{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T12:19:14Z","timestamp":1770725954687,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1007670","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,2,26]],"date-time":"2020-02-26T00:00:00Z","timestamp":1582675200000}}],"reference-count":65,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2020,2,13]],"date-time":"2020-02-13T00:00:00Z","timestamp":1581552000000},"content-version":"vor","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.1007670","type":"journal-article","created":{"date-parts":[[2020,2,13]],"date-time":"2020-02-13T13:50:09Z","timestamp":1581601809000},"page":"e1007670","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":41,"title":["Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis"],"prefix":"10.1371","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2821-0494","authenticated-orcid":true,"given":"Qian-Yuan","family":"Tang","sequence":"first","affiliation":[]},{"given":"Kunihiko","family":"Kaneko","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2020,2,13]]},"reference":[{"issue":"1","key":"pcbi.1007670.ref001","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1146\/annurev.bb.12.060183.001151","article-title":"Theoretical studies of protein folding","volume":"12","author":"N Go","year":"1983","journal-title":"Annu Rev Biophys Bioeng"},{"issue":"1","key":"pcbi.1007670.ref002","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1146\/annurev.physchem.48.1.545","article-title":"Theory of protein folding: the energy landscape perspective","volume":"48","author":"JN Onuchic","year":"1997","journal-title":"Annu Rev Phys Chem"},{"issue":"1","key":"pcbi.1007670.ref003","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.jmb.2004.06.063","article-title":"The protein folding network","volume":"342","author":"F Rao","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi.1007670.ref004","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1146\/annurev.biophys.36.040306.132808","article-title":"Physics of proteins","volume":"36","author":"JR Banavar","year":"2007","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"pcbi.1007670.ref005","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/0079-6107(83)90015-9","article-title":"The role of protein fluctuations in enzyme action: a review","volume":"39","author":"GR Welch","year":"1982","journal-title":"Prog Biophys Mol Biol"},{"issue":"12","key":"pcbi.1007670.ref006","doi-asserted-by":"crossref","first-page":"4282","DOI":"10.1073\/pnas.0407499102","article-title":"Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins","volume":"102","author":"ST Whitten","year":"2005","journal-title":"Proc Natl Acad Sci USA"},{"issue":"29","key":"pcbi.1007670.ref007","doi-asserted-by":"crossref","first-page":"11681","DOI":"10.1073\/pnas.1209309109","article-title":"Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites","volume":"109","author":"GR Bowman","year":"2012","journal-title":"Proc Natl Acad Sci USA"},{"issue":"11","key":"pcbi.1007670.ref008","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1038\/nchembio.232","article-title":"The role of dynamic conformational ensembles in biomolecular recognition","volume":"5","author":"DD Boehr","year":"2009","journal-title":"Nat Chem Biol"},{"issue":"42","key":"pcbi.1007670.ref009","doi-asserted-by":"crossref","first-page":"28680","DOI":"10.1074\/jbc.M800889200","article-title":"Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter","volume":"283","author":"IH Shrivastava","year":"2008","journal-title":"J Biol Chem"},{"issue":"2","key":"pcbi.1007670.ref010","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/S0959-440X(00)00061-0","article-title":"Collective protein dynamics in relation to function","volume":"10","author":"HJ Berendsen","year":"2000","journal-title":"Curr Opin Struct Biol"},{"issue":"6","key":"pcbi.1007670.ref011","doi-asserted-by":"crossref","first-page":"2902","DOI":"10.1016\/S0006-3495(00)76527-1","article-title":"Protein motions at zero-total angular momentum: the importance of long-range correlations","volume":"79","author":"Y Zhou","year":"2000","journal-title":"Biophys J"},{"issue":"27","key":"pcbi.1007670.ref012","doi-asserted-by":"crossref","first-page":"10336","DOI":"10.1021\/ja200461n","article-title":"Weak long-range correlated motions in a surface patch of ubiquitin involved in molecular recognition","volume":"133","author":"RB Fenwick","year":"2011","journal-title":"J Amer Chem Soc"},{"issue":"7496","key":"pcbi.1007670.ref013","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1038\/nature13001","article-title":"The ensemble nature of allostery","volume":"508","author":"HN Motlagh","year":"2014","journal-title":"Nature"},{"issue":"6","key":"pcbi.1007670.ref014","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1016\/j.bpj.2015.08.011","article-title":"Allosteric dynamic control of binding","volume":"109","author":"F