year = 2008,
+ month = jan,
+ address = {Department of Biochemistry G. Moruzzi,
+ University of Bologna, Bologna, Italy.},
+ journal = PLOS:BIO,
+ volume = 6,
+ number = 1,
+ pages = {e6},
+ issn = {1545-7885},
+ doi = {10.1371/journal.pbio.0060006},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/18198943},
+ language = {eng},
+ keywords = {Buffers},
+ keywords = {Circular Dichroism},
+ keywords = {Copper},
+ keywords = {Entropy},
+ keywords = {Models, Molecular},
+ keywords = {Molecular Sequence Data},
+ keywords = {Mutation},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Protein Structure, Tertiary},
+ keywords = {alpha-Synuclein},
+ abstract = {Human $\alpha$-Synuclein ($\alpha$Syn) is a natively
+ unfolded protein whose aggregation into amyloid fibrils is
+ involved in the pathology of Parkinson disease. A full
+ comprehension of the structure and dynamics of early intermediates
+ leading to the aggregated states is an unsolved problem of
+ essential importance to researchers attempting to decipher the
+ molecular mechanisms of $\alpha$Syn aggregation and formation of
+ fibrils. Traditional bulk techniques used so far to solve this
+ problem point to a direct correlation between $\alpha$Syn's unique
+ conformational properties and its propensity to aggregate, but
+ these techniques can only provide ensemble-averaged information
+ for monomers and oligomers alike. They therefore cannot
+ characterize the full complexity of the conformational equilibria
+ that trigger the aggregation process. We applied atomic force
+ microscopy-based single-molecule mechanical unfolding methodology
+ to study the conformational equilibrium of human wild-type and
+ mutant $\alpha$Syn. The conformational heterogeneity of monomeric
+ $\alpha$Syn was characterized at the single-molecule level. Three
+ main classes of conformations, including disordered and
+ ``$\beta$-like'' structures, were directly observed and quantified
+ without any interference from oligomeric soluble forms. The
+ relative abundance of the ``$\beta$-like'' structures
+ significantly increased in different conditions promoting the
+ aggregation of $\alpha$Syn: the presence of \Cu, the pathogenic
+ A30P mutation, and high ionic strength. This methodology can
+ explore the full conformational space of a protein at the
+ single-molecule level, detecting even poorly populated conformers
+ and measuring their distribution in a variety of biologically
+ important conditions. To the best of our knowledge, we present
+ for the first time evidence of a conformational equilibrium that
+ controls the population of a specific class of monomeric
+ $\alpha$Syn conformers, positively correlated with conditions
+ known to promote the formation of aggregates. A new tool is thus
+ made available to test directly the influence of mutations and
+ pharmacological strategies on the conformational equilibrium of
+ monomeric $\alpha$Syn.},
+}
+
@article{ sandal09,
author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "#
AGomezCasado #" and "# BSamori,
- title = "Hooke: an open software platform for force spectroscopy.",
+ title = "Hooke: An open software platform for force spectroscopy.",
journal = BIOINFO,
year = 2009,
month = jun,
language = "eng",
}
+@article{ materassi09,
+ author = DMaterassi #" and "# PBaschieri #" and "# BTiribilli #" and "#
+ GZuccheri #" and "# BSamori,
+ title = {An open source/real-time atomic force microscope
+ architecture to perform customizable force spectroscopy
+ experiments},
+ year = 2009,
+ month = aug,
+ address = {Department of Electrical and Computer Engineering,
+ University of Minnesota, 200 Union St. SE, Minneapolis,
+ Minnesota 55455, USA. mater013@umn.edu},
+ journal = RSI,
+ volume = 80,
+ number = 8,
+ pages = 084301,
+ issn = "1089-7623",
+ doi = "10.1063/1.3194046",
+ url = "http://www.ncbi.nlm.nih.gov/pubmed/19725671",
+ language = "eng",
+ keywords = {Algorithms},
+ keywords = {Animals},
+ keywords = {Calibration},
+ keywords = {Gold},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Muscle Proteins},
+ keywords = {Myocardium},
+ keywords = {Optics and Photonics},
+ keywords = {Ownership},
+ keywords = {Protein Kinases},
+ keywords = {Software},
+ keywords = {Spectrum Analysis},
+ keywords = {Time Factors},
+ abstract = {We describe the realization of an atomic force
+ microscope architecture designed to perform customizable
+ experiments in a flexible and automatic way. Novel technological
+ contributions are given by the software implementation platform
+ (RTAI-LINUX), which is free and open source, and from a functional
+ point of view, by the implementation of hard real-time control
+ algorithms. Some other technical solutions such as a new way to
+ estimate the optical lever constant are described as well. The
+ adoption of this architecture provides many degrees of freedom in
+ the device behavior and, furthermore, allows one to obtain a
+ flexible experimental instrument at a relatively low cost. In
+ particular, we show how such a system has been employed to obtain
+ measures in sophisticated single-molecule force spectroscopy
+ experiments\citep{fernandez04}. Experimental results on proteins
+ already studied using the same methodologies are provided in order
+ to show the reliability of the measure system.},
+ note = {Although this paper claims to present an open source
+ experiment control framework (on Linux!), it doesn't actually link
+ to any source code. This is puzzling and frusterating.},
+}
+
+@article{ aioanei11,
+ author = DAioanei #" and "# MBrucale #" and "# BSamori,
+ title = {Open source platform for the execution and analysis of
+ mechanical refolding experiments.},
+ year = 2011,
+ month = feb,
+ day = 1,
+ address = {Department of Biochemistry G.~Moruzzi,
+ University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
+ aioaneid@gmail.com},
+ journal = BIOINFO,
+ volume = 27,
+ number = 3,
+ pages = {423--425},
+ issn = {1367-4811},
+ doi = {10.1093/bioinformatics/btq663},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21123222},
+ language = {eng},
+ keywords = {Computational Biology},
+ keywords = {Kinetics},
+ keywords = {Protein Denaturation},
+ keywords = {Protein Refolding},
+ keywords = {Software},
+ abstract = {Single-molecule force spectroscopy has facilitated the
+ experimental investigation of biomolecular force-coupled kinetics,
+ from which the kinetics at zero force can be extrapolated via
+ explicit theoretical models. The atomic force microscope (AFM) in
+ particular is routinely used to study protein unfolding kinetics,
+ but only rarely protein folding kinetics. The discrepancy arises
+ because mechanical protein refolding studies are more technically
+ challenging.},
+ note = {\href{http://code.google.com/p/refolding/}{Refolding} is a
+ suite for performing and analyzing double-pulse refolding
