From b6543e48d37996450129523a56d136594f71aa9e Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Mon, 25 Jun 2012 19:24:10 -0400 Subject: [PATCH] Add several new citations to root.bib (mostly for the apparatus chapter). New keys: bartels03, berkemeier11, hager02 honda08 itoh04, kempe85, lo01, ma10, sakaki05, schmidt02, schmitt00, sundberg03, ulman96, --- src/root.bib | 661 ++++++++++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 648 insertions(+), 13 deletions(-) diff --git a/src/root.bib b/src/root.bib index 6f389eb..e351b5b 100644 --- a/src/root.bib +++ b/src/root.bib @@ -4,6 +4,7 @@ @string{DAbramavicius = "Abramavicius, Darius"} @string{JFAbril = "Abril, J. F."} @string{JAbu-Threideh = "Abu-Threideh, J."} +@string{KAdachi = "Adachi, Kengo"} @string{MDAdams = "Adams, M. D."} @string{AdvExpMedBiol = "Adv Exp Med Biol"} @string{SAinavarapu = "Ainavarapu, Sri Rama Koti"} @@ -18,11 +19,12 @@ @string{ASA = "American Statistical Association"} @string{HAn = "An, H."} @string{KNAn = "An, Kai-Nan"} +@string{ABioChem = "Analytical biochemistry"} @string{IAndricioaei = "Andricioaei, Ioan"} @string{ACIEE = "Angew. Chem. Int. Ed. Engl."} @string{ARBBS = "Annu Rev Biophys Biomol Struct"} @string{ARBC = "Annual Review of Biochemistry"} -@string{DAnselmetti = "Anselmetti, D."} +@string{DAnselmetti = "Anselmetti, Dario"} @string{AMC = "Applied Mathematics and Computation"} @string{SArcidiacono = "Arcidiacono, S"} @string{CArciola = "Arciola, Carla Renata"} @@ -31,6 +33,7 @@ @string{AAwe = "Awe, A."} @string{SBedard = "B\'edard, Sabrina"} @string{WBaase = "Baase, Walter A."} +@string{YBaba = "Baba, Y."} @string{HBaden = "Baden, H."} @string{CBadilla = "Badilla, Carmen L."} @string{VBafna = "Bafna, V."} @@ -45,17 +48,20 @@ @string{MBarnstead = "Barnstead, M."} @string{DBarrick = "Barrick, Doug"} @string{IBarrow = "Barrow, I."} -@string{FWBartels = "Bartels, F. W."} +@string{FWBartels = "Bartels, Frank Wilco"} @string{BBarz = "Barz, Bogdan"} @string{TBasche = "Basche, Th."} @string{ABasu = "Basu, A."} @string{LBaugh = "Baugh, Loren"} +@string{BBaumgarth = "Baumgarth, Birgit"} @string{SBaumhueter = "Baumhueter, S."} @string{JBaxendale = "Baxendale, J."} @string{EABayer = "Bayer, Edward A."} @string{EBeasley = "Beasley, E."} @string{JBechhoefer = "Bechhoefer, John"} +@string{ABecker = "Becker, Anke"} @string{GSBeddard = "Beddard, Godfrey S."} +@string{TBeebe = "Beebe, Thomas P."} @string{KBeeson = "Beeson, K."} @string{GIBell = "Bell, G. I."} @string{FBenedetti = "Benedetti, Fabrizio"} @@ -77,7 +83,8 @@ @string{Biochem = "Biochemistry"} @string{BBABE = "Biochimica et Biophysica Acta (BBA) - Bioenergetics"} @string{BIOINFO = "Bioinformatics (Oxford, England)",} -@string{BPJ = "Biophys. J."} +@string{BPJ = "Biophysical Journal"} +%@string{BPJ = "Biophys. J."} @string{BIOSENSE = "Biosensors and Bioelectronics"} @string{BIOTECH = "Biotechnology and Bioengineering"} @string{JBirchler = "Birchler, James A."} @@ -96,6 +103,7 @@ @string{DJBrockwell = "Brockwell, David J."} @string{SBroder = "Broder, S."} @string{SBroedel = "Broedel, Sheldon E."} +@string{ABrolo = "Brolo, Alexandre G."} @string{BrooksCole = "Brooks/Cole"} @string{BDBrowerToland = "Brower-Toland, Brent D."} @string{MBrucale = "Brucale, Marco"} @@ -105,6 +113,7 @@ @string{ABuguin = "Buguin, A."} @string{ABulhassan = "Bulhassan, Ahmed"} @string{BBullard = "Bullard, Belinda"} +@string{RBunk = "Bunk, Richard"} @string{DBusam = "Busam, D."} @string{CBustamante = "Bustamante, Carlos"} @string{YBustanji = "Bustanji, Yasser"} @@ -133,6 +142,7 @@ @string{KChaturvedi = "Chaturvedi, K."} @string{CChauzy = "Chauzy, C."} @string{SChe = "Che, Shunai"} +@string{CHEMREV = "Chemical reviews"} @string{CHEM = "Chemistry (Weinheim an der Bergstrasse, Germany)"} @string{CPC = "Chemphyschem"} @string{HCChen = "Chen, H. C."} @@ -144,6 +154,7 @@ @string{VGCheung = "Cheung, V. G."} @string{YHChiang = "Chiang, Y. H."} @string{AChinwalla = "Chinwalla, A."} +@string{FChow = "Chow, Flora"} @string{JChoy = "Choy, Jason"} @string{BChu = "Chu, Benjamin"} @string{XChu = "Chu, Xueying"} @@ -181,6 +192,7 @@ @string{WDeGrado = "DeGrado, William F."} @string{PDebrunner = "Debrunner, P."} @string{ADelcher = "Delcher, A."} +@string{WDeLorbe = "DeLorbe, William J."} @string{BDelpech = "Delpech, B."} @string{Demography = "Demography"} @string{ZDeng = "Deng, Z."} @@ -256,6 +268,7 @@ @string{RFulton = "Fulton, R."} @string{TFunck = "Funck, Theodor"} @string{TFurey = "Furey, T."} +@string{SFuruike = "Furuike, Shou"} @string{GLGaborMiklos = "Gabor Miklos, G. L."} @string{AEGabrielian = "Gabrielian, A. E."} @string{WGan = "Gan, W."} @@ -269,6 +282,7 @@ @string{LAGavrilov = "Gavrilov, L. A."} @string{NSGavrilova = "Gavrilova, N. S."} @string{WGe = "Ge, W."} +@string{GENE = "Gene"} @string{CGergely = "Gergely, C."} @string{RGibbs = "Gibbs, R."} @string{DGilbert = "Gilbert, D."} @@ -285,15 +299,15 @@ @string{FGong = "Gong, F."} @string{MGorokhov = "Gorokhov, M."} @string{JHGorrell = "Gorrell, J. H."} -@string{AGrutzner = {Gr\"utzner, Anika}} @string{KGraham = "Graham, K."} @string{HLGranzier = "Granzier, Henk L."} -@string{FGrater = "Grater, Frauke"} +@string{FGrater = "Gr{\"a}ter, Frauke"} @string{EDGreen = "Green, E. D."} @string{SGGregory = "Gregory, S. G."} @string{BGropman = "Gropman, B."} @string{CGrossman = "Grossman, C."} @string{HGrubmuller = {Grubm\"uller, Helmut}} +@string{AGrutzner = {Gr\"utzner, Anika}} @string{ZGu = "Gu, Z."} @string{PGuan = "Guan, P."