蛋白质相互作用的生物信息学.ppt

蛋白质相互作用的生物信息学,高友鹤,中国医学科学院基础医学研究所,蛋白质相互作用的生物信息学,实验数据蛋白质相互作用数据库高通量实验数据的验证蛋白质相互作用网络计算预测蛋白质相互作用,实验数据,蛋白质相互作用的知识来源于实验。高通量地应用传统实验方法获取大量相互作用信息。高通量的数据需要验证。,高通量实验方法,CurrOpinStructBiol2003,13:377,Yeasttwo-hybridassay,Benefits:invivo.Dontneedpureproteins.DontneedAb.Drawbacks:onlytwoproteinsaretestedatatime(nocooperativebinding);ittakesplaceinthenucleus,somanyproteinsarenotintheirnativecompartment;anditpredictspossibleinteractions,butisunrelatedtothephysiologicalsetting.,Massspectrometryofpurifiedcomplexes,Benefits:severalmembersofacomplexcanbetagged,givinganinternalcheckforconsistency;anditdetectsrealcomplexesinphysiologicalsettings.Drawbacks:itmightmisssomecomplexesthatarenotpresentunderthegivenconditions;taggingmaydisturbcomplexformation;andlooselyassociatedcomponentsmaybewashedoffduringpurification.,CorrelatedmRNAexpression,Benefits:itisaninvivotechnique,albeitanindirectone;andithasmuchbroadercoverageofcellularconditionsthanothermethods.Drawbacks:itisapowerfulmethodfordiscriminatingcellstatesordiseaseoutcomes,butisarelativelyinaccuratepredictorofdirectphysicalinteraction;anditisverysensitivetoparameterchoicesandclusteringmethodsduringanalysis.,Geneticinteractions(syntheticlethality).,Benefits:itisaninvivotechnique,albeitanindirectone;anditisamenabletounbiasedgenome-widescreens.Drawbacks:notnecessarilyphysicalinteractions,蛋白质相互作用的生物信息学,实验数据蛋白质相互作用数据库高通量实验数据的验证蛋白质相互作用网络计算预测蛋白质相互作用,蛋白质相互作用数据库,CurrOpinStructBiol2003,13:377,THEDIPDATABASE,DatabaseofInteractingProteinsTheDIPdatabasecatalogsexperimentallydeterminedinteractionsbetweenproteins.,DIP相互作用的表达,NucleicAcidsResearch,2000,28,289291,DIP数据库结构,NucleicAcidsResearch,2000,28,289291,BIND：theBiomolecularInteractionNetworkDatabase,NucleicAcidsResearch,2001,29,242-245,蛋白质相互作用的生物信息学,实验数据蛋白质相互作用数据库高通量实验数据的验证蛋白质相互作用网络计算预测蛋白质相互作用,高通量实验数据需要验证,CurrOpinStructBiol2003,13:377,与可信的数据相比,CurrOpinStructBiol2003,13:377,ExpressionProfileReliability,EPRIndexExpressionProfileReliabilityIndex(EPRIndex)evaluatesthequalityofalarge-scaleprotein-proteininteractiondatasetsbycomparingtheexpressionprofileoftheinteractingdatasetwiththatofthehigh-qualitysubsetoftheDIPdatabase.,高通量数据互相比,CurrOpinStructBiol2003,13:377,ParalogousVerificationMethod,PVMScoreTheParalogousVerification(PVM)methodjudgesaninteractionprobableiftheputativelyinteractingpairhasparalogsthatalsointeract.,DomainPairVerification,DPVScoreTheDomainPairVerification(DPV)methodjudgesaninteractionprobableifpotentialdomain-domaininteractionsbetweenthepairaredeemedprobable.,Correlationdistance,NatureBiotechnology2003,22,78,蛋白质相互作用网络,Nature2001,411,41-42,相互作用网络的用途,Themosthighlyconnectedproteinsinthecellarethemostimportantforitssurvival.,Nature2001,411,41-42,蛋白质相互作用的生物信息学,实验数据蛋白质相互作用数据库高通量实验数据的验证蛋白质相互作用网络计算预测蛋白质相互作用,计算预测蛋白质相互作用,CurrOpinStructBiol2003,13:377,Docking,Need3DStructuresCAPRI:CriticalAssessmentofPredictedInteractions,acommunity-wideexperimentforassessingthepredictivepoweroftheseprocedures.,ProteinFusion,Basedon:Somepairsofinteractingproteinsencodedinseparategenesinoneorganismarefusedtoproducesinglehomologousproteinsinotherorganism.CompareE.Coliwithothergenomes:6,809putativeprotein-proteininteractionsMarcotteEMScience285,751(1999)Compareyeastwithothers:45,502putativeinteractionsEnrightAJNature402,86(1999),GeneClustering,Basedon:Functionalcouplinggenesareinconservedgeneclustersindifferentgenomes.,GeneClustering,OverbeekRPNAS96,2896(1999),OverbeekRPNAS96,2896(1999),Phylogeneticprofile,PNAS(1999)96,4285-4288,ACombinedExperimentalandComputationalStrategy,1)Screenrandompeptidelibrariesbyphagedisplaytodefinetheconsensussequencesforpreferredligandsthatbindtoeachpeptiderecognitionmodule.2)Onthebasisoftheseconsensussequences,computationallyderiveaprotein-proteininteractionnetworkthatlinkseachpeptiderecognitionmoduletoproteinscontainingapreferredpeptideligand.,Science2002295,321,3)Experimentallyderiveaprotein-proteininteractionnetworkbytestingeachpeptiderecognitionmoduleforassociationtoeachproteinoftheinferredproteomeintheyeasttwo-hybridsyste