+ experiments. The experiment-driver is mostly written in Java with
+ the analysis code in Python. The driver is curious; it uses the
+ NanoScope scripting interface to drive the experiment through the
+ NanoScope software by impersonating a mouse-wielding user (like
+ Selenium does for web browsers). See the
+ \imint{sh}|RobotNanoDriver.java| code for details. There is also
+ support for automatic velocity clamp analysis.},
+}
+
+@article{ benedetti11,
+ author = FBenedetti #" and "# CMicheletti #" and "# GBussi #" and "#
+ SKSekatskii #" and "# GDietler,
+ title = {Nonkinetic modeling of the mechanical unfolding of
+ multimodular proteins: theory and experiments.},
+ year = 2011,
+ month = sep,
+ day = 21,
+ address = {Laboratory of Physics of Living Matter,
+ Ecole Polytechnique F{\'e}d{\'e}rale de Lausanne,
+ Lausanne, Switzerland.},
+ journal = BPJ,
+ volume = 101,
+ number = 6,
+ pages = {1504--1512},
+ issn = {1542-0086},
+ doi = {10.1016/j.bpj.2011.07.047},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21943432},
+ language = {eng},
+ keywords = {Kinetics},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Molecular},
+ keywords = {Monte Carlo Method},
+ keywords = {Protein Unfolding},
+ keywords = {Stochastic Processes},
+ abstract = {We introduce and discuss a novel approach called
+ back-calculation for analyzing force spectroscopy experiments on
+ multimodular proteins. The relationship between the histograms of
+ the unfolding forces for different peaks, corresponding to a
+ different number of not-yet-unfolded protein modules, is exploited
+ in such a manner that the sole distribution of the forces for one
+ unfolding peak can be used to predict the unfolding forces for
+ other peaks. The scheme is based on a bootstrap prediction method
+ and does not rely on any specific kinetic model for multimodular
+ unfolding. It is tested and validated in both
+ theoretical/computational contexts (based on stochastic
+ simulations) and atomic force microscopy experiments on (GB1)(8)
+ multimodular protein constructs. The prediction accuracy is so
+ high that the predicted average unfolding forces corresponding to
+ each peak for the GB1 construct are within only 5 pN of the
+ averaged directly-measured values. Experimental data are also used
+ to illustrate how the limitations of standard kinetic models can
+ be aptly circumvented by the proposed approach.},
+}
+
+@phdthesis{ benedetti12,
+ author = FBenedetti,
+ title = {Statistical Study of the Unfolding of Multimodular Proteins
+ and their Energy Landscape by Atomic Force Microscopy},
+ year = 2012,
+ address = {Lausanne},
+ affiliation = {EPFL},
+ doctoral = {EDPY},
+ pagecount = {153},
+ doi = {10.5075/epfl-thesis-5440},
+ url = {http://infoscience.epfl.ch/record/181215},
+ eprint = {http://infoscience.epfl.ch/record/181215/files/EPFL_TH5440.pdf},
+ keywords = {atomic force microscope (AFM); single molecule force
+ spectrosopy; velocity clamp AFM; Monte carlo simulations; force
+ modulation spectroscopy; energy barrier model; non kinetic methods
+ for force spectroscopy},
+ abstract = {The aim of the present thesis is to investigate several
+ aspects of: the proteins mechanics, interprotein interactions and
+ to study also new techniques, theoretical and technical, to obtain
+ and analyze the force spectroscopy experiments. The first section
+ is dedicated to the statistical properties of the unfolding forces
+ in a chain of homomeric multimodular proteins. The basic idea of
+ this kind of statistic is to divide the peaks observed in a force
+ extension curve in separate groups and then analyze these groups
+ considering their position in the force curves. In fact in a
+ multimodular homomeric protein the unfolding force is related to
+ the number of not yet unfolded modules (we call it "N"). Such
+ effect yields to a linear dependence of the most probable
+ unfolding force of a peak on ln(N). We demonstrate how such
+ dependence can be used to extract the kinetic parameters and how,
+ ignoring it, could lead to significant errors. Following this
+ topic we continue with non kinetic methods that, using the
+ resampling from the rupture forces of any peak, could reconstruct
+ the rupture forces for all the other peaks in a chain. Then a
+ discussion about the Monte Carlo simulation for protein pulling is
+ present. In fact a theoretical framework for such methodology has
+ to be introduced to understand the various simulations done. In
+ this chapter we also introduce a methodology to study the ligand
+ receptor interactions when we directly functionalize the AFM tip
+ and the substrate. In fact, in many of our experiments, we see a
+ "cloud of points" in the force vs loading rate graph. We have
+ modeled a system composed by "N" parallel springs, and studying
+ the distribution of forces obtained in the force vs loading rate
+ graph we have establish a procedure to restore the kinetic
+ parameters used. Such procedure has then been used to discuss real
+ experiments similar to biotin-avidin interaction. In the following
+ chapter we discuss a first order approximation of the Bell-Evans
+ model where a more explicit form of the potential is
+ considered. In particular the dependence of the curvature of the
+ potential on the applied force at the minimum and at the
+ metastable state is considered. In the well known Bell-Evans model
+ the prefactors of the transition rate are fixed at any force,
+ however this is not what happen in nature, where the prefactors
+ (that are the second local derivative of the interacting energy
+ with respect to the reaction coordinate in its minimum and
+ maximum) depend on the force applied. The results obtained with
+ the force spectroscopy of the Laminin-binding-protein are
+ discussed, in particular this protein showed a phase transition
+ when the pH was changed. The behavior of this protein changes,
+ from a normal WLC behavior to a plateau behavior. The analysis of
+ the force spectroscopy curves shows a distribution of length where
+ the maximum of the first prominent peak correspond to the full
+ length of the protein. However, length that could be associated
+ with dimers and trymers are also present in this
+ distribution. Later a new approach to study the lock and key
+ mechanism, using "handles" with a specific force extension
+ pattern, is introduced. In particular handles of (I27)3 and
+ (I27–SNase)3 were biochemically attached to: strept-actin
+ molecules, biotin molecules, RNase and Angiogenin. The main idea
+ is to have a system composed by "handle-(molecule A)-(molecule
+ B)-handle" where the handles are covalently attached to the
+ respective molecules and the two molecules "A and B" are attached
+ by secondary bonds. This approach allows a better recognition of
+ the protein-protein interaction enabling us to filter out spurious
