{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T03:23:53Z","timestamp":1774063433116,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006796","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,17]],"date-time":"2019-06-17T00:00:00Z","timestamp":1560729600000}}],"reference-count":81,"publisher":"Public Library of Science (PLoS)","issue":"5","license":[{"start":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T00:00:00Z","timestamp":1559260800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"crossref","award":["GM101277"],"award-info":[{"award-number":["GM101277"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000288","name":"Royal Society","doi-asserted-by":"crossref","award":["U1175.70592"],"award-info":[{"award-number":["U1175.70592"]}],"id":[{"id":"10.13039\/501100000288","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006796","type":"journal-article","created":{"date-parts":[[2019,5,31]],"date-time":"2019-05-31T13:28:56Z","timestamp":1559309336000},"page":"e1006796","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Conformational coupling by trans-phosphorylation in calcium calmodulin dependent kinase II"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4158-233X","authenticated-orcid":true,"given":"Alessandro","family":"Pandini","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0353-2315","authenticated-orcid":true,"given":"Howard","family":"Schulman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0361-6068","authenticated-orcid":true,"given":"Shahid","family":"Khan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2019,5,31]]},"reference":[{"issue":"10","key":"ref1","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.tins.2012.05.003","article-title":"CaMKII regulation in information processing and storage","volume":"35","author":"SJ Coultrap","year":"2012","journal-title":"Trends Neurosci"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"178","DOI":"10.3389\/fphar.2015.00178","article-title":"Regulation of CaMKII signaling in cardiovascular disease","volume":"6","author":"MY Mollova","year":"2015","journal-title":"Frontiers in pharmacology"},{"issue":"2","key":"ref3","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1016\/j.neuron.2013.12.024","article-title":"CaMKII: claiming center stage in postsynaptic function and organization","volume":"81","author":"JW Hell","year":"2014","journal-title":"Neuron"},{"issue":"3","key":"ref4","doi-asserted-by":"crossref","first-page":"275","DOI":"10.1016\/S0092-8674(02)00741-9","article-title":"The conformational plasticity of protein kinases","volume":"109","author":"M Huse","year":"2002","journal-title":"Cell"},{"issue":"31","key":"ref5","doi-asserted-by":"crossref","first-page":"23798","DOI":"10.1074\/jbc.M001471200","article-title":"Mechanism and regulation of calcium\/calmodulin-dependent protein kinase II targeting to the NR2B subunit of the N-methyl-D-aspartate receptor","volume":"275","author":"S Strack","year":"2000","journal-title":"J Biol Chem"},{"issue":"6839","key":"ref6","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1038\/35081080","article-title":"Interaction with the NMDA receptor locks CaMKII in an active conformation","volume":"411","author":"KU Bayer","year":"2001","journal-title":"Nature"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1016\/j.cell.2011.07.038","article-title":"A mechanism for tunable autoinhibition in the structure of a human Ca2+\/calmodulin- dependent kinase II holoenzyme","volume":"146","author":"LH Chao","year":"2011","journal-title":"Cell"},{"issue":"3","key":"ref8","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1038\/nsmb.1751","article-title":"Intersubunit capture of regulatory segments is a component of cooperative CaMKII activation","volume":"17","author":"LH Chao","year":"2010","journal-title":"Nature structural & molecular biology"},{"issue":"7","key":"ref9","doi-asserted-by":"crossref","first-page":"e1000426","DOI":"10.1371\/journal.pbio.1000426","article-title":"Structure of the CaMKIIdelta\/calmodulin complex reveals the molecular mechanism of CaMKII kinase activation","volume":"8","author":"P Rellos","year":"2010","journal-title":"PLoS biology"},{"issue":"24","key":"ref10","doi-asserted-by":"crossref","first-page":"17216","DOI":"10.1016\/S0021-9258(18)41915-1","article-title":"Inhibitory autophosphorylation of multifunctional Ca2+\/calmodulin-dependent protein kinase analyzed by site-directed mutagenesis","volume":"267","author":"PI Hanson","year":"1992","journal-title":"J Biol Chem"},{"issue":"6","key":"ref11","doi-asserted-by":"crossref","first-page":"2020","DOI":"10.1523\/JNEUROSCI.09-06-02020.1989","article-title":"Distinct autophosphorylation sites sequentially produce autonomy and inhibition of the multifunctional Ca2+\/calmodulin-dependent protein kinase","volume":"9","author":"LL Lou","year":"1989","journal-title":"J