{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,8]],"date-time":"2024-08-08T20:30:27Z","timestamp":1723149027785},"reference-count":38,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2011,7,19]],"date-time":"2011-07-19T00:00:00Z","timestamp":1311033600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0021809","type":"journal-article","created":{"date-parts":[[2011,7,19]],"date-time":"2011-07-19T20:52:07Z","timestamp":1311108727000},"page":"e21809","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":15,"title":["In Silico Investigation of Conformational Motions in Superfamily 2 Helicase Proteins"],"prefix":"10.1371","volume":"6","author":[{"given":"Holger","family":"Flechsig","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Denny","family":"Popp","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander S.","family":"Mikhailov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2011,7,19]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1016\/S0092-8674(00)80922-8","article-title":"The cell as a collection of protein machines: Preparing the next generation of molecular biologists.","volume":"92","author":"B Alberts","year":"1998","journal-title":"Cell"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1016\/j.sbi.2008.01.007","article-title":"On helicases and other motor proteins.","volume":"18","author":"EJ Enemark","year":"2008","journal-title":"Curr Opin Struct Biol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1016\/S0959-440X(02)00298-1","article-title":"Helicase structure and mechanism.","volume":"12","author":"JM Caruthers","year":"2002","journal-title":"Curr Opin Struct Biol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1146\/annurev.bi.65.070196.001125","article-title":"Mechanisms of helicase-catalyzed DNA unwinding.","volume":"65","author":"TM Lohman","year":"1996","journal-title":"Annu Rev Biochem"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1016\/j.sbi.2007.05.007","article-title":"RNA helicases - one fold for many functions.","volume":"17","author":"E Jankowsky","year":"2007","journal-title":"Curr Opin Struct Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1315","DOI":"10.2174\/138161206776361147","article-title":"Understanding helicases as a means of virus control.","volume":"12","author":"DN Frick","year":"2006","journal-title":"Curr Pharm Des"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nrd1853","article-title":"Viral and cellular RNA helicases as antiviral targets.","volume":"4","author":"AD Kwong","year":"2005","journal-title":"Nat Rev Drug Discovery"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.biochem.76.052305.115300","article-title":"Structure and mechanism of helicases und nucleic acid translocases.","volume":"76","author":"MR Singleton","year":"2007","journal-title":"Annu Rev Biochem"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1146\/annurev.biophys.37.032807.125908","article-title":"Translocation and unwinding mechanism of RNA and DNA helicases.","volume":"37","author":"AM Pyle","year":"2008","journal-title":"Annu Rev Biophys"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1038\/nrm2394","article-title":"Non-hexameric DNA helicases and translocases: mechanisms and regulation.","volume":"9","author":"TM Lohman","year":"2008","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"3209","DOI":"10.1038\/emboj.2008.232","article-title":"Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein.","volume":"27","author":"DH Luo","year":"2008","journal-title":"EMBO Journal"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1073\/pnas.0913380107","article-title":"Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism.","volume":"107","author":"M Gu","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1016\/j.jmb.2010.11.034","article-title":"Visualizing ATP-dependend RNA translocation by the NS3 helicase from HCV.","volume":"405","author":"TC Appleby","year":"2011","journal-title":"J Mol Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/S0959-440X(05)80116-2","article-title":"Helicases: amino acid sequence comparisons and structure-function relationships.","volume":"3","author":"AE Gorbalenya","year":"1993","journal-title":"Curr Opin Struct Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nature04331","article-title":"RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP.","volume":"439","author":"S Dumont","year":"2006","journal-title":"Nature"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1126\/science.1144130","article-title":"Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase.","volume":"317","author":"S Myong","year":"2007","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.sbi.2010.03.011","article-title":"SF1 and SF2 helicases: family matters.","volume":"20","author":"ME Fairman-Williams","year":"2010","journal-title":"Curr Opin Struct Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.sbi.2009.12.008","article-title":"Stepwise translocation of nucleic acid motors.","volume":"20","author":"S Myong","year":"2010","journal-title":"Curr Opin Struct Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/S0969-2126(98)00010-0","article-title":"Hepatitis C virus NS3 helicase domain with a bound oligonucleotide: The crystal structure provides insights into the mode of unwinding.","volume":"6","author":"JL Kim","year":"1998","journal-title":"Structure"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1531","DOI":"10.1002\/bip.1978.360170612","article-title":"Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A three-dimensional lattice model of lysozyme.","volume":"17","author":"Y Ueda","year":"1978","journal-title":"Biopolymers"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/j.sbi.2005.02.005","article-title":"Coarse-grained models for proteins.","volume":"15","author":"V Tozzini","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1905","DOI":"10.1103\/PhysRevLett.77.1905","article-title":"Large amplitude elastic motions in proteins from a single-parameter, atomic analysis.","volume":"77","author":"MM Tirion","year":"1996","journal-title":"Phys Rev Lett"},{"key":"ref23","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"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"13253","DOI":"10.1073\/pnas.2235686100","article-title":"A comparative study of motor-protein motions by using a simple elastic-network model.","volume":"100","author":"W Zheng","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref25","year":"2006"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"886","DOI":"10.1002\/prot.21326","article-title":"Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model.","volume":"67","author":"W Zheng","year":"2007","journal-title":"Proteins"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"8697","DOI":"10.1073\/pnas.0702950104","article-title":"Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines.","volume":"104","author":"Y Togashi","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1000814","DOI":"10.1371\/journal.pcbi.1000814","article-title":"Nonlinearity of mechanochemical motions in motor proteins.","volume":"6","author":"Y Togashi","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"20875","DOI":"10.1073\/pnas.1014631107","article-title":"Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations.","volume":"107","author":"H Flechsig","year":"2010","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/j.str.2004.11.008","article-title":"Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing.","volume":"13","author":"T Nishino","year":"2005","journal-title":"Structure"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/nsmb1246","article-title":"Structural basis for DNA duplex separation by a superfamily-2 helicase.","volume":"14","author":"K Buettner","year":"2007","journal-title":"Nat Struct Mol Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"801","DOI":"10.1016\/j.cell.2008.04.029","article-title":"Structure of the DNA repair helicase XPD.","volume":"133","author":"H Liu","year":"2008","journal-title":"Cell"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"5118","DOI":"10.1074\/jbc.M707548200","article-title":"Structure of the DNA repair helicase Hel308 reveals DNA binding and autoinihibitory domains.","volume":"283","author":"JD Richards","year":"2008","journal-title":"J Biol Chem"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1016\/j.jmb.2007.10.004","article-title":"Archaeal Hel308 domain V couples DNA binding to ATP hydrolysis and positions DNA for unwinding over the helicase ratchet.","volume":"374","author":"IL Woodman","year":"2007","journal-title":"J Mol Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/S0968-0004(00)01734-5","article-title":"Unwinding the Gordian knot of helicase action.","volume":"26","author":"P Soultanas","year":"2001","journal-title":"Trends Biochem Sci"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"074112","DOI":"10.1063\/1.3167410","article-title":"Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion.","volume":"131","author":"JN Stember","year":"2009","journal-title":"J Chem Phys"},{"key":"ref37","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 U S A"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD-visual molecular dynamics.","volume":"14","author":"W Humphrey","year":"1996","journal-title":"J Molec Graphics"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0021809","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T16:55:25Z","timestamp":1540227325000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0021809"}},"subtitle":[],"editor":[{"given":"J\u00f6rg","family":"Langowski","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2011,7,19]]},"references-count":38,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2011,7,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0021809","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,19]]}}}