+ events. Doing a statistic on the rupture forces and comparing this
+ with the statistic of the detachments of the system of the bare
+ handles, we are able to extract the information of the interaction
+ between the molecule A and B. The two last chapters are of more
+ preliminary character that the previous part of the thesis. A
+ section is dedicated to the estimation of effective mass and
+ viscous drag of the cantilevers studied by autocorrelation and
+ noise power spectrum. Usually the noise power spectrum method is
+ the most used, however the autocorrelation should give
+ approximately the same information. The parameters obtained are
+ important in high frequency modulation techniques. In fact, they
+ are needed to interpret the results. The results of these two
+ methods show a good agreement in the estimation of the mass and
+ the viscous drag of the various cantilever used. Afterwards a
+ chapter is dedicated to the discussion of the force spectroscopy
+ experiments using a low frequency modulation of the cantilever
+ base. Such experiments allow us to record the phase and the
+ amplitude shift of the modulation signal used. Using the amplitude
+ channel we managed to restore the static force signal with a lower
+ level of noise. Moreover these signals give us direct information
+ about the dynamic stiffness and the lose of energy in the system,
+ information that, using the standard technique would be difficult
+ (or even impossible) to obtain.},
+}
+
@article{ kempe85,
author = TKempe #" and "# SBHKent #" and "# FChow #" and "# SMPeterson
#" and "# WSundquist #" and "# JLItalien #" and "# DHarbrecht
#" and "# DPlunkett #" and "# WDeLorbe,
- title = "Multiple-copy genes: production and modification of
+ title = "Multiple-copy genes: Production and modification of
monomeric peptides from large multimeric fusion proteins.",
journal = GENE,
year = 1985,
year = 2003,
issn = "1572-6657",
doi = "10.1016/S0022-0728(03)00052-4",
- url = "http://www.sciencedirect.com/science/article/pii/S0022072803000524",
+ url = "http://dx.doi.org/10.1016/S0022-0728(03)00052-4",
keywords = "Thiol",
keywords = "Disulfide",
keywords = "Thiol adsorption",
}
@article{ radmacher92,
- author = MRadmacher #" and "# RWTillamnn #" and "# MFritz #" and "# HEGaub,
+ author = MRadmacher #" and "# RWTillmann #" and "# MFritz #" and "# HEGaub,
title = {From molecules to cells: imaging soft samples with the
atomic force microscope},
year = 1992,
}
@article{ williams86,
- author = CCWilliams #" and "# HWickramasinghe,
+ author = CCWilliams #" and "# HKWickramasinghe,
title = "Scanning thermal profiler",
journal = APL,
year = 1986,
language = "eng",
}
-@article{ martin87,
- author = MMartin #" and "# CCWilliams #" and "# HWickramasinghe,
- title = "Atomic force microscope-force mapping and profiling on a sub
- 100-\AA scale",
- journal = JAP,
- year = 1987,
- month = may,
- day = 15,
- volume = 61,
- number = 10,
- pages = "4723--4729",
- abstract = "A modified version of the atomic force microscope is
- introduced that enables a precise measurement of the force between
- a tip and a sample over a tip-sample distance range of 30--150
- \AA. As an application, the force signal is used to maintain the
- tip-sample spacing constant, so that profiling can be achieved
- with a spatial resolution of 50 \AA. A second scheme allows the
- simultaneous measurement of force and surface profile; this scheme
- has been used to obtain material-dependent information from
- surfaces of electronic materials.",
- issn = "0021-8979",
- issn_online = "1089-7550",
- doi = "10.1063/1.338807",
- URL = "http://jap.aip.org/resource/1/japiau/v61/i10/p4723_s1",
- language = "eng",
-}
-
@article{ meyer88,
author = GMeyer #" and "# NMAmer,
title = "Novel optical approach to atomic force microscopy",
}
@article{ aruliah12,
- author = DAruliah #" and "# CTBrown #" and "# MPCHong #" and "#
+ author = DAruliah #" and "# CTBrown #" and "# NPCHong #" and "#
MDavis #" and "# RTGuy #" and "# SHaddock #" and "# KHuff #" and "#
IMitchell #" and "# MPlumbley #" and "# BWaugh #" and "#
EPWhite #" and "# GWilson #" and "# PWilson,
pages = {699--714},
issn = "0967-0661",
doi = "10.1016/0967-0661(93)91394-C",
- url = "http://www.sciencedirect.com/science/article/pii/096706619391394C",
+ url = "http://dx.doi.org/10.1016/0967-0661(93)91394-C",
keywords = {Adaptive control},
keywords = {automatic tuning},
keywords = {gain scheduling},
are given. The reporting of the uncertainties of final results is
discussed.},
}
+
+@article{ livadaru03,
+ author = LLivadaru #" and "# RRNetz #" and "# HJKreuzer,
+ title = {Stretching Response of Discrete Semiflexible Polymers},
+ year = 2003,
+ month = apr,
+ day = 25,
+ journal = Macromol,
+ volume = 36,
+ number = 10,
+ pages = {3732--3744},
+ doi = {10.1021/ma020751g},
+ URL = {http://pubs.acs.org/doi/abs/10.1021/ma020751g},
+ eprint = {http://pubs.acs.org/doi/pdf/10.1021/ma020751g},
+ abstract = {We demonstrate that semiflexible polymer chains
+ (characterized by a persistence length $l$) made up of discrete
+ segments or bonds of length $b$ show at large stretching forces a
+ crossover from the standard wormlike chain (WLC) behavior to a
+ discrete-chain (DC) behavior. In the DC regime, the stretching
+ response is independent of the persistence length and shows a
+ different force dependence than in the WLC regime. We perform
+ extensive transfer-matrix calculations for the force-response of a
+ freely rotating chain (FRC) model as a function of varying bond
+ angle $\gamma$ (and thus varying persistence length) and chain
+ length. The FRC model is a first step toward the understanding of
+ the stretching behavior of synthetic polymers, denatured proteins,
+ and single-stranded DNA under large tensile forces. We also
+ present scaling results for the force response of the elastically
+ jointed chain (EJC) model, that is, a chain made up of freely
+ jointed bonds that are connected by joints with some bending
+ stiffness; this is the discretized version of the continuum WLC
+ model. The EJC model might be applicable to stiff biopolymers such
+ as double-stranded DNA or Actin. Both models show a similar
+ crossover from the WLC to the DC behavior, which occurs at a force
+ $f/k_BT\sim l/b^2$ and is thus (for polymers with a moderately
+ large persistence length) in the piconewton range probed in many
+ AFM experiments. We also give a heuristic simple function for the
+ force--distance relation of a FRC, valid in the global force
+ range, which can be used to fit experimental data. Our findings
+ might help to resolve the discrepancies encountered when trying to
+ fit experimental data for the stretching response of polymers in a
+ broad force range with a single effective persistence length.},
+ note = {There are two typos in \fref{equation}{46}.
