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 Don tneedpureproteins Don tneedAb 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 28 289 291 DIP数据库结构 NucleicAcidsResearch 2000 28 289 291 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 hybridsystem 4 Determinetheintersectionofthepredictedandexperimentalnetworksandtestinvivothebiologicalrelevanceofkeyinteractionswithinthisset ACombinedExperimentalandComputationalStrategy Science2002295 321 高友鹤gaoyouhe