杉田理论生物化学研究室

TheoreticalBiochemistryLaboratorySUGITA,Yuji1.1*1*2*3MonteCarlo1(REMD)2QM/MM*3*24QM/MMGeneralizedhybridorbital2.1*2ATP2FoF1-ATPaseεATP*4*2FoF1-ATPaseATPADPPi3ATPXNMRATP2ATP*1*2*3*4Westudyfunctionsofbiomoleculesbytheoreticalcalculationsbasedonthermodynamics,statisticalmechanics,andquantumchemistry.Inparticular,weareinterestedintheconformationaldynamicsofproteinsanditsrelationshipwiththefunctionsofproteins.Currentresearchtopicsareproteinfoldingandstabilityinsolution,ion-transportbymembraneproteins,enzymaticreactions,andsoon.Wealsodevelopnewcomputationalmodelsandmethodstoovercomecurrentlimitationsofcomputationalchemistryonbiomolecules.1.Developmentofnewcomputationalmethods(1)Conformationalsamplingmethodsforproteins(Miyashita,Yoda,Sato,andSugita)Inthefree-energylandscapesofproteinsorothersystemswithrugged-energysurfaces,thereareahugenumberofconformationalsubstates.However,theconventionalsimulationtechniques,suchasmoleculardynamicsorMonteCarlomethodsoftengettrappedatoneofthelocal-energyminima,andthereforecannotsamplewideconformationalspacesofproteins.Generalized-ensemblealgorithmscanovercomethedifficultybyperformingarandomwalkinthepotentialenergyspace,andalsocanevaluatethecanonicalensembleaveragesatanytemperaturebyasinglesimulationrun.Wehavedevelopednewgeneralized-ensemblealgorithmsincludingreplica-exchangemoleculardynamicsmethod(REMD)andaretryingtoimprovesamplingefficiencyofthesemethods.(2)QM/MMmethodsforenzymaticreactions(Re,Ten-no,andSugita)Tounderstandchemicalreactionsoccurredinproteinsorenzymesisoneofthecentralissuesinmolecularbiologyorbiochemistry.Tostudythereactionstheoretically,wehavetocalculatetheconformationalenergiesofthesystemsbyquantumchemicalmethods.However,thesize-dependencyofab-initioquantumchemistryissignificant(proportionalto,atleast,N4),indicatingthatitisimpossibletoapplythemethodtoafullproteinsystemwithsolventmolecules.Therefore,weuseQM/MMhybridmethodsforthestudyofenzymaticreactions.OneofthemajortechnicalproblemsintheQM/MMmethodswashowtotreattheboundaryatomsbetweenquantumandmolecularmechanicalregions.Wehaveovercometheproblembyimprovingthegeneralizedhybridorbital(GHO)method.WearecurrentlyimprovingthealgorithmsforQMandMMenergycalculationsforfastcomputationsandapplyingthemethodstoseveralenzymaticreactions.2.Moleculardynamicssimulationsofproteinsinsolutionormembrane(1)Moleculardynamicssimulationsonmembraneproteins(Ishitani,andSugita)Theconcentrationofionsorothersubstratesinsideoroutsideofcellsisstrictlyregulated.Membranetransportingproteins,suchaschannels,pumps,ortransporters,haveessentialrolestotransportthesesubstratesacrossbiologicalmembranes.ByusingX-raystructuresofmembraneproteins,wehaveperformedlarge-scalemoleculardynamicssimulationsofmembraneproteins,includingsarcoplasmicreticulum(SR)calciumpump.ThisproteintransportstwocalciumionsfromthecytoplasmtoSRlumenperATP-hydrolyzed.Bytheoreticalcalculations,wehaveelucidatedtherolesofprotonsattheion-bindingsitesofthecalciumpump.Wearealsosimulatingothermembranetransportingproteinswithbiologicalmembranestostudytheirstructuralandfunctionalrelationships.(2)εsubunitinFoF1-ATPase(Tsuji,Muneyuki,andSugita)FoF1-ATPaseisamembraneproteinthatcangenerateATPfromADPandPibyusingelectro-chemicalpotentials.Thismembraneproteinconsistsofthreeαandβ,γ,δ,andεsubunits.WestudytheeffectofATPonthestructureofεsubunit.X-raycrystallographyandNMRspectroscopyshowedthatlargeconformationalchangesoccurupontheATP-bindingorrelease.MoleculardynamicssimulationsonthesubunitinsolutionsuggestedthatlargeconformationalfluctuationsexistregardlessoftheATP-binding.However,thelargeconformationalchangesfromthefoldedforminthepresenceofATPtotheextendedformintheabsenceofATPcouldnotbeobservedinthecurrentsimulations.Muchlongercalculationsorbetterefficientconformationalsamplingmayberequiredforsimulatingthelargeconformationalchanges.StaffHeadDr.YujiSUGITAMembersDr.SuyongRE1Dr.DaisukeSATO1Ms.MaiUSUI2__________________________________________________1ContractResearcher,2SecretaryincollaborationwithDr.ToshinoriSUZUKI(ChemicalDynamicsLab.)Dr.NaoyukiMIYASHITA(Molecular-scaleResearchandDevelopmentteam,ResearchProgramforComputationalScience)ViitingMemberssDr.SeiichiroTEN-NO(NagoyaUniv.)Dr.TakaoYODA(Nagahama-BioUniv.)19Dr.EiroMUNEYUKI(ChuoUniv.)Dr.RyuichiroISHITANI(TokyoInst.ofTech.)TraineesMr.YosukeTsuji(ChuoUniv.)