ClassicalMolecularDynamicsSimulationsofProteins：经典的蛋白质的分子动力学模拟

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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