Neurosci"},{"issue":"26","key":"ref12","doi-asserted-by":"crossref","first-page":"8704","DOI":"10.1523\/JNEUROSCI.0133-10.2010","article-title":"Autonomous CaMKII can promote either long-term potentiation or long-term depression, depending on the state of T305\/T306 phosphorylation","volume":"30","author":"HJ Pi","year":"2010","journal-title":"J Neurosci"},{"issue":"7","key":"ref13","doi-asserted-by":"crossref","first-page":"1251","DOI":"10.1038\/emboj.2011.40","article-title":"Conformational changes underlying calcium\/calmodulin-dependent protein kinase II activation","volume":"30","author":"L Hoffman","year":"2011","journal-title":"EMBO J"},{"issue":"14","key":"ref14","doi-asserted-by":"crossref","first-page":"3590","DOI":"10.1093\/emboj\/cdf360","article-title":"Alternative splicing modulates the frequency-dependent response of CaMKII to Ca(2+) oscillations","volume":"21","author":"KU Bayer","year":"2002","journal-title":"EMBO J"},{"issue":"42","key":"ref15","doi-asserted-by":"crossref","first-page":"9324","DOI":"10.1523\/JNEUROSCI.2350-04.2004","article-title":"Persistent accumulation of calcium\/calmodulin-dependent protein kinase II in dendritic spines after induction of NMDA receptor-dependent chemical long-term potentiation","volume":"24","author":"N Otmakhov","year":"2004","journal-title":"J Neurosci"},{"issue":"9","key":"ref16","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/78783","article-title":"Molecular memory by reversible translocation of calcium\/calmodulin-dependent protein kinase II","volume":"3","author":"K Shen","year":"2000","journal-title":"Nat Neurosci"},{"issue":"3","key":"ref17","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1016\/S0896-6273(00)80569-3","article-title":"CaMKIIbeta functions as an F-actin targeting module that localizes CaMKIIalpha\/beta heterooligomers to dendritic spines","volume":"21","author":"K Shen","year":"1998","journal-title":"Neuron"},{"issue":"3","key":"ref18","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1002\/acn3.528","article-title":"De novo variants in CAMK2A and CAMK2B cause neurodevelopmental disorders","volume":"5","author":"T Akita","year":"2018","journal-title":"Ann Clin Transl Neurol"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1016\/j.ajhg.2017.10.003","article-title":"De Novo Mutations in Protein Kinase Genes CAMK2A and CAMK2B Cause Intellectual Disability","volume":"101","author":"S Kury","year":"2017","journal-title":"Am J Hum Genet"},{"issue":"4","key":"ref20","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1523\/JNEUROSCI.3116-05.2006","article-title":"Transition from reversible to persistent binding of CaMKII to postsynaptic sites and NR2B","volume":"26","author":"KU Bayer","year":"2006","journal-title":"J Neurosci"},{"issue":"37","key":"ref21","doi-asserted-by":"crossref","first-page":"26199","DOI":"10.1074\/jbc.274.37.26199","article-title":"Structural examination of autoregulation of multifunctional calcium\/calmodulin-dependent protein kinase II","volume":"274","author":"E Yang","year":"1999","journal-title":"J Biol Chem"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"21","DOI":"10.3389\/fphar.2014.00021","article-title":"CaMKII inhibitors: from research tools to therapeutic agents.","volume":"5","author":"P Pellicena","year":"2014","journal-title":"Frontiers in pharmacology"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1016\/j.cell.2005.10.029","article-title":"Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme","volume":"123","author":"OS Rosenberg","year":"2005","journal-title":"Cell"},{"issue":"5","key":"ref24","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1529\/biophysj.107.118505","article-title":"A simulation study on the activation of cardiac CaMKII delta-isoform and its regulation by phosphatases","volume":"95","author":"H Chiba","year":"2008","journal-title":"Biophys J"},{"issue":"11","key":"ref25","doi-asserted-by":"crossref","first-page":"1482","DOI":"10.1016\/j.str.2007.09.017","article-title":"Geometry-based sampling of conformational transitions in proteins","volume":"15","author":"D Seeliger","year":"2007","journal-title":"Structure"},{"issue":"43","key":"ref26","doi-asserted-by":"crossref","first-page":"E4623","DOI":"10.1073\/pnas.1418402111","article-title":"Dynamic architecture of a protein kinase","volume":"111","author":"CL McClendon","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9","key":"ref27","doi-asserted-by":"crossref","first-page":"e45064","DOI":"10.1371\/journal.pone.0045064","article-title":"Effect of multimeric structure of CaMKII in the GluN2B-mediated modulation of kinetic parameters of ATP","volume":"7","author":"J Cheriyan","year":"2012","journal-title":"PloS one"},{"issue":"3","key":"ref28","doi-asserted-by":"crossref","first-page":"e16495","DOI":"10.1371\/journal.pone.0016495","article-title":"Calcium\/calmodulin dependent protein kinase