Conformational changes associated with proteinprotein - PDF document

Conformationalchangesassociatedwithprotein–proteinChern-SingGoh,DuncanMilburnandMarkGersteinMotionsrelatedtoprotein–proteinbindingeventscanbesurveyedfromtheperspectiveoftheDatabaseofMacromolecularMovements.Thereareanumberofalternativeconceptualmodelsthatdescribetheseevents,particularlyinducedtandpre-existingequilibrium.Thereisevidencefor COSTBI113 www.sciencedirect.comCurrentOpinioninStructuralBiology describeoccurrencesofdynamicpopulationshiftinallos-tericregulationmechanisms.Table1providesamorecomprehensiveoverviewofmotionsandtheircorre-spondingmodels.InducedÞtAnelectroncryo-microscopystudyillustratesthattheclosingofmyosinsactin-bindingcleftisstructurallycoupledtotheopeningofthenucleotide-bindingpocketpocket].Initiationofbindingoccursthroughaweakstereospecicinteractionwherebythelowerdomainofmyosincontactstheactinlamentinanopenconforma-tion(Figure2a).Asthisinteractionprogressestowardstrongbinding,thecleftinthemyosindomaincloses,ashasbeenpreviouslysuggested[15].Theuppermyosindomainswingsaroundbyarotationof21,sothatthecardiomyopathyloopcomesincontactwiththeactinsurface,thusdoublingthetotalinteractionsurfaceareaFigure2b).Thiscreatesadisplacementmovementofintheswitch1element,whichcontainsthenucleotide-bindingpocket.Thesestudiesthereforeindicatethatstrongbindingtoactinopensupthe Figure1 L L LL L Current Opinion in Structural Biology Modelsofproteinbindingmechanisms.Lockandkeymodel.Induced-fitmodel.Pre-existingequilibriummodel.L,ligand. Table1Proteincomplexeswithobservedconformationalchanges.ProteinBindingConformation1(PDBcode)Conformation2(PDBcode)MaximumCdisplacement(AMyosinActinNANA9InducedYesAntibodySpe7TrxShear3NANA6.7EquilibriumYesGpIb-IX-VThrombin1P8V1OOK37EquilibriumYessubunitRGS141BOF1KJY10.2177InducedYesFliSFliC1ORJ1ORY29.3168.8InducedYesNtrCP1DC71DC812177EquilibriumYesR1Fc1OVZ1OWO11180InducedImportinSREPB-21GCJ1UKL19BtubColicinE31NQF1UJW13.4179InducedLeukemiainhibitoryfactorGP1301LKI1PVH7169InducedLir-1Hla-A21G0X1P7Q11177InducedGPCRkinase2G21BAK1OMW17171Induced-ATPaseIF1BMF1OHH4.5Her2HerceptinFab1N8Y1N8Z13.7170InducedErythropoietinErythropoietinreceptor1BUY1EER15.4149.5InducedGroELGroES1AON1OEL48.5169.6AllostericCalmodulinCalmodulin-bindingdomainofskeletallightchainmyosinkinase4CLN2BBM17961AllostericProto-oncogeneCblZAP-70kinase2CBL1B47758InducedCDK2CyclinA1FIN1HCK20176InducedMms2Ubc131J741J7D20.7164InducedSteroidreceptorcoactivator-11PRG1FM613169EquilibriumTRAF6RANK1LB41LB516.6133EitherXRCC4DNA-ligaseIV1FU11IK914119InducedRANRAN-bindingprotein21BYU1RRP53.4179InducedCheYCheA3CHY1EAY3.823InducedDatatakenfromtheliterature.Theclassificationsareassumedbasedontheexperimentaldataavailable.NA,notavailable.Foldingandbinding CurrentOpinioninStructuralBiology6www.sciencedirect.com