+ \citet{livadaru03} have
+ \begin{equation}
+ \frac{R_z}{L} = \begin{cases}
+ \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
+ 1 - \p({\frac{fl}{4k_BT}})^{-0.5}
+ & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
+ 1 - \p({\frac{fb}{ck_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
+ \end{cases}
+ \end{equation}
+ but the correct formula is
+ \begin{equation}
+ \frac{R_z}{L} = \begin{cases}
+ \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\
+ 1 - \p({\frac{4fl}{k_BT}})^{-0.5}
+ & \frac{b}{l} < \frac{fb}{k_BT} < \frac{l}{b} \\
+ 1 - \p({\frac{cfb}{k_BT}})^{-1} & \frac{1}{b} < \frac{fb}{k_BT} \;,
+ \end{cases}
+ \end{equation}
+ with both the $4$ and the $c$ moved into their respective
+ numerators. I pointed these errors out to Roland Netz in 2012,
+ along with the fact that even with the corrected formula there is
+ a discontinuity between the low- and moderate-force regimes. Netz
+ confirmed the errors, and pointed out that the discontinuity is
+ because \fref{equation}{46} only accounts for the scaling (without
+ prefactors). Unfortunately, there does not seem to be a published
+ erratum pointing out the error and at least \citet{puchner08} have
+ quoted the incorrect form.},
+}
+
+@misc{ punias,
+ author = PCarl #" and "# PDalhaimer,
+ title = {{PUNIAS}: Protein Unfolding and Nano-indentation Analysis
+ Software},
+ year = 2005,
+ month = oct,
+ day = 13,
+ note = {4 Int. Workshop, Scanning Probe Microscopy in Life Sciences},
+ address = {Berlin},
+ url = {http://punias.voila.net/},
+}
+
+@article{ carl08,
+ author = PCarl #" and "# HSchillers,
+ title = {Elasticity measurement of living cells with an atomic force
+ microscope: data acquisition and processing.},
+ year = 2008,
+ month = nov,
+ day = 15,
+ address = {Institute of Physiology II, University of M{\"u}nster,
+ Robert-Koch-Str. 27b, 48149, M{\"u}nster, Germany.},
+ journal = PA,
+ volume = 457,
+ number = 2,
+ pages = {551--559},
+ issn = {0031-6768},
+ doi = {10.1007/s00424-008-0524-3},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/18481081},
+ language = {eng},
+ keywords = {Animals},
+ keywords = {Biomechanics},
+ keywords = {CHO Cells},
+ keywords = {Cricetinae},
+ keywords = {Cricetulus},
+ keywords = {Cystic Fibrosis Transmembrane Conductance Regulator},
+ keywords = {Elastic Modulus},
+ keywords = {Equipment Design},
+ keywords = {Microscopy, Atomic Force},
+ keywords = {Models, Biological},
+ keywords = {Reproducibility of Results},
+ keywords = {Signal Processing, Computer-Assisted},
+ keywords = {Transfection},
+ abstract = {Elasticity of living cells is a parameter of increasing
+ importance in cellular physiology, and the atomic force microscope
+ is a suitable instrument to quantitatively measure it. The
+ principle of an elasticity measurement is to physically indent a
+ cell with a probe, to measure the applied force, and to process
+ this force-indentation data using an appropriate model. It is
+ crucial to know what extent the geometry of the indenting probe
+ influences the result. Therefore, we indented living Chinese
+ hamster ovary cells at 37 degrees C with sharp tips and colloidal
+ probes (spherical particle tips) of different sizes and
+ materials. We furthermore developed an implementation of the Hertz
+ model, which simplifies the data processing. Our results show (a)
+ that the size of the colloidal probe does not influence the result
+ over a wide range (radii $0.5$-$26\U{$\mu$m}$) and (b) indenting
+ cells with sharp tips results in higher Young's moduli
+ (approximately $1,300\U{Pa}$) than using colloidal probes
+ (approximately $400\U{Pa}$).},
+ note = {Mentions \citetalias{punias} as if it was in-house software,
+ which makes sense because Philippe Carl seems to be a major author.},
+}
+
+@article{ struckmeier08,
+ author = JStruckmeier #" and "# RWahl #" and "# MLeuschner #" and "#
+ JNunes #" and "# HJanovjak #" and "# UGeisler #" and "#
+ GHofmann #" and "# TJahnke #" and "# DJMuller,
+ title = {Fully automated single-molecule force spectroscopy for
+ screening applications},
+ year = 2008,
+ month = sep,
+ day = 24,
+ address = {Cellular Machines, Biotechnology Center,
+ Technische Universit{\"a}t Dresden, Tatzberg 47, D-01307
+ Dresden, Germany},
+ journal = NT,
+ volume = 19,
+ number = 38,
+ pages = 384020,
+ issn = {0957-4484},
+ doi = {10.1088/0957-4484/19/38/384020},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21832579},
+ language = {eng},
+ abstract = {With the introduction of single-molecule force
+ spectroscopy (SMFS) it has become possible to directly access the
+ interactions of various molecular systems. A bottleneck in
+ conventional SMFS is collecting the large amount of data required
+ for statistically meaningful analysis. Currently, atomic force
+ microscopy (AFM)-based SMFS requires the user to tediously `fish'
+ for single molecules. In addition, most experimental and
+ environmental conditions must be manually adjusted. Here, we
+ developed a fully automated single-molecule force
+ spectroscope. The instrument is able to perform SMFS while
+ monitoring and regulating experimental conditions such as buffer
+ composition and temperature. Cantilever alignment and calibration
+ can also be automatically performed during experiments. This,
+ combined with in-line data analysis, enables the instrument, once
+ set up, to perform complete SMFS experiments autonomously.},
+ note = {An advertisement for JPK's \citetalias{force-robot}.},
+}
+
+@article{ andreopoulos11,
+ author = BAndreopoulos #" and "# DLabudde,
+ title = {Efficient unfolding pattern recognition in single molecule
+ force spectroscopy data},
+ year = 2011,
+ month = jun,
+ day = 06,
+ address = {Department of Bioinformatics, Biotechnological Center,
+ University of Technology Dresden, Dresden, Germany.