} @string{RGuigo = "Guig\'o, R."} @@ -303,6 +317,7 @@ @string{PHanggi = {H\"anggi, Peter}} @string{THa = "Ha, Taekjip"} @string{JHaack = "Haack, Julie A."} +@string{GHager = "Hager, Gabriele"} @string{RHajjar = "Hajjar, Roger J."} @string{AHalpern = "Halpern, A."} @string{KHalvorsen = "Halvorsen, Ken"} @@ -310,6 +325,7 @@ @string{SHannenhalli = "Hannenhalli, S."} @string{HHansma = "Hansma, H. G."} @string{PHansma = "Hansma, Paul K."} +@string{DHarbrecht = "Harbrecht, Douglas"} @string{SHarper = "Harper, Sandy"} @string{MHarris = "Harris, M."} @string{BHart = "Hart, B."} @@ -330,6 +346,7 @@ @string{JHemmerle = "Hemmerle, J."} @string{SHenderson = "Henderson, S."} @string{BHeymann = "Heymann, Berthold"} +@string{NHiaro = "Hiaro, N." @string{MEHiggins = "Higgins, M. E."} @string{LHillier = "Hillier, L."} @string{HHinssen = "Hinssen, Horst"} @@ -341,6 +358,7 @@ @string{WHoff = "Hoff, Wouter D."} @string{JLHolden = "Holden, J. L."} @string{RAHolt = "Holt, R. A."} +@string{MHonda = "Honda, M."} @string{XHong = "Hong, Xia"} @string{LHood = "Hood, L."} @string{JHoover = "Hoover, J."} @@ -367,6 +385,7 @@ @string{SImprota = "Improta, S."} @string{TInoue = "Inoue, Tadashi"} @string{IJBMM = "International Journal of Biological Macromolecules"} +@string{HItoh = "Itoh, Hiroyasu"} @string{AIrback = "Irback, Anders"} @string{BIsralewitz = "Isralewitz, B."} @string{SIstrail = "Istrail, S."} @@ -377,7 +396,9 @@ @string{JACS = "Journal of the American Chemical Society"} @string{JBM = "J Biomech"} @string{JBT = "J Biotechnol"} +@string{JEChem = "Journal of Electroanalytical Chemistry"} @string{JMathBiol = "J Math Biol"} +@string{JStructBiol = "Journal of structural biology"} @string{JTB = "J Theor Biol"} @string{WJang = "Jang, W."} @string{LJanosi = "Janosi, Lorant"} @@ -389,6 +410,7 @@ @string{RRJi = "Ji, R. R."} @string{YJia = "Jia, Yiwei"} @string{SJiang = "Jiang, Shaoyi"} +@string{XJiang = "Jiang, Xingqun"} @string{DJohannsmann = "Johannsmann, Diethelm"} @string{CJohnson = "Johnson, Colin P."} @string{JJohnson = "Johnson, J."} @@ -402,6 +424,7 @@ @string{JCompP = "Journal of Computational Physics"} @string{JMB = "Journal of Molecular Biology"} @string{JP:CM = "Journal of Physics: Condensed Matter"} +@string{JP:CON = "Journal of Physics: Conference Series"} @string{JASA = "Journal of the American Statistical Association"} @string{DAJuckett = "Juckett, D. A."} @string{SRJun = "Jun, Se-Ran"} @@ -417,15 +440,16 @@ @string{KKawasaki = "Kawasaki, K."} @string{ZKe = "Ke, Z."} @string{AKejariwal = "Kejariwal, A."} -@string{MKellermayer = "Kellermayer, M."} -@string{MSKellermayer = "Kellermayer, M. S."} -@string{MSZKellermayer = "Kellermayer, Mikl\'os S. Z."} +@string{MSKellermayer = "Kellermayer, Mikl\'os S. Z."} +@string{TKempe = "Kempe, Thomas"} @string{SKennedy = "Kennedy, S."} +@string{SBHKent = "Kent, Stephen B. H."} @string{WJKent = "Kent, W. J."} @string{KAKetchum = "Ketchum, K. A."} @string{FKienberger = "Kienberger, Ferry"} @string{SHKim = "Kim, Sung-Hou"} @string{WKing = "King, William Trevor"} +@string{KKinosita = "{Kinosita Jr.}, Kazuhiko"} @string{IRKirsch = "Kirsch, I. R."} @string{JKlafter = "Klafter, J."} @string{AKleiner = "Kleiner, Ariel"} @@ -477,6 +501,7 @@ @string{ALevitsky = "Levitsky, A."} @string{SLevy = "Levy, S."} @string{MLewis = "Lewis, M."} +@string{JLItalien = "L'Italien, James J."} @string{BLi = "Li, Bing"} @string{CYLi = "Li, Christopher Y."} @string{HLi = "Li, Hongbin"} @@ -493,6 +518,7 @@ @string{JLin = "Lin, Jianhua"} @string{SHLin = "Lin, Sheng-Hsien"} @string{XLin = "Lin, X."} +@string{JLindahl = "Lindahl, Joakim"} @string{WALinke = "Linke, Wolfgang A."} @string{RLippert = "Lippert, R."} @string{JLis = "Lis, John T."} @@ -500,6 +526,7 @@ @string{WLiu = "Liu, W."} @string{XLiu = "Liu, X."} @string{YLiu = "Liu, Yichun"} +@string{YSLo = "Lo, Yu-Shiu"} @string{GLois = "Lois, Gregg"} @string{JLopez = "Lopez, J."} @string{LANL = "Los Alamos National Laboratory"} @@ -508,11 +535,12 @@ @string{FLu = "Lu, F."} @string{HLu = "Lu, Hui"} @string{QLu = "Lu, Qinghua"} -@string{MLudwig = "Ludwig, M."} +@string{MLudwig = "Ludwig, Markus"} @string{ZPLuo = "Luo, Zong-Ping"} @string{ZLuthey-Schulten = "Luthey-Schulten, Z."} @string{EMunck = {M\"unck, E.}} @string{DMa = "Ma, D."} +@string{LMa = "Ma, Liang"} @string{MMaaloum = "Maaloum, Mounir"} @string{Macromol = "Macromolecules"} @string{AMadan = "Madan, A."} @@ -525,6 +553,7 @@ @string{EMandello = "Mandello, Enrico"} @string{GManderson = "Manderson, Gavin"} @string{FMann = "Mann, F."} +@string{AMansson = "M{\aa}nsson, Alf"} @string{ERMardis = "Mardis, E. R."} @string{JMarion = "Marion, J."} @string{JFMarko = "Marko, John F."} @@ -568,6 +597,8 @@ @string{PJMohr = "Mohr, Peter J."} @string{VMontana = "Montana, Vedrana"} @string{LMontanaro = "Montanaro, Lucio"} +@string{LMontelius = "Montelius, Lars"} +@string{CMontemagno = "Montemagno, Carlo D."} @string{KTMontgomery = "Montgomery, K. T."} @string{HMMoore = "Moore, H. M."} @string{MMorgan = "Morgan, Michael"} @@ -576,6 +607,7 @@ @string{VMoy = "Moy, Vincent T."} @string{SMukamel = "Mukamel, Shaul"} @string{PMundel = "Mundel, P."} +@string{EMuneyuki = "Muneyuki, Eiro"} @string{RJMural = "Mural, R. J."} @string{BMurphy = "Murphy, B."} @string{SMurphy = "Murphy, S."} @@ -607,9 +639,11 @@ @string{NNguyen = "Nguyen, N."} @string{TNguyen = "Nguyen, T."} @string{MNguyen-Duong = "Nguyen-Duong, M."} +@string{INicholls = "Nicholls, Ian A."} @string{SNie = "Nie, S."