Sumbul","year":"2015","journal-title":"Biophys J"},{"issue":"8","key":"pcbi.1007670.ref015","doi-asserted-by":"crossref","first-page":"088102","DOI":"10.1103\/PhysRevLett.118.088102","article-title":"Critical Fluctuations in the Native State of Proteins","volume":"118","author":"QY Tang","year":"2017","journal-title":"Phys Rev Lett"},{"issue":"1","key":"pcbi.1007670.ref016","doi-asserted-by":"crossref","first-page":"011920","DOI":"10.1103\/PhysRevE.75.011920","article-title":"Amino acid hydrophobicity and accessible surface area","volume":"75","author":"MA Moret","year":"2007","journal-title":"Phys Rev E"},{"issue":"17","key":"pcbi.1007670.ref017","doi-asserted-by":"crossref","first-page":"3055","DOI":"10.1016\/j.physa.2011.04.008","article-title":"Self-organized critical model for protein folding","volume":"390","author":"MA Moret","year":"2011","journal-title":"Physica A"},{"key":"pcbi.1007670.ref018","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1016\/j.physa.2014.08.034","article-title":"Fractals and self-organized criticality in proteins","volume":"415","author":"JC Phillips","year":"2014","journal-title":"Physica A"},{"issue":"9","key":"pcbi.1007670.ref019","doi-asserted-by":"crossref","first-page":"3107","DOI":"10.1073\/pnas.0811262106","article-title":"Scaling and self-organized criticality in proteins I","volume":"106","author":"JC Phillips","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"pcbi.1007670.ref020","doi-asserted-by":"crossref","first-page":"3113","DOI":"10.1073\/pnas.0811308105","article-title":"Scaling and self-organized criticality in proteins II","volume":"106","author":"JC Phillips","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"issue":"20","key":"pcbi.1007670.ref021","doi-asserted-by":"crossref","first-page":"208101","DOI":"10.1103\/PhysRevLett.100.208101","article-title":"Proteins: coexistence of stability and flexibility","volume":"100","author":"S Reuveni","year":"2008","journal-title":"Phys Rev Lett"},{"issue":"18","key":"pcbi.1007670.ref022","doi-asserted-by":"crossref","first-page":"188103","DOI":"10.1103\/PhysRevLett.100.188103","article-title":"Subdiffusion in peptides originates from the fractal-like structure of configuration space","volume":"100","author":"T Neusius","year":"2008","journal-title":"Phys Rev Lett"},{"issue":"5395","key":"pcbi.1007670.ref023","doi-asserted-by":"crossref","first-page":"1877","DOI":"10.1126\/science.282.5395.1877","article-title":"Single-molecule enzymatic dynamics","volume":"282","author":"HP Lu","year":"1998","journal-title":"Science"},{"key":"pcbi.1007670.ref024","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1038\/nphys3553","article-title":"The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time","volume":"12","author":"X Hu","year":"2016","journal-title":"Nat Phys"},{"issue":"10","key":"pcbi.1007670.ref025","doi-asserted-by":"crossref","first-page":"3599","DOI":"10.1021\/jacs.6b12058","article-title":"Native State Volume Fluctuations in Proteins as a Mechanism for Dynamic Allostery","volume":"139","author":"AB Law","year":"2017","journal-title":"J Amer Chem Soc"},{"issue":"12","key":"pcbi.1007670.ref026","doi-asserted-by":"crossref","first-page":"2733","DOI":"10.1103\/PhysRevLett.80.2733","article-title":"Vibrational dynamics of folded proteins: significance of slow and fast motions in relation to function and stability","volume":"80","author":"I Bahar","year":"1998","journal-title":"Phys Rev Lett"},{"key":"pcbi.1007670.ref027","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.biophys.093008.131258","article-title":"Global dynamics of proteins: bridging between structure and function","volume":"39","author":"I Bahar","year":"2010","journal-title":"Annu Rev Biophys"},{"issue":"10","key":"pcbi.1007670.ref028","doi-asserted-by":"crossref","first-page":"1645","DOI":"10.1002\/pro.711","article-title":"Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins","volume":"20","author":"L Meireles","year":"2011","journal-title":"Protein Sci"},{"issue":"3","key":"pcbi.1007670.ref029","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1529\/biophysj.106.095927","article-title":"How well can we understand large-scale protein motions using normal modes of elastic network models?","volume":"93","author":"L Yang","year":"2007","journal-title":"Biophys J"},{"issue":"10","key":"pcbi.1007670.ref030","doi-asserted-by":"crossref","first-page":"3152","DOI":"10.3390\/ijms19103152","article-title":"Designed elastic networks: Models of complex protein machinery","volume":"19","author":"H Flechsig","year":"2018","journal-title":"Intl J Mol Sci"},{"issue":"3","key":"pcbi.1007670.ref031","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1002\/prot.340110305","article-title":"Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations","volume":"11","author":"T Ichiye","year":"1991","journal-title":"Proteins"},{"issue":"2","key":"pcbi.1007670.ref032","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S0959-440X(94)90321-2","article-title":"Normal