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大小:1014.00 KB
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时间:2019-08-18
《ClassicalMolecularDynamicsSimulationsofProteins:经典的蛋白质的分子动力学模拟》由会员上传分享,免费在线阅读,更多相关内容在教育资源-天天文库。
1、ProteinFolding&BiospectroscopyLecture5F14PFBDavidRobinsonProteinFoldingIntroductionProteinStructureInteractionsProteinFoldingModelsBiomolecularModellingBioinformaticsClassicalMolecularDynamicsSimulationsofProteins“everythingthatlivingthingsdocanbeunders
2、toodintermsofthejigglingsandwigglingsofatoms.”TheFeynmanLecturesinPhysicsvol.1,3-6(1963)WhatisMolecularDynamics?“Thescienceofsimulatingthemotionsofasystemofparticles”(Karplus&Petsko)FromsystemsAssmallasanatomAslargeasagalaxyEquationsofmotionTimeevolutionW
3、hy?EssentialElementsKnowledgeoftheinteractionpotentialfortheparticlesForcesClassicalNewtonianequationsofmotionManyparticlesystemssimulationMaxwell-Boltzmannaveragingprocessforthermodynamicproperties:timeaveragingOneparticleeasyanalyticallyManyparticlesimp
4、ossibleanalyticallyBasis:MolecularMechanicsTheoreticalfoundationPotentialenergyfunctionsEnergyminimizationMoleculardynamicsUsesofsimulation&modellingConformationalsearchingwithMDandminimizationExplorationofbiopolymerfluctuationsanddynamics&kineticsMDasane
5、nsemblesamplerFreeenergysimulationsExampleapplicationsEnergyminimizationasanestimatorofbindingfreeenergiesProteinstabilityApproximateassociationfreeenergyofmolecularassembliesApproximatepKacalculationsTheoreticalFoundationsForcefieldparametersforfamilieso
6、fchemicalcompoundsSystemmodelledusingNewton’sequationsofmotionExamples:hardspheressimulations(Alder&Wainwright,1959);Liquidwater(Rahman&Stillinger,1970);BPTI(McCammon&Karplus,1976);Villinheadpiece(Duan&Kollman,1998)ProteinMotionProteinmotionsofimportancea
7、retorsionaloscillationsaboutthebondsthatlinkgroupstogetherSubstantialdisplacementsofgroupsoccuroverlongtimeintervalsCollectivemotionseitherlocal(cagestructure)orrigid-body(displacementofdifferentregions)Whatistheimportanceofthesefluctuationsforbiologicalf
8、unction?EffectoffluctuationsThermodynamics:equilibriumbehaviourimportant;e.g.,energyofligandbindingDynamics:displacementsfromaveragestructureimportant;e.g.,localsidechainmotionsthatactasconformationalgatesinoxygentr
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