II bound to NMDA receptor 2B subunit exhibits increased ATP affinity and attenuated dephosphorylation","volume":"6","author":"J Cheriyan","year":"2011","journal-title":"PloS one"},{"issue":"5060","key":"ref29","doi-asserted-by":"crossref","first-page":"1199","DOI":"10.1126\/science.256.5060.1199","article-title":"Calmodulin trapping by calcium-calmodulin-dependent protein kinase","volume":"256","author":"T Meyer","year":"1992","journal-title":"Science"},{"issue":"2","key":"ref30","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1016\/j.bpj.2016.06.007","article-title":"Multiple CaMKII Binding Modes to the Actin Cytoskeleton Revealed by Single-Molecule Imaging","volume":"111","author":"S Khan","year":"2016","journal-title":"Biophys J"},{"issue":"9","key":"ref31","doi-asserted-by":"crossref","first-page":"2158","DOI":"10.1016\/j.bpj.2015.03.028","article-title":"3rd, Vogel SS. Covert Changes in CaMKII Holoenzyme Structure Identified for Activation and Subsequent Interactions","volume":"108","author":"TA Nguyen","year":"2015","journal-title":"Biophys J"},{"issue":"6","key":"ref32","doi-asserted-by":"crossref","first-page":"1270","DOI":"10.1016\/j.bpj.2017.02.005","article-title":"Deciphering CaMKII Multimerization Using Fluorescence Correlation Spectroscopy and Homo-FRET Analysis","volume":"112","author":"P Sarkar","year":"2017","journal-title":"Biophys J"},{"issue":"2","key":"ref33","doi-asserted-by":"crossref","first-page":"e1006021","DOI":"10.1371\/journal.pcbi.1006021","article-title":"Ligand-induced perturbation of the HIF-2alpha:ARNT dimer dynamics.","volume":"14","author":"S Motta","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"ref34","doi-asserted-by":"crossref","first-page":"e1004898","DOI":"10.1371\/journal.pcbi.1004898","article-title":"Non-degradative Ubiquitination of Protein Kinases","volume":"12","author":"KA Ball","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"ref35","doi-asserted-by":"crossref","first-page":"e1004826","DOI":"10.1371\/journal.pcbi.1004826","article-title":"Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases","volume":"12","author":"N Chopra","year":"2016","journal-title":"PLoS Comput Biol"},{"issue":"16","key":"ref36","doi-asserted-by":"crossref","first-page":"2053","DOI":"10.1093\/bioinformatics\/btt326","article-title":"GSATools: analysis of allosteric communication and functional local motions using a structural alphabet","volume":"29","author":"A Pandini","year":"2013","journal-title":"Bioinformatics"},{"issue":"23","key":"ref37","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 U S A"},{"issue":"5","key":"ref38","doi-asserted-by":"crossref","first-page":"056131","DOI":"10.1103\/PhysRevE.70.056131","article-title":"Analysis of weighted networks","volume":"70","author":"ME Newman","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"issue":"6","key":"ref39","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1016\/j.chembiol.2013.06.001","article-title":"Ins and outs of kinase DFG motifs","volume":"20","author":"DK Treiber","year":"2013","journal-title":"Chem Biol"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1002\/prot.22875","article-title":"Principal component and normal mode analysis of proteins; a quantitative comparison using the GroEL subunit","volume":"79","author":"L Skjaerven","year":"2011","journal-title":"Proteins"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"1707","DOI":"10.1016\/S0006-3495(96)79372-4","article-title":"The consistency of large concerted motions in proteins in molecular dynamics simulations","volume":"71","author":"BL de Groot","year":"1996","journal-title":"Biophys J"},{"issue":"3","key":"ref42","doi-asserted-by":"crossref","first-page":"031910","DOI":"10.1103\/PhysRevE.65.031910","article-title":"Convergence of sampling in protein simulations","volume":"65","author":"B. Hess","year":"2002","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys"},{"issue":"8","key":"ref43","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1021\/jp054359r","article-title":"Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics","volume":"110","author":"P Raiteri","year":"2006","journal-title":"J Phys Chem B"},{"issue":"1","key":"ref44","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1016\/S0006-3495(98)77529-0","article-title":"A helix propensity scale based on experimental studies of peptides and proteins","volume":"75","author":"CN Pace","year":"1998","journal-title":"Biophys J"},{"issue":"7","key":"ref45","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1016\/j.str.2016.05.012","article-title":"The Gearbox of the Bacterial Flagellar Motor Switch","volume":"24","author":"A Pandini","year":"2016","journal-title":"Structure"},{"issue":"1","key":"ref46","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"},{"issue":"2","key":"ref47","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.cell.2013.03.034","article-title":"Allostery