{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T18:21:57Z","timestamp":1761675717529},"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2009,11,20]],"date-time":"2009-11-20T00:00:00Z","timestamp":1258675200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000574","type":"journal-article","created":{"date-parts":[[2009,11,19]],"date-time":"2009-11-19T22:46:54Z","timestamp":1258670814000},"page":"e1000574","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":48,"title":["Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis"],"prefix":"10.1371","volume":"5","author":[{"given":"Wolfram","family":"Stacklies","sequence":"first","affiliation":[]},{"given":"Fei","family":"Xia","sequence":"additional","affiliation":[]},{"given":"Frauke","family":"Gr\u00e4ter","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,11,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1016\/j.sbi.2006.01.003","article-title":"The changing landscape of protein allostery.","volume":"16","author":"JF Swain","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"19813","DOI":"10.1073\/pnas.0708120104","article-title":"Principles underlying energetic coupling along an allosteric communication trajectory of a voltage-activated k+ channel.","volume":"104","author":"E Sadovsky","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1002\/prot.21426","article-title":"Using molecular dynamics to map interaction networks in an aminoacyl-trna synthetase.","volume":"68","author":"ME Budiman","year":"2007","journal-title":"Proteins"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nsb881","article-title":"Evolutionary conserved networks of residues mediate allosteric communication in proteins.","volume":"10","author":"G S\u00fcel","year":"2002","journal-title":"Nature Structural Biology"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1126\/science.1159052","article-title":"Surface sites for engineering allosteric control in proteins.","volume":"322","author":"J Lee","year":"2008","journal-title":"Science"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"8311","DOI":"10.1073\/pnas.0700329104","article-title":"Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins.","volume":"104","author":"VJ Hilser","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1039\/b819720b","article-title":"Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms.","volume":"5","author":"CJ Tsai","year":"2009","journal-title":"Mol Biosyst"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1110\/ps.03259908","article-title":"Allostery and cooperativity revisited.","volume":"17","author":"Q Cui","year":"2008","journal-title":"Protein Sci"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nsmb1132","article-title":"Dynamically driven protein allostery.","volume":"13","author":"N Popovych","year":"2006","journal-title":"Nat Struct Mol Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"13111","DOI":"10.1073\/pnas.0503732102","article-title":"Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.","volume":"102","author":"JW Chu","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","article-title":"Mechanochemical coupling in the myosin motor domain. ii. analysis of critical residues.","volume":"3","author":"H Yu","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"7664","DOI":"10.1073\/pnas.0510426103","article-title":"Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations.","volume":"103","author":"W Zheng","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1038\/msb4100075","article-title":"Markov propagation of allosteric effects in biomolecular systems: application to groel-groes.","volume":"2","author":"C Chennubhotla","year":"2006","journal-title":"Mol Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5000","DOI":"10.1073\/pnas.82.15.5000","article-title":"Protein states and proteinquakes.","volume":"82","author":"A Ansari","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/341705a0","article-title":"Three-dimensional crystal structures of escherichia coli met repressor with and without corepressor.","volume":"341","author":"JB Rafferty","year":"1989","journal-title":"Nature"},{"key":"ref16","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000306","article-title":"Mechanical network in titin immunoglobulin from force distribution analysis.","volume":"5","author":"W Stacklies","year":"2009","journal-title":"PLoS Comput Biol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"3997","DOI":"10.1016\/j.bpj.2009.02.052","article-title":"Mechanical response of silk crystalline units from force-distribution analysis.","volume":"96","author":"S Xiao","year":"2009","journal-title":"Biophys J"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1007\/978-1-59745-177-2_5","article-title":"Normal modes and essential dynamics.","volume":"443","author":"S Hayward","year":"2008","journal-title":"Methods Mol Biol"},{"key":"ref19","article-title":"Mechanisms of Cooperativity and Allosteric