+ williama@biotec.tu-dresden.de},
+ journal = AMB,
+ volume = 6,
+ number = 1,
+ pages = 16,
+ issn = {1748-7188},
+ doi = {10.1186/1748-7188-6-16},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21645400},
+ language = {eng},
+ abstract = {Single-molecule force spectroscopy (SMFS) is a technique
+ that measures the force necessary to unfold a protein. SMFS
+ experiments generate Force-Distance (F-D) curves. A statistical
+ analysis of a set of F-D curves reveals different unfolding
+ pathways. Information on protein structure, conformation,
+ functional states, and inter- and intra-molecular interactions can
+ be derived.},
+}
+
+@book{ turnbull59,
+ editor = HWTurnbull,
+ author = INewton,
+ title = {The correspondence of Isaac Newton},
+ year = 1959,
+ publisher = RSUP,
+ volume = 1,
+ numpages = 445,
+ url = {http://books.google.com/books?id=pr8WAQAAMAAJ},
+ note = {The ``Giants'' quote is on page 416, in a letter to Robert
+ Hooke dated February 5, 1676.},
+}
+
+@book{ whitehead11,
+ author = ANWhitehead,
+ title = {An introduction to mathematics},
+ year = 1911,
+ publisher = WN,
+ numpages = 274,
+ address = {London},
+ url = {http://archive.org/details/introductiontoma00whitiala},
+ note = {The ``civilization'' quote is on page 61.},
+}
+
+@article{ mlot11,
+ author = NJMlot #" and "# CATovey #" and "# DLHu,
+ title = {Fire ants self-assemble into waterproof rafts to survive floods},
+ year = 2011,
+ month = may,
+ day = 10,
+ address = {Schools of Mechanical Engineering, Industrial and
+ Systems Engineering, and Biology,
+ Georgia Institute of Technology, Atlanta, GA 30318, USA.},
+ journal = PNAS,
+ volume = 108,
+ number = 19,
+ pages = {7669--7673},
+ issn = {1091-6490},
+ doi = {10.1073/pnas.1016658108},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21518911},
+ language = {eng},
+ keywords = {Animals},
+ keywords = {Ants},
+ keywords = {Behavior, Animal},
+ keywords = {Biophysical Phenomena},
+ keywords = {Floods},
+ keywords = {Hydrophobic and Hydrophilic Interactions},
+ keywords = {Microscopy, Electron, Scanning},
+ keywords = {Models, Biological},
+ keywords = {Social Behavior},
+ keywords = {Surface Properties},
+ keywords = {Time-Lapse Imaging},
+ keywords = {Video Recording},
+ keywords = {Water},
+ abstract = {Why does a single fire ant \species{Solenopsis invicta}
+ struggle in water, whereas a group can float effortlessly for
+ days? We use time-lapse photography to investigate how fire ants
+ \species{S.~invicta} link their bodies together to build
+ waterproof rafts. Although water repellency in nature has been
+ previously viewed as a static material property of plant leaves
+ and insect cuticles, we here demonstrate a self-assembled
+ hydrophobic surface. We find that ants can considerably enhance
+ their water repellency by linking their bodies together, a process
+ analogous to the weaving of a waterproof fabric. We present a
+ model for the rate of raft construction based on observations of
+ ant trajectories atop the raft. Central to the construction
+ process is the trapping of ants at the raft edge by their
+ neighbors, suggesting that some ``cooperative'' behaviors may rely
+ upon coercion.},
+ note = {Higher resolution pictures are available at
+ \url{http://antlab.gatech.edu/antlab/The_Ant_Raft.html}.},
+}
+
+@article{ hofmeister88,
+ author = FHofmeister,
+ title = {Zur Lehre von der Wirkung der Salze.},
+ year = 1888,
+ month = mar,
+ address = {Prague},
+ journal = AEPP,
+ volume = 25,
+ number = 1,
+ pages = {1--30},
+ doi = {10.1007/BF01838161},
+ url = {http://link.springer.com/article/10.1007/BF01838161},
+ eprint = {http://link.springer.com/content/pdf/10.1007%2FBF01838161.pdf},
+ language = {de},
+}
+
+@article{ chauhan97,
+ author = VPChauhan #" and "# IRay #" and "# AChauhan #" and "#
+ JWegiel #" and "# HMWisniewski,
+ title = {Metal cations defibrillize the amyloid beta-protein fibrils.},
+ year = 1997,
+ month = jul,
+ address = {New York State Institute for Basic Research in
+ Developmental Disabilities, Staten Island 10314-6399,
+ USA.},
+ journal = NR,
+ volume = 22,
+ number = 7,
+ pages = {805--809},
+ issn = {0364-3190},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/9232632},
+ doi = {10.1023/A:1022079709085},
+ language = {eng},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Drug Evaluation, Preclinical},
+ keywords = {Humans},
+ keywords = {Metals},
+ keywords = {Peptide Fragments},
+ keywords = {Solubility},
+ abstract = {Amyloid beta-protein (A beta) is the major constituent
+ of amyloid fibrils composing beta-amyloid plaques and
+ cerebrovascular amyloid in Alzheimer's disease (AD). We studied
+ the effect of metal cations on preformed fibrils of synthetic A
+ beta by Thioflavin T (ThT) fluorescence spectroscopy and
+ electronmicroscopy (EM) in negative staining. The amount of cross
+ beta-pleated sheet structure of A beta 1-40 fibrils was found to
+ decrease by metal cations in a concentration-dependent manner as
+ measured by ThT fluorescence spectroscopy. The order of
+ defibrillization of A beta 1-40 fibrils by metal cations was: Ca2+
+ and Zn2+ (IC50 = 100 microM) > Mg3+ (IC50 = 300 microM) > Al3+
+ (IC50 = 1.1 mM). EM analysis in negative staining showed that A
+ beta 1-40 fibrils in the absence of cations were organized in a
+ fine network with a little or no amorphous material. The addition
+ of Ca2+, Mg2+, and Zn2+ to preformed A beta 1-40 fibrils
+ defibrillized the fibrils or converted them into short rods or to
+ amorphous material. Al3+ was less effective, and reduced the
+ fibril network by about 80\% of that in the absence of any metal
+ cation. Studies with A beta 1-42 showed that this peptide forms
+ more dense network of fibrils as compared to A beta 1-40. Both ThT
+ fluorescence spectroscopy and EM showed that similar to A beta
+ 1-40, A beta 1-42 fibrils are also defibrillized in the presence
+ of millimolar concentrations of Ca2+. These studies suggest that
+ metal cations can defibrillize the fibrils of synthetic A beta.},
+ note = {From page 806, ``The exact mechanism by which these metal
+ ions affect the fibrillization of A$\beta$ is not known.''},
+}
+
+@article{ friedman05,
+ author = RFriedman #" and "# ENachliel #" and "# MGutman,
+ title = {Molecular dynamics of a protein surface: ion-residues
+ interactions.},
+ year = 2005,
+ month = aug,
+ day = 13,
+ address = {Laser Laboratory for Fast Reactions in Biology,
+ Department of Biochemistry, The George S. Wise Faculty
+ for Life Sciences, Tel Aviv University, Israel.},
+ journal = BPJ,
+ volume = 89,
+ number = 2,
+ pages = {768--781},
+ issn = {0006-3495},
+ doi = {10.1529/biophysj.105.058917},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/15894639},
