{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,31]],"date-time":"2024-07-31T17:07:38Z","timestamp":1722445658101},"reference-count":49,"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.1000568","type":"journal-article","created":{"date-parts":[[2009,11,19]],"date-time":"2009-11-19T22:47:04Z","timestamp":1258670824000},"page":"e1000568","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":8,"title":["Circadian KaiC Phosphorylation: A Multi-Layer Network"],"prefix":"10.1371","volume":"5","author":[{"given":"Congxin","family":"Li","sequence":"first","affiliation":[]},{"given":"Xiaofang","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Pengye","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Weichi","family":"Wang","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,11,20]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.tim.2007.08.005","article-title":"Winding up the cyanobacterial circadian clock.","volume":"15","author":"SR Mackey","year":"2007","journal-title":"Trends Microbiol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"7051","DOI":"10.1073\/pnas.0609315104","article-title":"Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling.","volume":"104","author":"M Amdaoud","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nature02533","article-title":"Resilient circadian oscillator revealed in individual cyanobacteria.","volume":"430","author":"I Mihalcescu","year":"2004","journal-title":"Nature"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1126\/science.1108451","article-title":"Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro.","volume":"308","author":"M Nakajima","year":"2005","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/j.molcel.2006.05.039","article-title":"Cyanobacterial circadian pacemaker: Kai protein complex dynamics in the KaiC phosphorylation cycle in vitro.","volume":"23","author":"H Kageyama","year":"2006","journal-title":"Mol Cell"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"17203","DOI":"10.1073\/pnas.262578499","article-title":"Circadian clock protein KaiC forms ATP-dependent hexameric rings and binds DNA.","volume":"99","author":"T Mori","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1046\/j.1365-2443.2003.00633.x","article-title":"ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC.","volume":"8","author":"F Hayashi","year":"2003","journal-title":"Genes Cells"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1016\/j.bbrc.2006.07.143","article-title":"Hexamerization by the N-terminal domain and intersubunit phosphorylation by the C-terminal domain of cyanobacterial circadian clock protein KaiC.","volume":"348","author":"F Hayashi","year":"2006","journal-title":"Biochem Biophys Res Commun"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"13927","DOI":"10.1073\/pnas.0403906101","article-title":"Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942.","volume":"101","author":"T Nishiwaki","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"13933","DOI":"10.1073\/pnas.0404768101","article-title":"Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses.","volume":"101","author":"Y Xu","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"4029","DOI":"10.1038\/sj.emboj.7601832","article-title":"A sequential program of dual phosphorylation of KaiC as a basis for circadian rhythm in cyanobacteria.","volume":"26","author":"T Nishiwaki","year":"2007","journal-title":"Embo J"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1126\/science.1148596","article-title":"Ordered phosphorylation governs oscillation of a three-protein circadian clock.","volume":"318","author":"MJ Rust","year":"2007","journal-title":"Science"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"15788","DOI":"10.1073\/pnas.222467299","article-title":"KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria.","volume":"99","author":"H Iwasaki","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"2127","DOI":"10.1093\/emboj\/cdg212","article-title":"KaiB functions as an attenuator of KaiC phosphorylation in the cyanobacterial circadian clock system.","volume":"22","author":"Y Kitayama","year":"2003","journal-title":"Embo J"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"16377","DOI":"10.1073\/pnas.0706292104","article-title":"ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria.","volume":"104","author":"K Terauchi","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"038303","DOI":"10.1103\/PhysRevLett.96.038303","article-title":"Hourglass model for a protein-based circadian oscillator.","volume":"96","author":"E Emberly","year":"2006","journal-title":"Phys Rev Lett"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e93","DOI":"10.1371\/journal.pbio.0050093","article-title":"Elucidating the Ticking of an In Vitro Circadian Clockwork.","volume":"5","author":"T Mori","year":"2007","journal-title":"PLoS Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"7420","DOI":"10.1073\/pnas.0608665104","article-title":"An allosteric model of circadian KaiC phosphorylation.","volume":"104","author":"JS van Zon","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"e96","DOI":"10.1371\/journal.pcbi.0020096","article-title":"Circadian rhythmicity by autocatalysis.","volume":"2","author":"A Mehra","year":"2006","journal-title":"PLoS Comput Biol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"2015","DOI":"10.1529\/biophysj.105.076554","article-title":"A model for the circadian rhythm of cyanobacteria that maintains oscillation without gene expression.","volume":"91","author":"G Kurosawa","year":"2006","journal-title":"Biophys J"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/msb4100128","article-title":"Functioning and robustness of a bacterial circadian clock.","volume":"3","author":"S Clodong","year":"2007","journal-title":"Mol Syst Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1177\/0748730406295749","article-title":"A mathematical model for the kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria.","volume":"22","author":"F Miyoshi","year":"2007","journal-title":"J Biol Rhythms"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e408","DOI":"10.1371\/journal.pone.0000408","article-title":"Monomer-shuffling and allosteric transition in KaiC circadian oscillation.","volume":"2","author":"M Yoda","year":"2007","journal-title":"PLoS ONE"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1773","DOI":"10.1529\/biophysj.107.127555","article-title":"Mechanism