mode analysis of protein dynamics","volume":"4","author":"DA Case","year":"1994","journal-title":"Curr Opin Struct Biol"},{"issue":"6","key":"pcbi.1007670.ref033","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1007\/s12551-017-0330-2","article-title":"Normal mode analysis as a method to derive protein dynamics information from the Protein Data Bank","volume":"9","author":"H Wako","year":"2017","journal-title":"Biophys Rev"},{"key":"pcbi.1007670.ref034","volume-title":"Phase transitions and critical phenomena","author":"HE Stanley","year":"1971"},{"key":"pcbi.1007670.ref035","volume-title":"Lectures on phase transitions and the renormalization group","author":"N Goldenfeld","year":"1992"},{"key":"pcbi.1007670.ref036","doi-asserted-by":"crossref","DOI":"10.1007\/978-1-4757-5426-1","volume-title":"How nature works: the science of self-organized criticality","author":"P Bak","year":"1996"},{"issue":"16","key":"pcbi.1007670.ref037","doi-asserted-by":"crossref","first-page":"3090","DOI":"10.1103\/PhysRevLett.79.3090","article-title":"Gaussian dynamics of folded proteins","volume":"79","author":"T Haliloglu","year":"1997","journal-title":"Phys Rev Lett"},{"issue":"8","key":"pcbi.1007670.ref038","doi-asserted-by":"crossref","first-page":"088103","DOI":"10.1103\/PhysRevLett.102.088103","article-title":"Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding","volume":"102","author":"T Haliloglu","year":"2009","journal-title":"Phys Rev Lett"},{"issue":"26","key":"pcbi.1007670.ref039","doi-asserted-by":"crossref","first-page":"11865","DOI":"10.1073\/pnas.1005766107","article-title":"Scale-free correlations in starling flocks","volume":"107","author":"A Cavagna","year":"2010","journal-title":"Proc Natl Acad Sci USA"},{"issue":"23","key":"pcbi.1007670.ref040","doi-asserted-by":"crossref","first-page":"238102","DOI":"10.1103\/PhysRevLett.113.238102","article-title":"Finite-size scaling as a way to probe near-criticality in natural swarms","volume":"113","author":"A Attanasi","year":"2014","journal-title":"Phys Rev Lett"},{"issue":"4","key":"pcbi.1007670.ref041","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1093\/bioinformatics\/btm625","article-title":"Structural flexibility in proteins: impact of the crystal environment","volume":"24","author":"K Hinsen","year":"2007","journal-title":"Bioinformatics"},{"issue":"12","key":"pcbi.1007670.ref042","doi-asserted-by":"crossref","first-page":"5618","DOI":"10.1021\/ct400399x","article-title":"Evaluation of protein elastic network models based on an analysis of collective motions","volume":"9","author":"E Fuglebakk","year":"2013","journal-title":"J Chem Theor Comp"},{"issue":"30","key":"pcbi.1007670.ref043","doi-asserted-by":"crossref","first-page":"12347","DOI":"10.1073\/pnas.0902159106","article-title":"Protein elastic network models and the ranges of cooperativity","volume":"106","author":"L Yang","year":"2009","journal-title":"Proc Natl Acad Sci USA"},{"key":"pcbi.1007670.ref044","doi-asserted-by":"crossref","first-page":"032411","DOI":"10.1103\/PhysRevE.100.032411","article-title":"Parsimonious evolutionary scenario for the origin of allostery and coevolution patterns in proteins","volume":"100","author":"O Rivoire","year":"2019","journal-title":"Phys Rev E"},{"key":"pcbi.1007670.ref045","doi-asserted-by":"crossref","first-page":"031001","DOI":"10.1103\/RevModPhys.91.031001","article-title":"Colloquium: Proteins: The physics of amorphous evolving matter","volume":"91","author":"JP Eckmann","year":"2019","journal-title":"Rev Mod Phys"},{"issue":"3","key":"pcbi.1007670.ref046","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1110\/ps.04882105","article-title":"Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool","volume":"14","author":"U Lehnert","year":"2005","journal-title":"Protein Sci"},{"issue":"9","key":"pcbi.1007670.ref047","doi-asserted-by":"crossref","first-page":"3052","DOI":"10.1529\/biophysj.106.099440","article-title":"Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication","volume":"92","author":"AR Atilgan","year":"2007","journal-title":"Biophys J"},{"key":"pcbi.1007670.ref048","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1146\/annurev-biophys-050511-102305","article-title":"Network-based models as tools hinting at nonevident protein functionality","volume":"41","author":"C Atilgan","year":"2012","journal-title":"Annu Rev Biophys"},{"issue":"2","key":"pcbi.1007670.ref049","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1007\/s10955-011-0229-4","article-title":"Are biological systems poised at criticality?","volume":"144","author":"T Mora","year":"2011","journal-title":"J Stat Phys"},{"issue":"1","key":"pcbi.1007670.ref050","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.bbamem.2008.09.010","article-title":"An introduction to critical points for biophysicists: observations