+ language = {eng},
+ keywords = {Amino Acids},
+ keywords = {Binding Sites},
+ keywords = {Chlorine},
+ keywords = {Computer Simulation},
+ keywords = {Ions},
+ keywords = {Models, Chemical},
+ keywords = {Models, Molecular},
+ keywords = {Motion},
+ keywords = {Protein Binding},
+ keywords = {Protein Conformation},
+ keywords = {Ribosomal Protein S6},
+ keywords = {Sodium},
+ keywords = {Solutions},
+ keywords = {Static Electricity},
+ keywords = {Surface Properties},
+ keywords = {Water},
+ abstract = {Time-resolved measurements indicated that protons could
+ propagate on the surface of a protein or a membrane by a special
+ mechanism that enhanced the shuttle of the proton toward a
+ specific site. It was proposed that a suitable location of
+ residues on the surface contributes to the proton shuttling
+ function. In this study, this notion was further investigated by
+ the use of molecular dynamics simulations, where Na(+) and Cl(-)
+ are the ions under study, thus avoiding the necessity for quantum
+ mechanical calculations. Molecular dynamics simulations were
+ carried out using as a model a few Na(+) and Cl(-) ions enclosed
+ in a fully hydrated simulation box with a small globular protein
+ (the S6 of the bacterial ribosome). Three independent 10-ns-long
+ simulations indicated that the ions and the protein's surface were
+ in equilibrium, with rapid passage of the ions between the
+ protein's surface and the bulk. However, it was noted that close
+ to some domains the ions extended their duration near the surface,
+ thus suggesting that the local electrostatic potential hindered
+ their diffusion to the bulk. During the time frame in which the
+ ions were detained next to the surface, they could rapidly shuttle
+ between various attractor sites located under the electrostatic
+ umbrella. Statistical analysis of the molecular dynamics and
+ electrostatic potential/entropy consideration indicated that the
+ detainment state is an energetic compromise between attractive
+ forces and entropy of dilution. The similarity between the motion
+ of free ions next to a protein and the proton transfer on the
+ protein's surface are discussed.},
+}
+
+@article{ friedman11,
+ author = RFriedman,
+ title = {Ions and the protein surface revisited: extensive molecular
+ dynamics simulations and analysis of protein structures in
+ alkali-chloride solutions.},
+ year = 2011,
+ month = jul,
+ day = 28,
+ address = {School of Natural Sciences, Linn{\ae}us University,
+ 391 82 Kalmar, Sweden. ran.friedman@lnu.se},
+ journal = JPC:B,
+ volume = 115,
+ number = 29,
+ pages = {9213--9223},
+ issn = {1520-5207},
+ doi = {10.1021/jp112155m},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21688775},
+ language = {eng},
+ keywords = {Alkalies},
+ keywords = {Amyloid},
+ keywords = {Chlorides},
+ keywords = {Databases, Protein},
+ keywords = {Fungal Proteins},
+ keywords = {HIV Protease},
+ keywords = {Humans},
+ keywords = {Molecular Dynamics Simulation},
+ keywords = {Protein Multimerization},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Proteins},
+ keywords = {Ribosomal Protein S6},
+ keywords = {Solutions},
+ keywords = {Solvents},
+ keywords = {Surface Properties},
+ abstract = {Proteins interact with ions in various ways. The surface
+ of proteins has an innate capability to bind ions, and it is also
+ influenced by the screening of the electrostatic potential owing
+ to the presence of salts in the bulk solution. Alkali metal ions
+ and chlorides interact with the protein surface, but such
+ interactions are relatively weak and often transient. In this
+ paper, computer simulations and analysis of protein structures are
+ used to characterize the interactions between ions and the protein
+ surface. The results show that the ion-binding properties of
+ protein residues are highly variable. For example, alkali metal
+ ions are more often associated with aspartate residues than with
+ glutamates, whereas chlorides are most likely to be located near
+ arginines. When comparing NaCl and KCl solutions, it was found
+ that certain surface residues attract the anion more strongly in
+ NaCl. This study demonstrates that protein-salt interactions
+ should be accounted for in the planning and execution of
+ experiments and simulations involving proteins, particularly if
+ subtle structural details are sought after.},
+}
+
+@article{ zhang06,
+ author = YZhang #" and "# PSCremer,
+ title = {Interactions between macromolecules and ions: The
+ {H}ofmeister series.},
+ year = 2006,
+ month = dec,
+ day = 10,
+ address = {Department of Chemistry, Texas A\&M University,
+ College Station, TX 77843, USA.},
+ journal = COCB,
+ volume = 10,
+ number = 6,
+ pages = {658--663},
+ issn = {1367-5931},
+ doi = {10.1016/j.cbpa.2006.09.020},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/17035073},
+ language = {eng},
+ keywords = {Acrylamides},
+ keywords = {Biopolymers},
+ keywords = {Solubility},
+ keywords = {Thermodynamics},
+ keywords = {Water},
+ abstract = {The Hofmeister series, first noted in 1888, ranks the
+ relative influence of ions on the physical behavior of a wide
+ variety of aqueous processes ranging from colloidal assembly to
+ protein folding. Originally, it was thought that an ion's
+ influence on macromolecular properties was caused at least in part
+ by `making' or `breaking' bulk water structure. Recent
+ time-resolved and thermodynamic studies of water molecules in salt
+ solutions, however, demonstrate that bulk water structure is not
+ central to the Hofmeister effect. Instead, models are being
+ developed that depend upon direct ion-macromolecule interactions
+ as well as interactions with water molecules in the first
+ hydration shell of the macromolecule.},
+ note = {A quick pass through Hofmeister history, but no discussion
+ of cations (``A complete picture will inevitably involve an
+ integrated understanding of the role of cations (including
+ guanidinium ions) and osmolytes (such as urea and tri-methylamine
+ N-oxide) as well. There has been some progress in these fields,
+ although such subjects are generally beyond the scope of this
+ short review.'').},
+}
+
+@article{ isaacs06,
+ author = AMIsaacs #" and "# DBSenn #" and "# MYuan #" and "#
+ JPShine #" and "# BAYankner,
+ title = {Acceleration of Amyloid $\beta$-Peptide Aggregation by
+ Physiological Concentrations of Calcium.},
+ year = 2006,
+ month = sep,
+ day = 22,
+ address = {Department of Neurology and Division of Neuroscience,
+ The Children's Hospital, Harvard Medical School,
+ Boston, Massachusetts 02115, USA.},
+ journal = JBC,
+ volume = 281,
+ number = 38,
+ pages = {27916--27923},