of robust circadian oscillation of KaiC phosphorylation in vitro.","volume":"95","author":"K Eguchi","year":"2008","journal-title":"Biophys J"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1101\/gad.9.12.1469","article-title":"Circadian orchestration of gene expression in cyanobacteria.","volume":"9","author":"Y Liu","year":"1995","journal-title":"Genes Dev"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"4995","DOI":"10.1073\/pnas.82.15.4995","article-title":"Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.","volume":"82","author":"B Brooks","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/0022-2836(85)90230-X","article-title":"Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme.","volume":"181","author":"M Levitt","year":"1985","journal-title":"J Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1126\/science.1088172","article-title":"How enzymes work: analysis by modern rate theory and computer simulations.","volume":"303","author":"M Garcia-Viloca","year":"2004","journal-title":"Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/S0006-3495(04)74084-9","article-title":"Revisiting free energy calculations: a theoretical connection to MM\/PBSA and direct calculation of the association free energy.","volume":"86","author":"JM Swanson","year":"2004","journal-title":"Biophys J"},{"key":"ref30","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":"ref31","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1126\/science.1085515","article-title":"A Perspective on Enzyme Catalysis.","volume":"301","author":"SJ Benkovic","year":"2003","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev.biophys.27.1.1","article-title":"The stereochemical mechanism of the cooperative effects in hemoglobin revisited.","volume":"27","author":"MF Perutz","year":"1998","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/nature02239","article-title":"Conformational change and protein-protein interactions of the fusion protein of Semliki Forest virus.","volume":"427","author":"DL Gibbons","year":"2004","journal-title":"Nature"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1038\/41111","article-title":"Kinesin hydrolyses one ATP per 8-nm step.","volume":"388","author":"MJ Schnitzer","year":"1997","journal-title":"Nature"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/30018","article-title":"Receptor clustering as a cellular mechanism to control sensitivity.","volume":"393","author":"D Bray","year":"1998","journal-title":"Nature"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1111\/j.1432-1033.1990.tb15640.x","article-title":"Thermodynamics of information transfer between subunits in oligomeric enzymes and kinetic cooperativity. 1. Thermodynamics of subunit interactions, partition functions and enzyme reaction rate.","volume":"194","author":"J Ricard","year":"1990","journal-title":"Eur J Biochem"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"703","DOI":"10.1016\/j.molcel.2008.01.015","article-title":"Assembly and disassembly dynamics of the cyanobacterial periodosome.","volume":"29","author":"S Akiyama","year":"2008","journal-title":"Mol Cell"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1767","DOI":"10.1038\/emboj.2008.104","article-title":"Structural model of the circadian clock KaiB-KaiC complex and mechanism for modulation of KaiC phosphorylation.","volume":"27","author":"R Pattanayek","year":"2008","journal-title":"Embo J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions.","volume":"81","author":"DT Gillespie","year":"1977","journal-title":"J phys Chem"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1249","DOI":"10.1038\/nature06395","article-title":"Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock.","volume":"450","author":"JR Chabot","year":"2007","journal-title":"Nature"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1101\/gad.1661808","article-title":"Dual KaiC-based oscillations constitute the circadian system of cyanobacteria.","volume":"22","author":"Y Kitayama","year":"2008","journal-title":"Genes Dev"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1101\/gad.1686608","article-title":"Lego clocks: building a clock from parts.","volume":"22","author":"M Brunner","year":"2008","journal-title":"Genes Dev"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1084","DOI":"10.1038\/nsmb1312","article-title":"Autonomous synchronization of the circadian KaiC phosphorylation rhythm.","volume":"14","author":"H Ito","year":"2007","journal-title":"Nat Struct Mol Biol"},{"key":"ref44","doi-asserted-by":"crossref","DOI":"10.1137\/1.9780898718195","article-title":"Simulating, Analyzing, and Animating Dynamical Systems: Society for Industrial and Applied Mathematics, Philadelphia.","author":"B Ermentrout","year":"2002"},{"key":"ref45","first-page":"95","article-title":"Response curves in circadian periodicity.","author":"J Aschoff","year":"1965"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"8564","DOI":"10.1073\/pnas.0508696103","article-title":"Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus.","volume":"103","author":"RM Smith","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"18819","DOI":"10.1073\/pnas.0706069104","article-title":"Circadian rhythms of superhelical status of DNA in cyanobacteria.","volume":"104","author":"MA Woelfle","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"12109","DOI":"10.1073\/pnas.0602955103","article-title":"A KaiC-associating SasA-RpaA two-component regulatory system as a major circadian timing mediator in cyanobacteria.","volume":"103","author":"N Takai","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1101\/gad.1488107","article-title":"labA: a novel gene required for negative feedback regulation of the cyanobacterial circadian clock protein KaiC.","volume":"21","author":"Y Taniguchi","year":"2007","journal-title":"Genes Dev"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000568","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,23]],"date-time":"2018-10-23T04:48:44Z","timestamp":1540270124000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000568"}},"subtitle":[],"editor":[{"given":"Jorg","family":"Stelling","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,11,20]]},"references-count":49,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2009,11,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000568","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,20]]}}}