Regulation in Proteins.","author":"MF Perutz","year":"1990","journal-title":"CUP Archive"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1016\/0079-6107(91)90012-H","article-title":"Regulation of methionine biosynthesis in the enterobacteriaceae.","volume":"56","author":"IG Old","year":"1991","journal-title":"Prog Biophys Mol Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1042\/BJ20060021","article-title":"Transcript analysis reveals an extended regulon and the importance of protein-protein co-operativity for the escherichia coli methionine repressor.","volume":"396","author":"F Marincs","year":"2006","journal-title":"Biochem J"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"6104","DOI":"10.1073\/pnas.82.18.6104","article-title":"Isolation and characterization of the product of the methionine-regulatory gene metj of escherichia coli k-12.","volume":"82","author":"AA Smith","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"34269","DOI":"10.1074\/jbc.M605763200","article-title":"Structural basis for the differential regulation of dna by the methionine repressor metj.","volume":"281","author":"AM Augustus","year":"2006","journal-title":"J Biol Chem"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"10936","DOI":"10.1016\/S0021-9258(18)67477-0","article-title":"Interactions of the escherichia coli methionine repressor with the metf operator and with its corepressor, s-adenosylmethionine.","volume":"261","author":"I Saint-Girons","year":"1986","journal-title":"J Biol Chem"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3212","DOI":"10.1021\/bi00010a010","article-title":"Thermodynamic evaluation of binding interactions in the methionine repressor system of escherichia coli using isothermal titration calorimetry.","volume":"34","author":"DE Hyre","year":"1995","journal-title":"Biochemistry"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/359387a0","article-title":"Crystal structure of the met repressor-operator complex at 2.8 a resolution reveals dna recognition by beta-strands.","volume":"359","author":"WS Somers","year":"1992","journal-title":"Nature"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/S0969-2126(00)00032-0","article-title":"Electrostatic activation of escherichia coli methionine repressor.","volume":"2","author":"K Phillips","year":"1994","journal-title":"Structure"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/S0014-5793(04)00336-9","article-title":"Kinetic analysis of operator binding by the e. coli methionine repressor highlights the role(s) of electrostatic interactions.","volume":"564","author":"ID Lawrenson","year":"2004","journal-title":"FEBS Lett"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1016\/S0969-2126(00)00182-9","article-title":"Direct and indirect readout in mutant met repressor-operator complexes.","volume":"8","author":"CW Garvie","year":"2000","journal-title":"Structure"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1002\/jcc.10349","article-title":"A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.","volume":"24","author":"Y Duan","year":"2003","journal-title":"J Comput Chem"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/359431a0","article-title":"Probing met repressor-operator recognition in solution.","volume":"359","author":"YY He","year":"1992","journal-title":"Nature"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1016\/0009-2614(93)89366-P","article-title":"Estimation of absolute and relative entropies of macromolecules using the covariance matrix.","volume":"215","author":"J Schlitter","year":"1993","journal-title":"Chemical Physics Letters"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1002\/jcc.10379","article-title":"Converging free energy estimates: Mm-pb(gb)sa studies on the protein-protein complex ras-raf.","volume":"25","author":"H Gohlke","year":"2004","journal-title":"J Comput Chem"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1002\/prot.20528","article-title":"Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition.","volume":"61","author":"V Zoete","year":"2005","journal-title":"Proteins"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1039\/B816495A","article-title":"Identification of stable s-adenosylmethionine (sam) analogues derivatised with bioorthogonal tags: effect of ligands on the affinity of the e. coli methionine repressor, metj, for its operator dna.","volume":"7","author":"C Joce","year":"2009","journal-title":"Org Biomol Chem"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"5065","DOI":"10.1073\/pnas.0811130106","article-title":"Metj repressor interactions with dna probed by in-cell nmr.","volume":"106","author":"AM Augustus","year":"2009","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"2055","DOI":"10.1529\/biophysj.106.082180","article-title":"Coupling of global and local vibrational modes in dynamic allostery of proteins.","volume":"91","author":"RJ Hawkins","year":"2006","journal-title":"Biophys