} @string{MNodell = "Nodell, M."} @string{AANoegel = "Noegel, Angelika A."} +@string{HNoji = "Noji, Hiroyuki"} @string{RNome = "Nome, Rene A."} @string{NNowak = "Nowak, N."} @string{ANoy = "Noy, Aleksandr"} @@ -626,6 +660,7 @@ @string{PDOlmsted = "Olmsted, Peter D."} @string{AOlsen = "Olsen, A."} @string{SJOlshansky = "Olshansky, S. J."} +@string{POmling = {Omlink, P{\"a}r}} @string{JNOnuchic = "Onuchic, J. N."} @string{YOono = "Oono, Y."} @string{COpitz = "Optiz, Christiane A."} @@ -647,6 +682,7 @@ @string{OPerisic = "Perisic, Ognjen"} @string{CPeterson = "Peterson, Craig L."} @string{MPeterson = "Peterson, M."} +@string{SMPeterson = "Peterson, Susan M."} @string{CPfannkoch = "Pfannkoch, C."} @string{PA = "Pflugers Arch"} @string{PTRSL = "Philosophical Transactions of the Royal Society of London"} @@ -654,13 +690,16 @@ @string{PRL = "Phys Rev Lett"} @string{Physica = "Physica"} @string{GPing = "Ping, Guanghui"} +@string{NPinotsis = "Pinotsis, Nikos"} +@string{DPlunkett = "Plunkett, David"} @string{PPodsiadlo = "Podsiadlo, Paul"} @string{ASPolitou = "Politou, A. S."} @string{APoustka = "Poustka, A."} @string{GPratesi = "Pratesi, G."} @string{EPratts = "Pratts, E."} @string{WPress = "Press, W."} -@string{PNAS = "Proceedings of the National Academy of Sciences USA"} +@string{PNAS = "Proceedings of the National Academy of Sciences of the + United States of America"} @string{PBPMB = "Progress in Biophysics and Molecular Biology"} @string{PS = "Protein Science"} @string{PROT = "Proteins"} @@ -697,8 +736,9 @@ @string{SRogic = "Rogic, S."} @string{MRoman = "Roman, Marisa"} @string{DRomblad = "Romblad, D."} -@string{RRos = "Ros, R."} +@string{RRos = "Ros, Robert"} @string{BRosenberg = "Rosenberg, B."} +@string{JRosengren = "Rosengren, Jenny P."} @string{ARosenthal = "Rosenthal, A."} @string{ARoters = "Roters, Andreas"} @string{WRowe = "Rowe, W."} @@ -706,6 +746,7 @@ @string{BRuhfel = "Ruhfel, B."} @string{DBRusch = "Rusch, D. B."} @string{JPRyckaert = "Ryckaert, Jean-Paul"} +@string{NSakaki = "Sakaki, Naoyoshi"} @string{YSakaki = "Sakaki, Y."} @string{SSalzberg = "Salzberg, S."} @string{BSamori = "Samor{\`i}, Bruno"} @@ -723,6 +764,8 @@ @string{BSchlegelberger = "Schlegelberger, B."} @string{MSchleicher = "Schleicher, Michael"} @string{MSchlierf = "Schlierf, Michael"} +@string{JSchmidt = "Schmidt, Jacob J."} +@string{LSchmitt = "Schmitt, Lutz"} @string{JSchmutz = "Schmutz, J."} @string{GSchuler = "Schuler, G."} @string{GDSchuler = "Schuler, G. D."} @@ -737,6 +780,7 @@ @string{RScott = "Scott, R."} @string{USeifert = "Seifert, Udo"} @string{MSekhon = "Sekhon, M."} +@string{TSekiguchi = "Sekiguchi, T."} @string{BSenger = "Senger, B."} @string{PSeranski = "Seranski, P."} @string{RSesboue = {Sesbo\"u\'e, R.}} @@ -750,6 +794,7 @@ @string{JShillcock = "Shillcock, Julian"} @string{AShimizu = "Shimizu, A."} @string{NShimizu = "Shimizu, N."} +@string{RShimoKon = "Shimo-Kon, Rieko"} @string{AShintani = "Shintani, A."} @string{BShue = "Shue, B."} @string{RSiebert = "Siebert, R."} @@ -798,13 +843,18 @@ @string{ESuh = "Suh, E."} @string{JSun = "Sun, J."} @string{YLSun = "Sun, Yu-Long"} +@string{MSundberg = "Sundberg, Mark"} +@string{WSundquist = "Sundquist, Wesley I."} @string{KSurewicz = "Surewicz, Krystyna"} @string{WKSurewicz = "Surewicz, Witold K."} @string{GGSutton = "Sutton, G. G."} @string{ASzabo = "Szabo, Attila"} +@string{STagerud = "T{\aa}gerud, Sven"} @string{PTabor = "Tabor, P."} +@string{ATakahashi = "Takahashi, Akiri"} @string{DTalaga = "Talaga, David S."} @string{PTalkner = "Talkner, Peter"} +@string{RTampe = "Tamp{\'e}, Robert"} @string{JTang = "Tang, Jianyong"} @string{BNTaylor = "Taylor, Barry N."} @string{STeukolsky = "Teukolsky, S."} @@ -833,8 +883,10 @@ @string{JCMTsibris = "Tsibris, J.C.M."} @string{LTskhovrebova = "Tskhovrebova, Larissa"} @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{KJVanVliet = "Van Vliet, Krystyn J."} @string{CVech = "Vech, C."} @@ -878,6 +930,7 @@ @string{Williams = "Williams"} @string{MWilliams = "Williams, M."} @string{SWilliams = "Williams, S."} +@strinf{MWilmanns = "Wilmanns, Matthias"} @string{RKWilson = "Wilson, R. K."} @string{SWilson = "Wilson, Scott"} @string{SWindsor = "Windsor, S."} @@ -900,16 +953,19 @@ @string{JXi = "Xi, Jun"} @string{AXia = "Xia, A."} @string{CXiao = "Xiao, C."} +@string{SXiao = "Xiao, Senbo"} @string{TYada = "Yada, T."} @string{CYan = "Yan, C."} @string{MYandell = "Yandell, M."} @string{GYang = "Yang, Guoliang"} @string{YYang = "Yang, Yao"} @string{AYao = "Yao, A."} +@string{RYasuda = "Yaduso, Ryohei"} @string{JYe = "Ye, J."} @string{RYeh = "Yeh, Richard C."} @string{RYonescu = "Yonescu, R."} @string{SYooseph = "Yooseph, S."} +@string{MYoshida = "Yoshida, Masasuke"} @string{WYu = "Yu, Weichang"} @string{JMYuan = "Yuan, Jian-Min"} @string{AZandieh = "Zandieh, A."} @@ -933,6 +989,7 @@ @string{HXZhou = "Zhou, Huan-Xiang"} @string{SZhu = "Zhu, S."} @string{XZhu = "Zhu, X."} +@string{YJZhu = "Zhu, Ying-Jie"} @string{WZhuang = "Zhuang, Wei"} @string{NZinder = "Zinder, N."} @string{RCZinober = "Zinober, Rebecca C."