nucleotide-bindingpocket.Thisandotherstudiessug-gestthatstrongbindingofthemyosincross-bridgetoactinprobablyclosestheactin-bindingcleft[16,17]AstructureoftheFliSFliCcomplexdemonstratesthebindingmechanismofthebacterialexportchaperoneanditsroleintypeIIIsecretionetion].FliCmonomerspoly-merizetoformthetaillamentofthebacterialagellumellum.ExportchaperoneFliSbindsspecicallytoFliC[20,21]toaidthecorrectassemblyofthebacterialgellumandtoavoidprematureinteractionswithotherstructuralcomponentsoftheagellum[22,23].ThestructureofFliSisanantiparallelfour-helixbundlewithaquasi-helicalcapformedby16N-terminalresiduesresidues].UponbindingFliC,theN-terminalcapofFliSisdisplacedandre-orientstoformashorthelixononesideofthehelicalbundle(Figure3),whileahelicalsegmentofFliC(residues499505)movesintothepositionthatwasformerlyoccupiedbytheFliSN-terminalcap.ThissuggeststhattheN-terminalcapofFliSworksasamolecularstoppertoblockthehydrophobicbindingsitewhenFliSisnotboundtoFliC.TherecentcrystalstructureofaG-proteinboundtotheGoLocomotiffoundinregulatoryproteinshighlightsimportantresiduesthatcontrolthespecicityoftheGoLocointeractionandsuggestsmechanismsforpreventingthebindingofGG].Regulatoryproteinswiththe19aminoacidGoLocomotif[25,26]canbindtoGsubunitsandmaintainG-proteinsubunitdisassociationiation,27–30].GoLocomotifproteinsinter-actspecicallywithGDP-boundGsubunits,preventingbothGDPreleaseease,27–29]andGreassembly[29,30].Kimpleetal..]determinedthecrystalstructureoftheRGS14GoLocoregionboundtotheadenylylcyclaseinhibitoryGsubunit(InteractionwiththeR14GLpeptide(residues496530ofratRGS14containingtheGoLocoregion)isshowntoaltertheconformationofswitchesIIIIrelativetoGbound.Inparticular,thedeviationinswitchII(whereArg208moves)couldhinderbindingtoGoLoco-complexedGDP.ThelargestchangeoccursintheCloopoftheGhelicaldomain,whereAla114isdisplaced11AawayfromtheRas-likedomain. Figure2 (a)(b)CardiomyopathyCurrent Opinion in Structural Biology Overviewofmyosin(yellow)anditsupper50kDadomain(red)dockedtoactin(blue)usingarigid-bodyX-raymodelofmyosininitsopencleft,weakbindingformandfitwithanindependentupper50kDadomainthatillustratesitsclosed,strongbindingform.Figureproducedwith Figure3 (a)(b)Current Opinion in Structural Biology StructuralconformationsofuncomplexedFliSandFliSboundtoFliC.ConformationalchangesassociatedwithproteinproteininteractionsGoh,MilburnandGerstein3 www.sciencedirect.comCurrentOpinioninStructuralBiology Pre-existingequilibriumTherearesomeexperimentaldatathatcandiscriminatebetweeninducedtandpre-existingequilibriummodels.Forhemoglobin,numerousconvincingexperimentssup-porttheMWCmodelandruleouttheinduced-tmodelmodel.Recently,therehavebeenanumberofstudiesre-portedthatsupportthepre-existingequilibriumhypo-thesis.AbreakthroughstudyreportedbyJamesetal.al.]presentscrystalstructuresofamonoclonalIgEantibody,Spe7,thatexistsintwoverydifferentconfor-mations,eachbindingstructurallydistinctantigens.Thepredominantunboundisomer(Ab)hasaat,regularbindingsite,whichisreminiscentofantibodiesthatbindproteinsorpeptides.Thealternativeisomer(Ab)con-tainsadeeper,funnel-shapedpocket,typicalofantibo-diesthatbindhaptens(smallmoleculesthatbecomeantigenicwhenboundtoproteins).TherecombinantproteinantigenTrxShear3bindstoAb,butdoesnotbindtoAb,andhaptensdonotbindtoAb.TheseconformationsresultfromlargebackbonealterationsoftheH3andL3loops,withCatomsdeviatingbyupto6.7AFigure4).TheH3loopipsbetweentheAbisomer,displayingdifferentsidechainrotamers.Thisstudyhighlightsthepotentialroleofconformationaldiversityincross-reactivity,whichcanleadtoauto-immunediseaseandallergyallergy.TwocrystalstructuresrecentlydeterminedbyCelikeletal.al.]andDumasetal.al.](Figure5)illustratetheexistenceofanensembleofpossibleconformationsforboundproteins.Theauthorsdescribethethrombininteraction,butobtainverydifferentcrystalforms.BoththesepapersshowtwothrombinsboundtoeachglycoproteinGpIbonethrombinboundthroughexositeIandtheotherboundthroughexositeII.AlthoughtherstthrombinisboundtoapproximatelythesameregionofGpIbinbothstructures,thestruc-turesdisplaycompletelydifferentcontactsandarerotatedapproximately180aboutanaxisperpendiculartotheinterface.Additionally,structuresofthesecondthrombininterfaceshowtheexibleanionicsegmentofGpIbrotated90,resultingina37AdisplacementofTyr279,asulfatedtyrosinelocatedontheanionicsegmentandshowntobenecessaryforoptimalthrombinbinding[36].ThesetwostructuresofthrombinGpIbbindingillustratetheverydifferentconformationsthatGpIbhavewhileboundtothesameprotein(Figure5).Furtherstudiesmaybeabletoelucidatethepredominantstruc-turalinterfaceandleadtoabetterfunctionalunderstand-ingofthethrombinGpIbinteraction.AllostericregulationthedynamicpopulationshiftmodelAlthoughallostericregulationiswellacceptedformulti-domainproteins,itisnotascommonlythoughtofforsingle-domainproteins.ItwasntuntilarecentNMR Figure4 MainchainconfigurationsoftheIgEantibodySpe7:freeisomersAb(green)andAb(purple),hapten-boundisomerAb(blue)andTrxShear3-boundisomerAb(pink).FigureprovidedbyDanTawfik. Figure5 90iTIITIITIITIIGplb Gplb Gplb TITITI (b) TheGpIbthrombininterface.SurfacerepresentationsoftheCelikeletalal]and(b)Dumasetalal]crystalstructures.TheGpIbN-terminalfragment(gray)isshownwithitsanionicsegment(orange).ThepartofthrombinthatbindstoGpIbthroughexositeI(TI,darkblue)isshowninpaleblueandthepartthatbindsthroughexositeII(TII,darkgreen)isshowninpalegreen.FigurereprintedwithpermissionfromJESadlerr.Copyright2003AmericanAssociationfortheAdvancementofScience.Foldingandbinding CurrentOpinioninStructuralBiology6www.sciencedirect.com studybyVolkmanetal.al.thatevidencewaspresentedforallosteryinasingle-domainsignalingprotein.Thestudydescribesapopulationshiftinducedbyligandbindingtothephosphorylation-regulatedbacterialresponseregulatorNtrC.ThisworkcharacterizedthemotionsofNtrCintheunphosphorylatedandphosphory-latedstates(Figure6).ForunphosphorylatedNtrC,boththeactiveandinactiveconformationsareevident.However,uponphosphorylation,theproteinisactivatedandtheequilibriumisshiftedtowardtheactiveconfor-mation.Similarly,apreviousstudyhadreportedmultipleconformationalstatesforapo-calmodulin,illustratingaconformationalexchangeprocessprocess.Itwasshownthatunboundcalmodulinexistsinapredominantlyclosedconformation,withasmallerpopulationofmoreopenconformations.Formembraneproteins,kineticstudiesperformedontheallosterictransitionsofTorpedoacet-ylcholinereceptorsshowedthat,withoutligand,11%ofthereceptorspre-existintheactivated(desensitized)conformationmation].Inthepresenceofligand,thispop-ulationincreasesto85%.Nevoetal.al.]presentedfurtherevidenceofmultipleconformationalstatesformacromolecularcomplexessuchastheRanimportin1bindinginteraction.Thisstudydemonstratedtheexistenceoftwodistinctboundconformationalstateswhenimportin1isassociatedwithRanthatisloadedwithanonhydrolyzableGTPanalog(GppNHp).Asmoreexperimentalworkisperformedtocharacterizethedynamicsofbindinginteractions,itisbecomingincreasinglyevidentthatproteinscanexistinanensem-bleofconformationalstates.Ifthishypothesisistrue,thenunboundproteinsshouldhaveapopulationofactivatedconformersandexhibitsomeactivity.Thisseemstobethecaseforproteinssuchasthesingle-domainresponseregulatorCheY,whichshowsalowlevelofactivityinitsunphosphorylatedstatestate.However,otherproteinsdonotexhibitabasallevelofactivityintheirunboundstate.Itispossiblethattheseproteins,suchasNtrC,mayrequireacertainnumberofactivatedconformerstodemonstrateactivityactivityandshowasharpsignalresponse.Theresultsreportedhereshowthatunboundproteinscanexistindifferentconformationalstates.Flexibilitywithinregionsofaproteinallowsittoadoptnewcon-formationsand,inturn,bindstructurallydistinctligands.Thisabilityofproteinstoadoptmultiplestructuresallowsfunctionaldiversitywithoutdependingontheevolutionofsequencediversity,whichcangreatlyfacilitatethepotentialforrapidlyevolvingnewfunctionsandstruc-struc-].SupplementarymaterialMostofthestructuresdiscussedforwhichthree-dimensionaldataareavailablearelistedonlineathttp://molmovdb.org/cosb.Theselistingsincludeaddi-tionalimagesandanimations.TheauthorswouldliketothankNathanielEcholsforscienticandtechnicalcontributions.ReferencesandrecommendedreadingPapersofparticularinterest,publishedwithintheannualperiodofreview,havebeenhighlightedas:ofspecialinterestofoutstandinginterest1.GersteinM,KrebsW:AdatabaseofmacromolecularmotionsNucleicAcidsRes2.EcholsN,MilburnD,GersteinM:MolMovDB:analysisandvisualizationofconformationalchangeandstructuralNucleicAcidsRes3.KrebsWG,GersteinM:Themorphserver:astandardizedsystemforanalyzingandvisualizingmacromolecularmotionsinadatabaseframeworkNucleicAcidsRes4.KoshlandD:ApplicationofatheoryofenzymespecicitytoproteinsynthesisProcNatlAcadSciUSA5.TsaiCJ,KumarS,MaB,NussinovR:Foldingfunnels,bindingfunnels,andproteinfunctionProteinSci6.FrauenfelderH,SligarSG,WolynesPG:Theenergylandscapesandmotionsofproteins:1598-1603.7.BryngelsonJD,OnuchicJN,SocciND,WolynesPG:pathways,andtheenergylandscapeofproteinfolding:aProteins8.KarplusM:TheLevinthalparadox:yesterdayandtodayFoldDes:S69-S75.9.DillKA,ChanHS:FromLevinthaltopathwaystofunnelsNatStructBiol10.MonodJ,WymanJ,ChangeuxJ:Ontheallosterictransitions:aplausiblemodelJMolBiol11.KoshlandDEJr,HamadaniK:ProteomicsandmodelsforenzymecooperativityJBiolChem:46841-46844.12.KoshlandDEJr,NemethyG,FilmerD:Comparisonofexperimentalbindingdataandtheoreticalmodelsinproteinscontainingsubunits Figure6 (a)(b)Current Opinion in Structural Biology StructuralconformationsoftheunphosphorylatedformofNtrC,andthephosphorylatedformofNtrC(cyan)superimposedontheunphosphorylatedform(gray).FigureproducedwithPyMOLPyMOL.ConformationalchangesassociatedwithproteinproteininteractionsGoh,MilburnandGerstein5 www.sciencedirect.comCurrentOpinioninStructuralBiology 13.FreireE:Thepropagationofbindinginteractionstoremotesitesinproteins:analysisofthebindingofthemonoclonalantibodyD1.3tolysozymeProcNatlAcadSciUSA:10118-10122.HolmesKC,AngertI,KullFJ,JahnW,SchroderRR:Electroncryo-microscopyshowshowstrongbindingofmyosintoactinreleasesnucleotide:423-427.Cryo-EMofthemyosinactincomplexrevealsaconformationalchangeuponbinding.Thesestudiessuggestthattheclosingoftheactin-bindingcleftisstructurallylinkedtotheopeningofthenucleotide-bindingpocket.15.RaymentI,HoldenHM,WhittakerM,YohnBC,LorenzM,HolmesKC,MilliganRA:Structureoftheactin-myosincomplexanditsimplicationsformusclecontractionScience16.YengoCM,DeLaCruzEM,ChrinLR,GaffneyDPII,BergerCL:Actin-inducedclosureoftheactin-bindingcleftofsmoothmusclemyosinJBiolChem:24114-24119.17.ConibearPB,BagshawCR,FajerPG,KovacsM,Malnasi-CsizmadiaA:MyosincleftmovementanditscouplingtoactomyosindissociationNatStructBiolEvdokimovAG,PhanJ,TropeaJE,RoutzahnKM,PetersHK,PokrossM,WaughDS:SimilarmodesofpolypeptiderecognitionbyexportchaperonesinagellarbiosynthesisandtypeIIIsecretionNatStructBiolrstcrystallographicstructureofaagellarexportchaperone,AquifexaeolicusFliS,anditscomplexwithFliC(agellin).19.AldridgeP,HughesKT:RegulationofagellarassemblyCurrOpinMicrobiol:160-165.20.FraserGM,BennettJC,HughesC:Substrate-specicbindingofhook-associatedproteinsbyFlgNandFliT,putativechaperonesforagellumassemblyMolMicrobiol21.AuvrayF,ThomasJ,FraserGM,HughesC:polymerisationcontrolbyacytosolicexportchaperoneJMolBiol22.BennettJC,HughesC:agellumassemblytovirulence:theextendedfamilyoftypeIIIexportchaperonesTrendsMicrobiol23.PageAL,ParsotC:ChaperonesofthetypeIIIsecretionpathway:jacksofalltradesMolMicrobiolKimpleRJ,KimpleME,BettsL,SondekJ,SiderovskiDP:StructuraldeterminantsforGoLoco-inducedinhibitionofnucleotidereleasebyGalphasubunitsNature2002,416:878-881.TheauthorspresentthecrystalstructureoftheRGS14GoLocoregionboundtotheadenylylcyclaseinhibitoryGsubunit(GDP).Thestructurerevealstheconformationalchangesthatprecludeconcurrentbindingtothecomplex.25.SiderovskiDP,Diverse-PierluissiM,DeVriesL:TheGoLocomotif:aGalphai/obindingmotifandpotentialguanine-nucleotideexchangefactorTrendsBiochemSci26.TakesonoA,CismowskiMJ,RibasC,BernardM,ChungP,HazardSIII,DuzicE,LanierSM:Receptor-independentactivatorsofheterotrimericG-proteinsignalingpathwaysJBiolChem27.DeVriesL,FischerT,TronchereH,BrothersGM,StrockbineB,SiderovskiDP,FarquharMG:ActivatorofGproteinsignaling3isaguaninedissociationinhibitorforGalphaisubunitsProcNatlAcadSciUSA:14364-14369.28.NatochinM,LesterB,PetersonYK,BernardML,LanierSM,ArtemyevNO:AGS3inhibitsGDPdissociationfromgalphasubunitsoftheGifamilyandrhodopsin-dependentactivationoftransducinJBiolChem:40981-40985