J"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2008.02.034","article-title":"Allostery: absence of a change in shape does not imply that allostery is not at play.","volume":"378","author":"CJ Tsai","year":"2008","journal-title":"J Mol Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1038\/71280","article-title":"Redistribution and loss of side chain entropy upon formation of a calmodulin-peptide complex.","volume":"7","author":"AL Lee","year":"2000","journal-title":"Nat Struct Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.jmb.2003.11.010","article-title":"Ligand-dependent dynamics and intramolecular signaling in a pdz domain.","volume":"335","author":"EJ Fuentes","year":"2004","journal-title":"J Mol Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation.","volume":"4","author":"B Hess","year":"2008","journal-title":"Journal of Chemical Theory and Computation"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water.","volume":"79","author":"WL Jorgensen","year":"1982","journal-title":"J Chem Phys"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1016\/0263-7855(90)80070-V","article-title":"WHAT IF: a molecular modelling and drug design program.","volume":"8","author":"G Vriend","year":"1990","journal-title":"J Mol Graph"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"4069","DOI":"10.1063\/1.449071","article-title":"The nose\u2013hoover thermostat.","volume":"83","author":"DJ Evans","year":"1985","journal-title":"The Journal of Chemical Physics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1080\/00268978300102851","article-title":"Constant pressure molecular dynamics for molecular systems.","volume":"50","author":"S Nos\u017d","year":"1983","journal-title":"Molecular Physics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations.","volume":"18","author":"B Hess","year":"1997","journal-title":"J Comp Chem"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"10089","DOI":"10.1063\/1.464397","article-title":"Particle Mesh Ewald \u2014 An <italic>N<\/italic>log(N) method for Ewald sums in large systems.","volume":"98","author":"T Darden","year":"1993","journal-title":"J Chem Phys"},{"key":"ref48","article-title":"R: A Language and Environment for Statistical Computing.","year":"2008"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1002\/jcc.20035","article-title":"Development and testing of a general amber force field.","volume":"25","author":"J Wang","year":"2004","journal-title":"J Comput Chem"},{"key":"ref50","article-title":"Gaussian 03, Revision C.02","author":"MJ Frisch","year":"2004"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1103\/PhysRevB.37.785","article-title":"Development of the colle-salvetti correlation-energy formula into a functional of the electron density.","volume":"37","author":"C Lee","year":"1988","journal-title":"Phys Rev B Condens Matter"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry. iii. the role of exact exchange.","volume":"98","author":"AD Becke","year":"1993","journal-title":"The Journal of Chemical Physics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"6796","DOI":"10.1063\/1.462569","article-title":"Electron affinities of the first-row atoms revisited. systematic basis sets and wave functions.","volume":"96","author":"RA Kendall","year":"1992","journal-title":"The Journal of Chemical Physics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/jcc.540050204","article-title":"An approach to computing electrostatic charges for molecules.","volume":"5","author":"PAK U C Singh","year":"1984","journal-title":"J Comp Chem"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1002\/jcc.540110404","article-title":"Atomic charges derived from semiempirical methods.","volume":"11","author":"BH Besler PAK","year":"1990","journal-title":"J Comp Chem"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"3032","DOI":"10.1063\/1.474659","article-title":"A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics.","volume":"107","author":"E Canc\u00e8s","year":"1997","journal-title":"The Journal of Chemical Physics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"5151","DOI":"10.1063\/1.473558","article-title":"Continuum solvation models: A new approach to the problem of solute&apos;s charge distribution and cavity boundaries.","volume":"106","author":"B Mennucci","year":"1997","journal-title":"The Journal of Chemical Physics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000574","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,14]],"date-time":"2021-10-14T13:06:07Z","timestamp":1634216767000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000574"}},"subtitle":[],"editor":[{"given":"Ruth","family":"Nussinov","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,11,20]]},"references-count":57,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2009,11,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000574","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,20]]}}}