} @@ -2304,6 +2361,57 @@ later." } +@article{ berkemeier11, + author = FBerkemeier #" and "# MBertz #" and "# SXiao #" and "# + NPinotsis #" and "# MWilmanns #" and "# FGrater #" and "# MRief, + title = "Fast-folding $\alpha$-helices as reversible strain absorbers + in the muscle protein myomesin.", + journal = PNAS, + year = 2011, + month = aug, + day = 23, + address = "Physik Department E22, Technische Universit{\"a}t + M{\"u}nchen, James-Franck-Stra{\ss}e, 85748 Garching, Germany.", + volume = 108, + number = 34, + pages = "14139--14144", + keywords = "Biomechanics", + keywords = "Kinetics", + keywords = "Microscopy, Atomic Force", + keywords = "Molecular Dynamics Simulation", + keywords = "Muscle Proteins", + keywords = "Protein Folding", + keywords = "Protein Multimerization", + keywords = "Protein Stability", + keywords = "Protein Structure, Secondary", + keywords = "Protein Structure, Tertiary", + keywords = "Protein Unfolding", + abstract = "The highly oriented filamentous protein network of + muscle constantly experiences significant mechanical load during + muscle operation. The dimeric protein myomesin has been identified + as an important M-band component supporting the mechanical + integrity of the entire sarcomere. Recent structural studies have + revealed a long $\alpha$-helical linker between the C-terminal + immunoglobulin (Ig) domains My12 and My13 of myomesin. In this + paper, we have used single-molecule force spectroscopy in + combination with molecular dynamics simulations to characterize + the mechanics of the myomesin dimer comprising immunoglobulin + domains My12-My13. We find that at forces of approximately 30?pN + the $\alpha$-helical linker reversibly elongates allowing the + molecule to extend by more than the folded extension of a full + domain. High-resolution measurements directly reveal the + equilibrium folding/unfolding kinetics of the individual helix. We + show that $\alpha$-helix unfolding mechanically protects the + molecule homodimerization from dissociation at physiologically + relevant forces. As fast and reversible molecular springs the + myomesin $\alpha$-helical linkers are an essential component for + the structural integrity of the M band.", + ISSN = "1091-6490", + doi = "10.1073/pnas.1105734108", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/21825161", + language = "eng", +} + @article { dill97, author = KADill #" and "# HSChan, title = "From Levinthal to pathways to funnels.", @@ -3036,7 +3144,7 @@ } @article { granzier97, - author = HLGranzier #" and "# MKellermayer #" and "# MHelmes #" and "# + author = HLGranzier #" and "# MSKellermayer #" and "# MHelmes #" and "# KTrombitas, title = "Titin elasticity and mechanism of passive force development in rat cardiac myocytes probed by thin-filament extraction", @@ -3609,7 +3717,7 @@ } @article { kellermayer03, - author = MSZKellermayer #" and "# CBustamante #" and "# HLGranzier, + author = MSKellermayer #" and "# CBustamante #" and "# HLGranzier, title = "Mechanics and structure of titin oligomers explored with atomic force microscopy", year = 2003, @@ -5690,6 +5798,64 @@ between theory and rupture data from several different experiments." } +@article{ bartels03, + author = FWBartels #" and "# BBaumgarth #" and "# DAnselmetti + #" and "# RRos #" and "# ABecker, + title = "Specific binding of the regulatory protein Exp{G} to + promoter regions of the galactoglucan biosynthesis gene cluster of + Sinorhizobium meliloti--a combined molecular biology and force + spectroscopy investigation.", + journal = JStructBiol, + year = 2003, + month = aug, + address = "Experimentelle Biophysik, Fakult{\"a}t f{\"u}r Physik, + Universit{\"a}t Bielefeld, 33615 Bielefeld, Germany.", + volume = 143, + number = 2, + pages = "145--152", + keywords = "Base Sequence", + keywords = "Binding Sites", + keywords = "Conserved Sequence", + keywords = "Fungal Proteins", + keywords = "Galactans", + keywords = "Glucans", + keywords = "Kinetics", + keywords = "Microscopy, Atomic Force", + keywords = "Multigene Family", + keywords = "Polysaccharides, Bacterial", + keywords = "Promoter Regions, Genetic", + keywords = "Protein Binding", + keywords = "Sinorhizobium meliloti", + keywords = "Trans-Activators", + abstract = "Specific protein-DNA interaction is fundamental for all + aspects of gene transcription. We focus on a regulatory + DNA-binding protein in the Gram-negative soil bacterium + Sinorhizobium meliloti 2011, which is capable of fixing molecular + nitrogen in a symbiotic interaction with alfalfa plants. The ExpG + protein plays a central role in regulation of the biosynthesis of + the exopolysaccharide galactoglucan, which promotes the + establishment of symbiosis. ExpG is a transcriptional activator of + exp gene expression. We investigated the molecular mechanism of + binding of ExpG to three associated target sequences in the exp + gene cluster with standard biochemical methods and single molecule + force spectroscopy based on the atomic force microscope + (AFM). Binding of ExpG to expA1, expG-expD1, and expE1 promoter + fragments in a sequence specific manner was demonstrated, and a 28 + bp conserved region was found. AFM force spectroscopy experiments + confirmed the specific binding of ExpG to the promoter regions, + with unbinding forces ranging from 50 to 165 pN in a logarithmic + dependence from the loading rates of 70-79000 pN/s. Two different + regimes of loading rate-dependent behaviour were + identified. Thermal off-rates in the range of k(off)=(1.2+/-1.0) x + 10(-3)s(-1) were derived from the lower loading rate regime for + all promoter regions. In the upper loading rate regime, however, + these fragments exhibited distinct differences which are + attributed to the molecular binding mechanism.", + ISSN = "1047-8477", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/12972351", + language = "eng", +} + @article { rief02, author = MRief #" and "# HGrubmuller, title = "Force spectroscopy of single biomolecules", @@ -5833,6 +5999,57 @@ to be 20 +/- 3 pN and for A-T to be 9 +/- 3 pN." } +@article{ schmitt00, + author = LSchmitt #" and "# MLudwig #" and "# HEGaub #" and "# RTampe, + title = "A metal-chelating microscopy tip as a new toolbox for + single-molecule experiments by atomic force microscopy.", + journal = BPJ, + year = 2000, + month = jun, + address = "Institut f{\"u}r Physiologische Chemie, + Philipps-Universit{\"a}t Marburg, 35033 Marburg, + Germany. schmittl@mailer.uni-marburg.de", + volume = 78, + number = 6, + pages = "3275--3285", + keywords = "Chelating Agents", + keywords = "Edetic Acid", + keywords = "Histidine", + keywords = "Metals", + keywords = "Microscopy, Atomic Force", + keywords = "Nitrilotriacetic Acid", + keywords = "Peptides", + keywords = "Recombinant Fusion Proteins", + abstract = "In recent years, the atomic force microscope (AFM) has + contributed much to our understanding of the molecular forces + involved in various high-affinity receptor-ligand + systems. However, a universal anchor system for such measurements + is still required. This would open up new possibilities for the + study of biological recognition processes and for the + establishment of high-throughput screening applications. One such + candidate is the N-nitrilo-triacetic acid (NTA)/His-tag system, + which is widely used in molecular biology to isolate and purify + histidine-tagged fusion proteins. Here the histidine tag acts as a + high-affinity recognition site for the NTA chelator. Accordingly, + we have investigated the possibility of using this approach in + single-molecule force measurements. Using a histidine-peptide as a + model system, we have determined the binding force for various + metal ions. At a loading rate of 0.5 microm/s, the determined + forces varied from 22 +/- 4 to 58 +/- 5 pN. Most importantly, no + interaction was detected for Ca(2+) and Mg(2+) up to + concentrations of 10 mM. Furthermore, EDTA and a metal ion + reloading step demonstrated the reversibility of the + approach. Here the molecular interactions were turned off (EDTA) + and on (metal reloading) in a switch-like fashion. Our results + show that the NTA/His-tag system will expand the ``molecular + toolboxes'' with which receptor-ligand systems can be investigated + at the single-molecule level.", + ISSN = "0006-3495", + doi = "10.1016/S0006-3495(00)76863-9", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/10828003", + language = "eng", +} + @article { roters96, author = ARoters #" and "# DJohannsmann, title = "Distance-dependent noise measurements in scanning force @@ -7801,3 +8018,421 @@ URL = "http://www.ncbi.nlm.nih.gov/pubmed/19336443", language = "eng", } + +@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 + monomeric peptides from large multimeric fusion proteins.", + journal = GENE, + year = 1985, + volume = 39, + number = "2-3", + pages = "239--245", + keywords = "Cloning, Molecular", + keywords = "Cyanogen Bromide", + keywords = "DNA, Recombinant", + keywords = "Escherichia coli", + keywords = "Gene Expression Regulation", + keywords = "Genetic Vectors", + keywords = "Humans", + keywords = "Molecular Weight", + keywords = "Peptide Fragments", + keywords = "Plasmids", + keywords = "Substance P", + keywords = "beta-Galactosidase", + abstract = "A vector system has been designed for obtaining high + yields of polypeptides synthesized in Escherichia coli. Multiple + copies of a synthetic gene encoding the neuropeptide substance P + (SP) (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Met-NH2) have been + linked and fused to the lacZ gene. Each copy of the SP gene was + flanked by codons for methionine to create sites for cleavage by + cyanogen bromide (CNBr). The isolated multimeric SP fusion + protein was converted to monomers of SP analog, each containing a + carboxyl-terminal homoserine lactone (Hse-lactone) residue + (Arg-Pro-Lys-Pro-Gln-Gln-Phe-Phe-Gly-Leu-Hse-lactone), upon + treatment with CNBr in formic acid. The Hse-lactone moiety was + subjected to chemical modifications to produce an SP Hse + amide. This method permits synthesis of peptide amide analogs and + other peptide derivatives by combining recombinant DNA techniques + and chemical methods.", + ISSN = "0378-1119", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/2419204", + language = "eng", +} + +@article{ honda08 + author = MHonda #" and "# YBaba #" and "# NHiaro #" and "# TSekiguchi, + title = "Metal-molecular interface of sulfur-containing amino acid + and thiophene on gold surface", + journal = JP:CON, + volume = 100, + number = 5, + pages = "052071", + url = "http://dx.doi.org/10.1088/1742-6596/100/5/052071", + year = 2008, + abstract = "Chemical-bonding states of metal-molecular interface + have been investigated for L-cysteine and thiophene on gold by + x-ray photoelectron spectroscopy (XPS) and near edge x-ray + adsorption fine structure (NEXAFS). A remarkable difference in + Au-S bonding states was found between L-cysteine and + thiophene. For mono-layered L-cysteine on gold, the binding energy + of S 1s in XPS and the resonance energy at the S K-edge in NEXAFS + are higher by 8–9 eV than those for multi-layered film (molecular + L-cysteine). In contrast, the S K-edge resonance energy for + mono-layered thiophene