MOE-HomologyModeling

CCG&InforSenseAllRightsReservedAdvancedApplicationinMOEHomologyModelingCCG&InforSenseAllRightsReservedBackground•Purpose:Buildingall-atom3Dstructureofunknownstructuresequencefromhomologytemplate•Hypothesis：AligntwosequencesA(unknownstructure)andB(knownstructure),iftheidentitypercentageinsequenceAexceeds30%,thenBcanbeconsideredashomologytemplateofA.CCG&InforSenseAllRightsReservedHomologyModelingMethodologyinMOE•Fromsequence-to-structureFold/FamilyIdentification(FamilyDatabase)Fold/FamilyIdentification(FamilyDatabase)HomologyModelingRotamerLibraryHomologyModelingRotamerLibraryStructureRefinementEnergyMinimizationStructureRefinementEnergyMinimizationProteinSequencePIR,FastA,…StructureValidationGeometryScoringStructureValidationGeometryScoringMultipleAlignmentConservedCoreDetectionMultipleAlignmentConservedCoreDetectionProteinStructuregi|2073144MIRLVLLLALTAHCVNAGCP...1AFA.1AIEVKLANMEAEINTLKSKL...1HUPAASERKALQTEMARIKKWLT...1TN3ALQTVCLKGTKVHMKCFLAF...1MSB.ASGKKFFVTNHERMPFSKVKA...MDYEILFSDETMNYADAGTYCQSRGMALVSSAMRDSTMVKAILAFTEV...CCG&InforSenseAllRightsReservedMOEProteinDatabase•1.Non-redundantPDB–$MOE/lib/pdb.mdb–Non-redundantclusteredproteinfamilystructuredatabase–Servesas“templatedictionary”forhomologymodeling•2.ProteinFamilies–$MOE/lib/pdb.fam–containstheclusterinformationofthestructurefamilydatabaseon1Dlevel•3.RemediatedPDB(separateDVD)–cleanedPDBentries–pdb_2008_09_09.mdb•4.AntibodyDatabaseandFamilies--$MOE/lib/fab.mdb--$MOE/lib/fab.fam--beusedwhenmakinghomologymodelsofantibodies•5.RotamerLibrary--$MOE/lib/amino.mdbCCG&InforSenseAllRightsReservedForcefield•Beforemodeling,checkthecurrentlyloadedforcefield.•EnsurethatAMPER99oranyother“protein”forcefieldisloadedin(MOE/SE|Window|PotentialSetup).•Click“Load...”tochangeforcefield:–CHARMMandAMBERperformbestonproteins.–MMFF94xisthedefaultforcefield.Itisagoodcompromiseformodelingprotein-ligandinteractions.CCG&InforSenseAllRightsReservedExample1：BuildingHomologyModelforcasp_t69•Predicta3DstructureofaproteinsequencewiththeHomologyModelingtools.1.(SE|File|Open)$MOE/sample/mol/casp_t69.pirNotethatthechainhasonlysequenceandnostructuredata.TheOpenSequenceFilebuttonbecomesactiveifMOErecognizesthefileasasequencefile.CCG&InforSenseAllRightsReservedExample1:PDBSearch•Searchforsuitabletemplatestructuresinthebuilt-instructurefamilydatabase(see$MOE/lib/pdb.fam)tobuilda3Dproteinmodel.2.(SE|Homology|PDBSearch).CCG&InforSenseAllRightsReservedExample1：PDBSearch3.PressonChain“1”toloadthequerysequenceintothesearchpanel.4.PressSearchtostartsearchingthequeryagainstMOE’sclusteredstructuredictionary.•Thefastscanisapair-wiseFasta-typesearch(localalignments).TheresultfromthefastscanisvalidatedbyaglobalNeedleman-WunschalignmentprocedureapplyingZ-Scorescrambling.CCG&InforSenseAllRightsReservedExample1:PDBSearchAsthesearchprogresses,pre-alignedfamiliesappearintheResultssectionofthepanelwiththeircalculatedE-values.Ifappropriate,MOEperformsaZ-scorecalculation.Familieswhichhavepassedbothfilterswillremainlistedoncethesearchiscompleted.5.Examinethepre-alignedfamiliesbydouble-clickoneach“hit”.Selectthe1sthitandLoadAlignment.6.PresstheLoadAllbutton.CCG&InforSenseAllRightsReservedExample1:PDBSearchAllsequencesandtheircorrespondingstructures(ifavailable)areloadedintotheMOEsystem.7.Changerenderingto(MOEpop-up|Backbone|Line)and(MOEpop-up|Hide|All).NotethatthestructuresarestillNOTsuperposed.CCG&InforSenseAllRightsReservedExample1:AlignmentCreatea“PercentResidueIdentityMatrix”tochooseasuitablesingletemplateforhomologymodelling.8.(SE|Homology|Align).9.SelectChain1first,then(SE|Selection|InvertChains)toselectalltemplatechainsintheSE.10.IntheAlignpanel,changetheChainSelectionoptiontofreeze,sincethesequencesarealreadypre-aligned.PressOK.CCG&InforSenseAllRightsReservedExample1:IdentityMatrix11.OpentheSVLCommandsWindowbypressing“SVL”atthetoprightofthemainMOEWindow.The“PercentResidueIdentityMatrix”iswrittentotheSVLCommandsWindow.Identitypercentageinchain1CCG&InforSenseAllRightsReservedManuallyAdjustAlignment•Residuescanbemovedbymiddlemousedragginginconjunctionwithmetakeysifinneed.MiddledragMiddledragGapsarenotpreservedGapsarenotpreservedctrl-Middledragctrl-MiddledragEntirechainmoves&gapsarepreservedEntirechainmoves&gapsarepreservedshift-Middledragshift-MiddledragGapsarepreserved&residuesontherightmoveGapsarepreserved&residuesontherightmovealt-MiddleDragselectedresiduesalt-MiddleDragselectedresidues“BeadsonaString”“BeadsonaString”CCG&InforSenseAllRightsReservedExample1:Modeling•OpentheHomologypanel(SE|Homology|HomologyModel).InputdataInputdataModelparameter.Modelparameter.SequencewithunknownstructureSequencewithunknownstructureTemplatestructureTemplatestructureOptionsOptionsNumberofmodelsNumberofmodelsLoopdatabaseLoopdatabaseDegreeofrefinementDegreeofrefinementOutputdataOutputdataCCG&InforSenseAllRightsReservedExample1:ModelingBuildahomologymodelusingthechosentemplate.12.OpentheHomologypanel(SE|Homology|HomologyModel)13.Setoptionsasfollows:–Select“Chain#2(1PWB.A)”asTemplate)–Changedefaultfilenamestocasp