in disease and in drug discovery","volume":"153","author":"R Nussinov","year":"2013","journal-title":"Cell"},{"issue":"11","key":"ref48","doi-asserted-by":"crossref","first-page":"628","DOI":"10.1016\/j.tibs.2015.09.002","article-title":"Dynamics-Driven Allostery in Protein Kinases","volume":"40","author":"AP Kornev","year":"2015","journal-title":"Trends Biochem Sci"},{"issue":"2","key":"ref49","doi-asserted-by":"crossref","first-page":"e1003394","DOI":"10.1371\/journal.pcbi.1003394","article-title":"A unified view of &quot;how allostery works&quot;.","volume":"10","author":"CJ Tsai","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref50","article-title":"A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation.","volume":"7","author":"EF Ruff","year":"2018","journal-title":"eLife"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"15742","DOI":"10.1038\/ncomms15742","article-title":"The CaMKII holoenzyme structure in activation-competent conformations","volume":"8","author":"JB Myers","year":"2017","journal-title":"Nat Commun"},{"issue":"4","key":"ref52","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1038\/nchembio.2296","article-title":"A water-mediated allosteric network governs activation of Aurora kinase A","volume":"13","author":"S Cyphers","year":"2017","journal-title":"Nat Chem Biol"},{"issue":"4","key":"ref53","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1016\/j.cell.2007.03.039","article-title":"Structural basis for the inhibition of tyrosine kinase activity of ZAP-70","volume":"129","author":"S Deindl","year":"2007","journal-title":"Cell"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"5939","DOI":"10.1038\/ncomms6939","article-title":"A dynamically coupled allosteric network underlies binding cooperativity in Src kinase","volume":"6","author":"ZH Foda","year":"2015","journal-title":"Nat Commun"},{"issue":"52","key":"ref55","doi-asserted-by":"crossref","first-page":"26739","DOI":"10.1074\/jbc.M116.749507","article-title":"Evolution of Negative Cooperativity in Glutathione Transferase Enabled Preservation of Enzyme Function","volume":"291","author":"A Bocedi","year":"2016","journal-title":"J Biol Chem"},{"issue":"405","key":"ref56","doi-asserted-by":"crossref","first-page":"rs13","DOI":"10.1126\/scisignal.aaa6711","article-title":"Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases","volume":"8","author":"Q Xu","year":"2015","journal-title":"Sci Signal"},{"issue":"219","key":"ref57","doi-asserted-by":"crossref","first-page":"pl5","DOI":"10.1126\/stke.2192004pl5","article-title":"Imaging calcium concentration dynamics in small neuronal compartments","volume":"2004","author":"R Yasuda","year":"2004","journal-title":"Science's STKE: signal transduction knowledge environment"},{"issue":"5348","key":"ref58","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1126\/science.279.5348.227","article-title":"Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations","volume":"279","author":"P De Koninck","year":"1998","journal-title":"Science"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"e01610","DOI":"10.7554\/eLife.01610","article-title":"Activation-triggered subunit exchange between CaMKII holoenzymes facilitates the spread of kinase activity.","volume":"3","author":"M Stratton","year":"2014","journal-title":"eLife"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"9601046","DOI":"10.1155\/2017\/9601046","article-title":"Activation State-Dependent Substrate Gating in Ca(2+)\/Calmodulin-Dependent Protein Kinase II","volume":"2017","author":"DE Johnson","year":"2017","journal-title":"Neural Plast"},{"issue":"3","key":"ref61","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.celrep.2014.01.005","article-title":"Autonomous CaMKII mediates both LTP and LTD using a mechanism for differential substrate site selection","volume":"6","author":"SJ Coultrap","year":"2014","journal-title":"Cell Rep"},{"issue":"6","key":"ref62","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1016\/S0143-4160(03)00152-0","article-title":"Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations: a simple model","volume":"34","author":"G Dupont","year":"2003","journal-title":"Cell Calcium"},{"issue":"3","key":"ref63","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1006\/jmbi.2001.4610","article-title":"Conformational spread in a ring of proteins: a stochastic approach to allostery","volume":"308","author":"TA Duke","year":"2001","journal-title":"J Mol Biol"},{"issue":"e13405","key":"ref64","article-title":"Molecular mechanism of activation-triggered subunit exchange in Ca(2+)\/calmodulin-dependent protein kinase II","volume":"5","author":"M Bhattacharyya","year":"2016","journal-title":"eLife"},{"issue":"3","key":"ref65","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1096\/fj.13-236992","article-title":"BCR-ABL residues