on gold was 2475.0 eV, which is the same as + that for molecular L-cysteine. In S 1s XPS for mono-layered + thiophene, two peaks were observed. The higher binging-energy and + more intense peak at 2473.4 eV are identified as gold sulfide. The + binding energy of smaller peak, whose intensity is less than 1/3 + of the higher binding energy peak, is 2472.2 eV, which is the same + as that for molecular thiophene. These observations indicate that + Au-S interface behavior shows characteristic chemical bond only + for the Au-S interface of L-cysteine monolayer on gold + substrate.", +} + +@article{ ulman96, + author = AUlman, + title = "Formation and Structure of Self-Assembled Monolayers.", + journal = CHEMREV, + year = 1996, + month = jun, + day = 20, + address = "Department of Chemical Engineering, Chemistry and + Materials Science, and the Herman F. Mark Polymer Research + Institute, Polytechnic University, Six MetroTech Center, Brooklyn, + New York 11201.", + volume = 96, + number = 4, + pages = "1533--1554", + ISSN = "1520-6890", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/11848802", + language = "eng", +} + +@article{ hager02 + author = GHager #" and "# ABrolo, + title = "Adsorption/desorption behaviour of cysteine and cystine in + neutral and basic media: electrochemical evidence for differing + thiol and disulfide adsorption to a {Au(111)} single crystal + electrode", + journal = JEChem, + volume = "550--551", + number = 0, + pages = "291--301", + year = 2003, + issn = "1572-6657", + doi = "10.1016/S0022-0728(03)00052-4", + url = "http://www.sciencedirect.com/science/article/pii/S0022072803000524", + keywords = "Thiol", + keywords = "Disulfide", + keywords = "Thiol adsorption", + keywords = "Self-assembled monolayers", + keywords = "Au(111) single crystal electrode", + keywords = "Cysteine", + keywords = "Cystine", + abstract = "The adsorption/desorption behaviour of the + thiol/disulfide redox couple, cysteine/cystine, was monitored at a + Au(111) single crystal electrode. The monolayers were formed + electrochemically from 0.1 M KClO4 and 0.1 M NaOH solutions + containing either the thiol or the disulfide. Distinct features in + the adsorption potential were noted. An adsorption peak was + observed in the cyclic voltammograms (CVs) from Au(111) in 0.1 M + KClO4 solutions containing cystine at $-0.57$ V vs. saturated + calomel electrode. Under the same conditions, the CVs from + solutions containing cysteine showed an adsorption peak at $-0.43$ + V (0.14 V more positive than the corresponding peak from disulfide + solutions). This showed that the thiol and disulfide species have + different adsorption properties. Similar behaviour was observed in + 0.1 M NaOH. Cyclic voltammetric and chronocoulometric data were + employed to determine the surface coverage of the different + monolayers. Cysteine solutions prepared in 0.1 M KClO4 provided + coverages of $3.0\times10^{-10}$ and $2.5\times10^{-10}$ + mol~cm$^{-2}$ for the L and the D--L species, respectively as + evaluated from the desorption peaks. Desorption of cystine in the + same medium yielded coverages of $1.2\times10^{-10}$ mol~cm$^{-2}$ + for both L and D--L solutions (or $2.4\times10^{-10}$ + mol~cm$^{-2}$ in cysteine equivalents). Surface coverages obtained + from Au(111) in 0.1 M NaOH corresponded to $3.9\times10^{10}$ + mol~cm$^{-2}$ for L-cysteine, and $1.2\times10^{-10}$ + mol~cm$^{-2}$ (or $2.4\times10^{-10}$ mol~cm$^{-2}$ cysteine + equivalents) for L and D--L cystine.", +} + +@phdthesis{ ma10, + author = LMa, + title = "The Nanomechanics of Polycystin-1: A Kidney Mechanosensor", + school = UTMB, + year = 2010, + month = aug, + url = "http://etd.utmb.edu/theses/available/etd-07072010-132038/", + keywords = "ADPKD", + keywords = "Polycystin-1", + keywords = "Missense mutations", + keywords = "Atomic Force Microscopy", + keywords = "Osmolyte", + keywords = "Mechanosensor", + abstract = "Mutations in polycystin-1 (PC1) can cause Autosomal + Dominant Polycystic Kidney Disease (ADPKD), which is a leading + cause of renal failure. The available evidence suggests that PC1 + acts as a mechanosensor, receiving signals from the primary cilia, + neighboring cells, and extracellular matrix. PC1 is a large + membrane protein that has a long N-terminal extracellular region + (about 3000 aa) with a multimodular structure including sixteen + Ig-like PKD domains, which are targeted by many naturally + occurring missense mutations. Nothing is known about the effects + of these mutations on the biophysical properties of PKD + domains. In addition, PC1 is expressed along the renal tubule, + where it is exposed to a wide range of concentration of urea. Urea + is known to destabilize proteins. Other osmolytes found in the + kidney such as sorbitol, betaine and TMAO are known to counteract + urea's negative effects on proteins. Nothing is known about how + the mechanical properties of PC1 are affected by these + osmolytes. Here I use nano-mechanical techniques to study the + effects of missense mutations and effects of denaturants and + various osmolytes on the mechanical properties of PKD + domains. Several missense mutations were found to alter the + mechanical stability of PKD domains resulting in distinct + mechanical phenotypes. Based on these findings, I hypothesize that + missense mutations may cause ADPKD by altering the stability of + the PC1 ectodomain, thereby perturbing its ability to