+ issn = {0021-9258},
+ doi = {10.1074/jbc.M602061200},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/16870617},
+ language = {eng},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Animals},
+ keywords = {Calcium},
+ keywords = {Cells, Cultured},
+ keywords = {Copper},
+ keywords = {Neurons},
+ keywords = {Rats},
+ keywords = {Zinc},
+ abstract = {Alzheimer disease is characterized by the accumulation
+ of aggregated amyloid beta-peptide (Abeta) in the brain. The
+ physiological mechanisms and factors that predispose to Abeta
+ aggregation and deposition are not well understood. In this
+ report, we show that calcium can predispose to Abeta aggregation
+ and fibril formation. Calcium increased the aggregation of early
+ forming protofibrillar structures and markedly increased
+ conversion of protofibrils to mature amyloid fibrils. This
+ occurred at levels 20-fold below the calcium concentration in the
+ extracellular space of the brain, the site at which amyloid plaque
+ deposition occurs. In the absence of calcium, protofibrils can
+ remain stable in vitro for several days. Using this approach, we
+ directly compared the neurotoxicity of protofibrils and mature
+ amyloid fibrils and demonstrate that both species are inherently
+ toxic to neurons in culture. Thus, calcium may be an important
+ predisposing factor for Abeta aggregation and toxicity. The high
+ extracellular concentration of calcium in the brain, together with
+ impaired intraneuronal calcium regulation in the aging brain and
+ Alzheimer disease, may play an important role in the onset of
+ amyloid-related pathology.},
+ note = {Physiological levels of \NaCl\ are $\sim 150\U{mM}$. \Ca\
+ is $\sim 2\U{mM}$.},
+}
+
+@article{ itkin11,
+ author = AItkin #" and "# VDupres #" and "# YFDufrene #" and "#
+ BBechinger #" and "# JMRuysschaert #" and "# VRaussens,
+ title = {Calcium ions promote formation of amyloid $\beta$-peptide
+ (1-40) oligomers causally implicated in neuronal toxicity of
+ {A}lzheimer's disease.},
+ year = 2011,
+ month = mar,
+ day = 28,
+ address = {Laboratory of Structure and Function of Biological
+ Membranes, Center for Structural Biology and
+ Bioinformatics, Universit{\'e} Libre de Bruxelles,
+ Brussels, Belgium.},
+ journal = PLOS:ONE,
+ volume = 6,
+ number = 3,
+ pages = {e18250},
+ keywords = {Alzheimer Disease},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Blotting, Western},
+ keywords = {Calcium},
+ keywords = {Fluorescence},
+ keywords = {Humans},
+ keywords = {Ions},
+ keywords = {Models, Biological},
+ keywords = {Mutant Proteins},
+ keywords = {Neurons},
+ keywords = {Protein Structure, Quaternary},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Spectroscopy, Fourier Transform Infrared},
+ keywords = {Thiazoles},
+ ISSN = {1932-6203},
+ doi = {10.1371/journal.pone.0018250},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21464905},
+ language = {eng},
+ abstract = {Amyloid $\beta$-peptide (A$\beta$) is directly linked to
+ Alzheimer's disease (AD). In its monomeric form, A$\beta$
+ aggregates to produce fibrils and a range of oligomers, the latter
+ being the most neurotoxic. Dysregulation of Ca(2+) homeostasis in
+ aging brains and in neurodegenerative disorders plays a crucial
+ role in numerous processes and contributes to cell dysfunction and
+ death. Here we postulated that calcium may enable or accelerate
+ the aggregation of A$\beta$. We compared the aggregation pattern
+ of A$\beta$(1-40) and that of A$\beta$(1-40)E22G, an amyloid
+ peptide carrying the Arctic mutation that causes early onset of
+ the disease. We found that in the presence of Ca(2+),
+ A$\beta$(1-40) preferentially formed oligomers similar to those
+ formed by A$\beta$(1-40)E22G with or without added Ca(2+), whereas
+ in the absence of added Ca(2+) the A$\beta$(1-40) aggregated to
+ form fibrils. Morphological similarities of the oligomers were
+ confirmed by contact mode atomic force microscopy imaging. The
+ distribution of oligomeric and fibrillar species in different
+ samples was detected by gel electrophoresis and Western blot
+ analysis, the results of which were further supported by
+ thioflavin T fluorescence experiments. In the samples without
+ Ca(2+), Fourier transform infrared spectroscopy revealed
+ conversion of oligomers from an anti-parallel $\beta$-sheet to the
+ parallel $\beta$-sheet conformation characteristic of
+ fibrils. Overall, these results led us to conclude that calcium
+ ions stimulate the formation of oligomers of A$\beta$(1-40), that
+ have been implicated in the pathogenesis of AD.},
+ note = {$2\U{mM}$ of \Ca\ is the \emph{extracellular} concentration.
+ Cytosol concetrations are in the $\mu$M range.},
+}
+
+@article{ zidar11,
+ author = JZidar #" and "# FMerzel,
+ title = {Probing amyloid-beta fibril stability by increasing ionic
+ strengths.},
+ year = 2011,
+ month = mar,
+ day = 10,
+ address = {National Institute of Chemistry, Hajdrihova 19,
+ SI-1000 Ljubljana, Slovenia.},
+ journal = JPC:B,
+ volume = 115,
+ number = 9,
+ pages = {2075--2081},
+ issn = {1520-5207},
+ doi = {10.1021/jp109025b},
+ URL = {http://www.ncbi.nlm.nih.gov/pubmed/21329333},
+ language = {eng},
+ keywords = {Amyloid beta-Peptides},
+ keywords = {Entropy},
+ keywords = {Hydrogen Bonding},
+ keywords = {Molecular Dynamics Simulation},
+ keywords = {Osmolar Concentration},
+ keywords = {Protein Multimerization},
+ keywords = {Protein Stability},
+ keywords = {Protein Structure, Secondary},
+ keywords = {Solvents},
+ keywords = {Vibration},
+ abstract = {Previous experimental studies have demonstrated changing
+ the ionic strength of the solvent to have a great impact on the
+ mechanism of aggregation of amyloid-beta (A$\beta$) protein
+ leading to distinct fibril morphology at high and low ionic
+ strength. Here, we use molecular dynamics simulations to elucidate
+ the ionic strength-dependent effects on the structure and dynamics
+ of the model A$\beta$ fibril. The change in ionic strength was
+ brought forth by varying the NaCl concentration in the environment
+ surrounding the A$\beta$ fibril. Comparison of the calculated
+ vibrational spectra of A$\beta$ derived from 40 ns all-atom
+ molecular dynamics simulations at different ionic strength reveals
+ the fibril structure to be stiffer with increasing ionic
+ strength. This finding is further corroborated by the calculation
+ of the stretching force constants. Decomposition of binding and
+ dynamical properties into contributions from different structural
+ segments indicates the elongation of the fibril at low ionic
+ strength is most likely promoted by hydrogen bonding between
+ N-terminal parts of the fibril, whereas aggregation at higher
