Classication of Domain Movements in Proteins Using Dynamic Contact Graphs.docVIP

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Classication of Domain Movements in Proteins Using Dynamic Contact Graphs.doc

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Classication of Domain Movements in Proteins Using Dynamic Contact Graphs

ClassificationofDomainMovementsinProteinsUsing DynamicContactGraphs DanielTaylor,GavinCawley,StevenHayward* D’ArcyThompsonCentreforComputationalBiology,SchoolofComputingSciences,UniversityofEastAnglia,Norwich,UnitedKingdom Abstract Anewmethodfortheclassificationofdomainmovementsinproteinsisdescribedandappliedto1822pairsofstructures fromtheProteinDataBankthatrepresentadomainmovementintwo-domainproteins.Themethodisbasedonchangesin contactsbetweenresiduesfromthetwodomainsinmovingfromoneconformationtotheother.Wearguethatthereare five types of elemental contact changes and that these relate to five model domain movements called: ‘‘free’’, ‘‘open- closed’’, ‘‘anchored’’, ‘‘sliding-twist’’, and ‘‘see-saw.’’ A directed graph is introduced called the ‘‘Dynamic Contact Graph’’ whichrepresentsthecontactchangesinadomainmovement.Inmanycasesagraph,orpartofagraph,providesaclear visualmetaphorforthemovementitrepresentsandisamotifthatcanbeeasilyrecognised.TheDynamicContactGraphs are often comprised of disconnected subgraphs indicating independent regions which may play different roles in the domain movement. The Dynamic Contact Graph for each domain movement is decomposed into elemental Dynamic ContactGraphs,thosethatrepresentelementalcontactchanges,allowingustocountthenumberofinstancesofeachtype ofelementalcontactchangeinthedomainmovement.Thisnaturallyleadstosixteenclassesintowhichthe1822domain movementsareclassified. Citation: Taylor D, Cawley G, Hayward S (2013) Classification of Domain Movements in Proteins Using Dynamic Contact Graphs. PLoS ONE 8(11): e81224. doi:10.1371/journal.pone.0081224 Editor:DaniloRoccatano,JacobsUniversityBremen,Germany ReceivedJuly31,2013;AcceptedOctober9,2013;PublishedNovember18,2013 Copyright: ? 2013 Taylor et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:Theauthor