sense + mechanical signals. I also found that urea has a significant + impact on both the mechanical stability and refolding rate of PKD + domains. It not only lowers their mechanical stability, but also + slows down their refolding rate. Moreover, several osmolytes were + found to effectively counteract the effects of urea. Our data + provide the evidence that naturally occurring osmolytes can help + to maintain Polycystin-1 mechanical stability and folding + kinetics. This study has the potential to provide new therapeutic + approaches (e.g. through the use of osmolytes or chemical + chaperones) for rescuing destabilized and misfolded PKD domains.", + language = "eng", +} + +@article{ sundberg03, + author = MSundberg #" and "# JRosengren #" and "# RBunk + #" and "# JLindahl #" and "# INicholls #" and "# STagerud + #" and "# POmling #" and "# LMontelius #" and "# AMansson, + title = "Silanized surfaces for in vitro studies of actomyosin + function and nanotechnology applications.", + journal = ABioChem, + year = 2003, + month = dec, + day = 01, + address = "Department of Chemistry and Biomedical Sciences, + University of Kalmar, SE-391 82 Kalmar, Sweden.", + volume = 323, + number = 1, + pages = "127--138", + keywords = "Actomyosin", + keywords = "Adsorption", + keywords = "Animals", + keywords = "Collodion", + keywords = "Kinetics", + keywords = "Methods", + keywords = "Movement", + keywords = "Nanotechnology", + keywords = "Rabbits", + keywords = "Silicon", + keywords = "Surface Properties", + keywords = "Trimethylsilyl Compounds", + abstract = "We have previously shown that selective heavy meromyosin + (HMM) adsorption to predefined regions of nanostructured polymer + resist surfaces may be used to produce a nanostructured in vitro + motility assay. However, actomyosin function was of lower quality + than on conventional nitrocellulose films. We have therefore + studied actomyosin function on differently derivatized glass + surfaces with the aim to find a substitute for the polymer + resists. We have found that surfaces derivatized with + trimethylchlorosilane (TMCS) were superior to all other surfaces + tested, including nitrocellulose. High-quality actin filament + motility was observed up to 6 days after incubation with HMM and + the fraction of motile actin filaments and the velocity of smooth + sliding were generally higher on TMCS than on nitrocellulose. The + actomyosin function on TMCS-derivatized glass and nitrocellulose + is considered in relation to roughness and hydrophobicity of these + surfaces. The results suggest that TMCS is an ideal substitute for + polymer resists in the nanostructured in vitro motility + assay. Furthermore, TMCS derivatized glass also seems to offer + several advantages over nitrocellulose for HMM adsorption in the + ordinary in /vitro motility assay.", + ISSN = "0003-2697", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/14622967", + doi = "10.1016/j.ab.2003.07.022", + language = "eng", +} + +@article{ itoh04, + author = HItoh #" and "# ATakahashi #" and "# KAdachi #" and "# + HNoji #" and "# RYasuda #" and "# MYoshida #" and "# + KKinosita, + title = "Mechanically driven {ATP} synthesis by {F1}-{ATP}ase.", + journal = NAT, + year = 2004, + month = jan, + day = 29, + address = "Tsukuba Research Laboratory, Hamamatsu Photonics KK, + Joko, Hamamatsu 431-3103, Japan. + hiritoh@hpk.trc-net.co.jp", + volume = 427, + number = 6973, + pages = "465--468", + keywords = "Adenosine Diphosphate", + keywords = "Adenosine Triphosphate", + keywords = "Bacillus", + keywords = "Catalysis", + keywords = "Glass", + keywords = "Magnetics", + keywords = "Microchemistry", + keywords = "Microspheres", + keywords = "Molecular Motor Proteins", + keywords = "Proton-Translocating ATPases", + keywords = "Rotation", + keywords = "Torque", + abstract = "ATP, the main biological energy currency, is synthesized + from ADP and inorganic phosphate by ATP synthase in an + energy-requiring reaction. The F1 portion of ATP synthase, also + known as F1-ATPase, functions as a rotary molecular motor: in + vitro its gamma-subunit rotates against the surrounding + alpha3beta3 subunits, hydrolysing ATP in three separate catalytic + sites on the beta-subunits. It is widely believed that reverse + rotation of the gamma-subunit, driven by proton flow through the + associated F(o) portion of ATP synthase, leads to ATP synthesis in + biological systems. Here we present direct evidence for the + chemical synthesis of ATP driven by mechanical energy. We attached + a magnetic bead to the gamma-subunit of isolated F1 on a glass + surface, and rotated the bead using electrical magnets. Rotation + in the appropriate direction resulted in the appearance of ATP in + the medium as detected by the luciferase-luciferin reaction. This + shows that a vectorial force (torque) working at one particular + point on a protein machine can influence a chemical reaction + occurring in physically remote catalytic sites, driving the + reaction far from equilibrium.", + ISSN = "1476-4687", + doi = "10.1038/nature02212", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/14749837", + language = "eng", +} + +@article{ sakaki05, + author = NSakaki #" and "# RShimoKon #" and "# KAdachi + #" and "# HItoh #" and "# SFuruike #" and "# EMuneyuki + #" and "# MYoshida #" and "# KKinosita, + title = "One rotary mechanism for {F1}-{ATP}ase over {ATP} + concentrations from millimolar down