+ ionic strength is suggested to be driven by the hydrophobic
+ interaction.},
+ note = {Only study \NaCl\ over the range to $308\U{mM}$, but show a
+ general decreased hydrogen bonding as concentration increases.},
+}
+
+@article{ miao11,
+ author = LMiao #" and "# HQin #" and "# PKoehl #" and "# JSong,
+ title = {Selective and specific ion binding on proteins at
+ physiologically-relevant concentrations.},
+ year = 2011,
+ month = oct,
+ day = 03,
+ address = {Department of Biological Sciences, Faculty of Science,
+ National University of Singapore, Singapore.},
+ journal = FEBS,
+ volume = 585,
+ number = 19,
+ pages = {3126--3132},
+ issn = {1873-3468},
+ doi = {10.1016/j.febslet.2011.08.048},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/21907714},
+ language = {eng},
+ keywords = {Amino Acid Sequence},
+ keywords = {Ephrin-B2},
+ keywords = {Ions},
+ keywords = {Models, Molecular},
+ keywords = {Molecular Sequence Data},
+ keywords = {Nuclear Magnetic Resonance, Biomolecular},
+ keywords = {Protein Binding},
+ keywords = {Protein Folding},
+ keywords = {Protein Structure, Tertiary},
+ keywords = {Salts},
+ keywords = {Solutions},
+ keywords = {Thermodynamics},
+ keywords = {Water},
+ abstract = {Insoluble proteins dissolved in unsalted water appear to
+ have no well-folded tertiary structures. This raises a fundamental
+ question as to whether being unstructured is due to the absence of
+ salt ions. To address this issue, we solubilized the insoluble
+ ephrin-B2 cytoplasmic domain in unsalted water and first confirmed
+ using NMR spectroscopy that it is only partially folded. Using NMR
+ HSQC titrations with 14 different salts, we further demonstrate
+ that the addition of salt triggers no significant folding of the
+ protein within physiologically relevant ion concentrations. We
+ reveal however that their 8 anions bind to the ephrin-B2 protein
+ with high affinity and specificity at biologically-relevant
+ concentrations. Interestingly, the binding is found to be both
+ salt- and residue-specific.},
+ note = {They suggest that for low concentrations ($<100\U{mM}$),
+ protein-ion interactions are mostly electrostatic. The Hofmeister
+ effects only kick in at higher consentrations.},
+}
+
+@article{ smith13,
+ author = MDSmith #" and "# LCCruz,
+ title = {Effect of Ionic Aqueous Environments on the Structure and
+ Dynamics of the A$\beta_{21-30}$ Fragment: a Molecular-Dynamics
+ Study.},
+ year = 2013,
+ month = jun,
+ day = 6,
+ address = {Department of Physics, 3141 Chestnut Street,
+ Drexel University, Philadelphia, Pennsylvania 19104,
+ United States.},
+ journal = JPC:B,
+ volume = 117,
+ number = 22,
+ pages = {6614--6624},
+ issn = {1520-5207},
+ doi = {10.1021/jp312653h},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/23675877},
+ language = {eng},
+ abstract = {The amyloid $\beta$-protein (A$\beta$) has been
+ implicated in the pathogenesis of Alzheimer's disease. The role
+ of the structure and dynamics of the central A$\beta_{21-30}$
+ decapeptide region of the full-length A$\beta$ is considered
+ crucial in the aggregation pathway of A$\beta$. Here we report
+ results of isobaric--isothermal (NPT) all-atom explicit water
+ molecular dynamics simulations of the monomeric form of the
+ wild-type A$\beta_{21-30}$ fragment in aqueous salt environments
+ formed by neurobiologically important group IA (\NaCl, \KCl) and
+ group IIA (\CaCl, \MgCl) salts. Our simulations reveal the
+ existence of salt-specific changes to secondary structure
+ propensities, lifetimes, hydrogen bonding, salt-bridge formation,
+ and decapeptide--ion contacts of this decapeptide. These results
+ suggest that aqueous environments with the \CaCl\ salt, and to a
+ much lesser extent the \MgCl\ salt, have profound effects by
+ increasing random coil structure propensities and lifetimes and
+ diminishing intrapeptide hydrogen bonding. These effects are
+ rationalized in terms of direct cation--decapeptide contacts and
+ changes to the hydration-shell water molecules. On the other side
+ of the spectrum, environments with the \NaCl\ and \KCl\ salts have
+ little influence on the decapeptide's secondary structure despite
+ increasing hydrogen bonding, salt-bridge formation, and lifetime
+ of turn structures. The observed enhancement of open structures
+ by group IIA may be of importance in the folding and aggregation
+ pathway of the full-length A$\beta$.},
+}
+
+@article{ dyson05,
+ author = HJDyson #" and "# PEWright,
+ title = {Intrinsically unstructured proteins and their functions.},
+ journal = NRMCB,
+ year = 2005,
+ month = mar,
+ address = {Department of Molecular Biology and Skaggs Institute
+ for Chemical Biology, The Scripps Research Institute,
+ 10550 North Torrey Pines Road, La Jolla, California
+ 92037, USA. dyson@scripps.edu},
+ volume = 6,
+ number = 3,
+ pages = {197--208},
+ issn = {1471-0072},
+ doi = {10.1038/nrm1589},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/15738986},
+ language = {eng},
+ keywords = {CREB-Binding Protein},
+ keywords = {Humans},
+ keywords = {Nuclear Proteins},
+ keywords = {Nucleic Acids},
+ keywords = {Protein Binding},
+ keywords = {Protein Processing, Post-Translational},
+ keywords = {Protein Structure, Tertiary},
+ keywords = {Proteins},
+ keywords = {Trans-Activators},
+ keywords = {Tumor Suppressor Protein p53},
+ abstract = {Many gene sequences in eukaryotic genomes encode entire
+ proteins or large segments of proteins that lack a well-structured
+ three-dimensional fold. Disordered regions can be highly conserved
+ between species in both composition and sequence and, contrary to
+ the traditional view that protein function equates with a stable
+ three-dimensional structure, disordered regions are often
+ functional, in ways that we are only beginning to discover. Many
+ disordered segments fold on binding to their biological targets
+ (coupled folding and binding), whereas others constitute flexible
+ linkers that have a role in the assembly of macromolecular
+ arrays.},
+}
+
+@article{ cleland64,
+ author = WWCleland,
+ title = {Dithiothreitol, a New Protective Reagent for SH Groups},
+ journal = Biochem,
+ year = 1964,
+ month = apr,
+ volume = 3,
+ number = 4,
+ pages = {480--482},
+ keywords = {Alcohols},
+ keywords = {Chromatography},
+ keywords = {Coenzyme A},
+ keywords = {Oxidation-Reduction},
+ keywords = {Research},
+ keywords = {Sulfhydryl Compounds},
+ keywords = {Sulfides},
+ keywords = {Ultraviolet Rays},
+ issn = {0006-2960},
+ doi = {10.1021/bi00892a002},
+ url = {http://www.ncbi.nlm.nih.gov/pubmed/14192894},
+ eprint = {http://pubs.acs.org/doi/pdf/10.1021/bi00892a002},
+ language = {eng},
+}
projects / thesis.git / blobdiff