of compositional heterogeneity in lipid membranes","volume":"1788","author":"AR Honerkamp-Smith","year":"2009","journal-title":"Biochim Biophys Acta"},{"issue":"10","key":"pcbi.1007670.ref051","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1038\/nphys1803","article-title":"Emergent complex neural dynamics","volume":"6","author":"DR Chialvo","year":"2010","journal-title":"Nat Phys"},{"issue":"8","key":"pcbi.1007670.ref052","doi-asserted-by":"crossref","first-page":"088102","DOI":"10.1103\/PhysRevLett.90.088102","article-title":"Zipf\u2019s law in gene expression","volume":"90","author":"C Furusawa","year":"2003","journal-title":"Phys Rev Lett"},{"issue":"20","key":"pcbi.1007670.ref053","doi-asserted-by":"crossref","first-page":"208103","DOI":"10.1103\/PhysRevLett.108.208103","article-title":"Adaptation to optimal cell growth through self-organized criticality","volume":"108","author":"C Furusawa","year":"2012","journal-title":"Phys Rev Lett"},{"key":"pcbi.1007670.ref054","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1103\/Physics.7.120","article-title":"Viewpoint: Insect Swarms Go Critical","volume":"7","author":"H Chat\u00e9","year":"2014","journal-title":"Physics"},{"issue":"3","key":"pcbi.1007670.ref055","doi-asserted-by":"crossref","first-page":"031001","DOI":"10.1103\/RevModPhys.90.031001","article-title":"Colloquium: Criticality and dynamical scaling in living systems","volume":"90","author":"MA Mu\u00f1oz","year":"2018","journal-title":"Rev Mod Phys"},{"issue":"2","key":"pcbi.1007670.ref056","doi-asserted-by":"crossref","first-page":"026113","DOI":"10.1103\/PhysRevE.69.026113","article-title":"Finding and evaluating community structure in networks","volume":"69","author":"ME Newman","year":"2004","journal-title":"Phys Rev E"},{"issue":"23","key":"pcbi.1007670.ref057","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1073\/pnas.0601602103","article-title":"Modularity and community structure in networks","volume":"103","author":"ME Newman","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"issue":"2","key":"pcbi.1007670.ref058","doi-asserted-by":"crossref","first-page":"025101","DOI":"10.1103\/PhysRevE.70.025101","article-title":"Modularity from fluctuations in random graphs and complex networks","volume":"70","author":"R Guimera","year":"2004","journal-title":"Phys Rev E"},{"issue":"2","key":"pcbi.1007670.ref059","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1140\/epjb\/e2004-00124-y","article-title":"Detecting community structure in networks","volume":"38","author":"ME Newman","year":"2004","journal-title":"Euro Phys J B"},{"issue":"2","key":"pcbi.1007670.ref060","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/S0022-2836(03)00755-1","article-title":"The structure of the receptor-binding domain of the bacteriophage T4 short tail fibre reveals a knitted trimeric metal-binding fold","volume":"331","author":"E Thomassen","year":"2003","journal-title":"J Mol Biol"},{"issue":"4","key":"pcbi.1007670.ref061","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1093\/abbs\/gms001","article-title":"Structure insights into mechanisms of ATP hydrolysis and the activation of human heat-shock protein 90","volume":"44","author":"J Li","year":"2012","journal-title":"Acta Biochim Biophys Sin"},{"issue":"7583","key":"pcbi.1007670.ref062","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/nature16162","article-title":"Exploring the repeat protein universe through computational protein design","volume":"528","author":"TJ Brunette","year":"2015","journal-title":"Nature"},{"issue":"1","key":"pcbi.1007670.ref063","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"pcbi.1007670.ref064","doi-asserted-by":"crossref","first-page":"042822","DOI":"10.1103\/PhysRevE.88.042822","article-title":"Spectral methods for community detection and graph partitioning","volume":"88","author":"ME Newman","year":"2013","journal-title":"Phys Rev E"},{"issue":"10","key":"pcbi.1007670.ref065","doi-asserted-by":"crossref","first-page":"P10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"VD Blondel","year":"2008","journal-title":"J Stat Mech"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1007670","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,2,26]],"date-time":"2020-02-26T00:00:00Z","timestamp":1582675200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007670","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,26]],"date-time":"2020-02-26T13:38:41Z","timestamp":1582724321000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1007670"}},"subtitle":[],"editor":[{"given":"Bert L.","family":"de Groot","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,13]]},"references-count":65,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2020,2,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1007670","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1007670","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,2,13]]}}}