.29.NatochinM,GasimovKG,ArtemyevNO:InhibitionofGDP/GTPexchangeonGalphasubunitsbyproteinscontainingG-proteinregulatorymotifs30.SchaeferM,PetronczkiM,DornerD,ForteM,KnoblichJA:HeterotrimericGproteinsdirecttwomodesofasymmetriccelldivisioninthenervoussystem:183-194.31.EatonWA,HenryER,HofrichterJ,MozzarelliA:Iscooperativeoxygenbindingbyhemoglobinreallyunderstood?NatStructJamesLC,RoversiP,TawkDS:AntibodymultispecimediatedbyconformationaldiversityScience:1362-1367.ThisstudyreportsthecrystalstructuresoftwodifferentconformationsoftheunboundantibodySpe7.Thetwoconformationsarefoundtobindstructurallydistinctligandsusingverydifferentbindingsites.Thecon-formationthatbindstheantigenisatwithashallowgroove,whereastheconformationthatbindstohaptensisadeephole.33.OldstoneMB:MolecularmimicryandautoimmunediseaseCelikelR,McClintockRA,RobertsJR,MendolicchioGL,WareJ,VarugheseKI,RuggeriZM:Modulationofalpha-thrombinfunctionbydistinctinteractionswithplateletglycoproteinScienceThispaperdescribesthedeterminedstructureofplateletglycoproteinIb(GpIb)boundtothrombinat2.3Aresolution.ThestructuredisplaysadifferentcrystalformandadistinctmodeofthrombinbindingcomparedtotheDumasetal.al.].35.DumasJJ,KumarR,SeehraJ,SomersWS,MosyakL:structureoftheGpIbalpha-thrombincomplexessentialforplateletaggregationScienceThispaperreportsthecrystalstructureoftheGpIbthrombincomplexat2.6Aresolutionn].36.MarcheseP,MurataM,MazzucatoM,PradellaP,DeMarcoL,WareJ,RuggeriZM:cationofthreetyrosineresiduesofglycoproteinIbalphawithdistinctrolesinvonWillebrandfactorandalpha-thrombinbindingJBiolChem:9571-9578.37.VolkmanBF,LipsonD,WemmerDE,KernD:Two-stateallostericbehaviorinasingle-domainsignalingprotein:2429-2433.38.MalmendalA,EvenasJ,ForsenS,AkkeM:StructuraldynamicsintheC-terminaldomainofcalmodulinatlowcalciumlevelsJMolBiolMartinezKL,GohonY,CorringerPJ,TribetC,MerolaF,ChangeuxJP,PopotJL:AllosterictransitionsofTorpedoacetylcholinereceptorinlipids,detergentandamphipols:molecularinteractionsvs.physicalconstraintsFEBSLett:251-256.KineticexperimentsrevealtwoconformationalstatesfortheunboundTorpedoacetylcholinereceptor.NevoR,StrohC,KienbergerF,KaftanD,BrumfeldV,ElbaumM,ReichZ,HinterdorferP:AmolecularswitchbetweenalternativeconformationalstatesinthecomplexofRanandimportinNatStructBiol:553-557.DynamicforcespectroscopyanalysisoftheRanimportin1complexrevealstwodistinctboundstates.41.BarakR,EisenbachM:CorrelationbetweenphosphorylationofthechemotaxisproteinCheYanditsactivityattheBiochemistry:1821-1826.42.WymanC,RombelI,NorthAK,BustamanteC,KustuS:UnusualoligomerizationrequiredforactivityofNtrC,abacterialenhancer-bindingproteinScienceJamesLC,TawkDS:Conformationaldiversityandproteina60-year-oldhypothesisrevisitedTrendsBiochem:361-368.Thisinterestingdiscussionfocusesonthehypothesisthatagivenproteinsequencecanadoptmultiplestructuresandfunctions.44.ThePyMOLMolecularGraphicsSystemonWorldWideWebURL:http://www.pymol.org45.SadlerJE:Structuralbiology.Amenageatroisintwogurations:177-179.Foldingandbinding CurrentOpinioninStructuralBiology6www.sciencedirect.com