interacting with ponatinib are critical to preserve the tumorigenic potential of the oncoprotein","volume":"28","author":"P Buffa","year":"2014","journal-title":"FASEB J"},{"issue":"2","key":"ref66","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1073\/pnas.0709214104","article-title":"Allosteric cooperativity in protein kinase A","volume":"105","author":"LR Masterson","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"D1","key":"ref67","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"10","key":"ref68","doi-asserted-by":"crossref","first-page":"1559","DOI":"10.1002\/pro.5560021003","article-title":"Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations","volume":"2","author":"J Zheng","year":"1993","journal-title":"Protein Sci"},{"issue":"5","key":"ref69","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1016\/j.bpj.2015.07.005","article-title":"The Phylogenetic Signature Underlying ATP Synthase c-Ring Compliance","volume":"109","author":"A Pandini","year":"2015","journal-title":"Biophysical journal"},{"issue":"2","key":"ref70","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1002\/(SICI)1097-0134(199710)29:2<240::AID-PROT11>3.0.CO;2-O","article-title":"Prediction of protein conformational freedom from distance constraints","volume":"29","author":"BL de Groot","year":"1997","journal-title":"Proteins"},{"issue":"2","key":"ref71","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1002\/prot.24350","article-title":"Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics","volume":"82","author":"AE Aliev","year":"2014","journal-title":"Proteins"},{"issue":"11","key":"ref72","doi-asserted-by":"crossref","first-page":"5127","DOI":"10.1021\/ct400486p","article-title":"Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles","volume":"9","author":"A Fornili","year":"2013","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"ref73","doi-asserted-by":"crossref","first-page":"014101","DOI":"10.1063\/1.2408420","article-title":"Canonical sampling through velocity rescaling","volume":"126","author":"G Bussi","year":"2007","journal-title":"J Chem Phys"},{"issue":"9","key":"ref74","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic transitions in single crystals. A new molecular dynamics method","volume":"52","author":"M Parrinello","year":"1981","journal-title":"J Appl Phys"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"W665","DOI":"10.1093\/nar\/gkh381","article-title":"PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations","volume":"32","author":"TJ Dolinsky","year":"2004","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ref76","doi-asserted-by":"crossref","first-page":"868","DOI":"10.1096\/fj.11-190868","article-title":"Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics","volume":"26","author":"A Pandini","year":"2012","journal-title":"FASEB J"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S0167-2789(98)00269-3","article-title":"Estimating the errors on measured entropy and mutual information","volume":"125","author":"MS Roulston","year":"1999","journal-title":"Physica D"},{"issue":"9","key":"ref78","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1016\/j.bpj.2014.09.019","article-title":"Kinesin-5 allosteric inhibitors uncouple the dynamics of nucleotide, microtubule, and neck-linker binding sites","volume":"107","author":"G Scarabelli","year":"2014","journal-title":"Biophys J"},{"issue":"9","key":"ref79","doi-asserted-by":"crossref","first-page":"2486","DOI":"10.1021\/ct9001812","article-title":"Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles","volume":"5","author":"CL McClendon","year":"2009","journal-title":"J Chem Theory Comput"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1186\/1471-2105-11-97","article-title":"Structural alphabets derived from attractors in conformational space","volume":"11","author":"A Pandini","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref81","article-title":"The igraph software package for complex network research","author":"G Csardi","year":"2006","journal-title":"InterJournal"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006796","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,6,17]],"date-time":"2019-06-17T00:00:00Z","timestamp":1560729600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006796","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,18]],"date-time":"2022-09-18T21:16:03Z","timestamp":1663535763000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006796"}},"subtitle":[],"editor":[{"given":"Bert L.","family":"de Groot","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,5,31]]},"references-count":81,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2019,5,31]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006796","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/524660","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,5,31]]}}}