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Similarity Measures for Protein Ensembles 英文参考文献.doc

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Similarity Measures for Protein Ensembles 英文参考文献

SimilarityMeasuresforProteinEnsembles KrestenLindorff-Larsen1¤*,JesperFerkinghoff-Borg2 1DepartmentofMolecularBiology,UniversityofCopenhagen,Copenhagen?,Denmark,2?rstedDTU,TechnicalUniversityofDenmark,?rstedsPlads,Lyngby,Denmark Abstract Analysesofsimilaritiesandchangesinproteinconformationcanprovideimportantinformationregardingproteinfunction andevolution.Manyscores,includingthecommonlyusedrootmeansquaredeviation,havethereforebeendevelopedto quantifythesimilaritiesofdifferentproteinconformations.However,insteadofexaminingindividualconformationsitisin manycasesmorerelevanttoanalyseensemblesofconformationsthathavebeenobtainedeitherthroughexperimentsor frommethodssuchasmoleculardynamicssimulations.Weherepresentthreeapproachesthatcanbeusedtocompare conformational ensembles in the same way as the root mean square deviation is used to compare individual pairs of structures. The methods are based on the estimation of the probability distributions underlying the ensembles and subsequent comparison of these distributions. We first validate the methods using a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformationsbetterthanstandardsingle-moleculerefinement. Citation:Lindorff-LarsenK,Ferkinghoff-BorgJ(2009)SimilarityMeasuresforProteinEnsembles.PLoSONE4(1):e4203.doi:10.1371/journal.pone.0004203 Editor:MarkIsalan,CenterforGenomicRegulation,Spain ReceivedOctober28,2008;AcceptedNovember25,2008;PublishedJanuary15,2009 Copyright:?2009Lindorff-Larsenetal.Thisisanopen-accessarticledistributedunderthetermsoftheCreativeCommonsAttributionLicense,whichpermits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Theauthorshavenosupportorfundingtoreport. CompetingInterests:Theauthorshavedeclaredthatnocompetingin