to nanomolar.", + journal = BPJ, + year = 2005, + month = mar, + day = 30, + address = "Department of Functional Molecular Science, The Graduate + University for Advanced Studies, Nishigonaka 38, Myodaiji, Okazaki + 444-8585, Japan.", + volume = 88, + number = 3, + pages = "2047--2056", + keywords = "Adenosine Triphosphate", + keywords = "Hydrolysis", + keywords = "Kinetics", + keywords = "Microchemistry", + keywords = "Molecular Motor Proteins", + keywords = "Nanostructures", + keywords = "Protein Binding", + keywords = "Protein Conformation", + keywords = "Proton-Translocating ATPases", + keywords = "Rotation", + keywords = "Torque", + abstract = "F(1)-ATPase is a rotary molecular motor in which the + central gamma-subunit rotates inside a cylinder made of + alpha(3)beta(3)-subunits. The rotation is driven by ATP hydrolysis + in three catalytic sites on the beta-subunits. How many of the + three catalytic sites are filled with a nucleotide during the + course of rotation is an important yet unsettled question. Here we + inquire whether F(1) rotates at extremely low ATP concentrations + where the site occupancy is expected to be low. We observed under + an optical microscope rotation of individual F(1) molecules that + carried a bead duplex on the gamma-subunit. Time-averaged rotation + rate was proportional to the ATP concentration down to 200 pM, + giving an apparent rate constant for ATP binding of 2 x 10(7) + M(-1)s(-1). A similar rate constant characterized bulk ATP + hydrolysis in solution, which obeyed a simple Michaelis-Menten + scheme between 6 mM and 60 nM ATP. F(1) produced the same torque + of approximately 40 pN.nm at 2 mM, 60 nM, and 2 nM ATP. These + results point to one rotary mechanism governing the entire range + of nanomolar to millimolar ATP, although a switchover between two + mechanisms cannot be dismissed. Below 1 nM ATP, we observed less + regular rotations, indicative of the appearance of another + reaction scheme.", + ISSN = "0006-3495", + doi = "10.1529/biophysj.104.054668", + URL = "http://www.ncbi.nlm.nih.gov/pubmed/15626703", + language = "eng", +} + +@article{ schmidt02, + author = JSchmidt #" and "# XJiang #" and "# CMontemagno, + title = "Force Tolerances of Hybrid Nanodevices", + journal = NANO, + volume = 2, + number = 11, + pages = "1229--1233", + year = 2002, + doi = "10.1021/nl025773v", + URL = "http://pubs.acs.org/doi/abs/10.1021/nl025773v", + eprint = "http://pubs.acs.org/doi/pdf/10.1021/nl025773v", + abstract = "We have created hybrid devices consisting of nanoscale + fabricated inorganic components integrated with and powered by a + genetically engineered motor protein. We wish to increase the + assembly yield and lifetime of these devices through + identification, measurement, and improvement of weak internal + bonds. Using dynamic force spectroscopy, we have measured the bond + rupture force of (histidine)\textsubscript{6} on a number of + different surfaces as a function of loading rate. The bond sizes, + lifetimes, and energy barrier heights were derived from these + measurements. We compare the (His)\textsubscript{6}--nickel bonds + to other bonds composing the hybrid device and describe + preliminary measurements of the force tolerances of the protein + itself. Pathways for improvement of device longevity and + robustness are discussed.", +} + +@article{ lo01, + author = YSLo #" and "# YJZhu #" and "# TBeebe, + title = "Loading-Rate Dependence of Individual Ligand−Receptor + Bond-Rupture Forces Studied by Atomic Force Microscopy", + journal = LANG, + volume = 17, + number = 12, + pages = "3741--3748", + year = 2001, + doi = "10.1021/la001569g", + URL = "http://pubs.acs.org/doi/abs/10.1021/la001569g", + eprint = "http://pubs.acs.org/doi/pdf/10.1021/la001569g", + abstract = "It is known that bond strength is a dynamic property + that is dependent upon the force loading rate applied during the + rupturing of a bond. For biotin--avidin and biotin--streptavidin + systems, dynamic force spectra, which are plots of bond strength + vs loge(loading rate), have been acquired in a recent biomembrane + force probe (BFP) study at force loading rates in the range + 0.05--60 000 pN/s. In the present study, the dynamic force spectrum + of the biotin--streptavidin bond strength in solution was extended + from loading rates of ∼104 to ∼107 pN/s with the atomic force + microscope (AFM). A Poisson statistical analysis method was + applied to extract the magnitude of individual bond-rupture forces + and nonspecific interactions from the AFM force--distance curve + measurements. The bond strengths were found to scale linearly with + the logarithm of the loading rate. The nonspecific interactions + also exhibited a linear dependence on the logarithm of loading + rate, although not increasing as rapidly as the specific + interactions. The dynamic force spectra acquired here with the AFM + combined well with BFP measurements by Merkel et al. The combined + spectrum exhibited two linear regimes, consistent with the view + that multiple energy barriers are present along the unbinding + coordinate of the biotin--streptavidin complex. This study + demonstrated that unbinding forces measured by different + techniques are in agreement and can be used together to obtain a + dynamic force spectrum covering 9 orders of magnitude in loading + rate.", + note = "These guys seem to be pretty thorough, give this one another read.", +} -- 2.26.2