Allosteric Transitions of Supramolecular Systems Explored by Network Models Application to Chaperonin GroEL 英文参考文献.docVIP

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Allosteric Transitions of Supramolecular Systems Explored by Network Models Application to Chaperonin GroEL 英文参考文献.doc

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Allosteric Transitions of Supramolecular Systems Explored by Network Models Application to Chaperonin GroEL 英文参考文献

AllostericTransitionsofSupramolecularSystems ExploredbyNetworkModels:ApplicationtoChaperonin GroEL ZhengYang1,2,PeterMa′jek3,IvetBahar1* 1DepartmentofComputationalBiology,SchoolofMedicine,UniversityofPittsburgh,Pittsburgh,Pennsylvania,UnitedStatesofAmerica,2DepartmentofPhysicsand Astronomy,SchoolofArtsSciences,UniversityofPittsburgh,Pittsburgh,Pennsylvania,UnitedStatesofAmerica,3DepartmentofComputerScience,CornellUniversity, Ithaca,NewYork,UnitedStatesofAmerica Abstract Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensionalenergylandscape.Thistaskbecomesevenmorechallenginginexploringmolecularsystemsontheorder ofmegadaltons.Coarse-grainedmodelsthatlendthemselvestoanalyticalsolutionsappeartobetheonlypossiblemeans of approaching such cases. Motivated by the utility of elastic network models for describing the collective dynamics of biomolecularsystemsandbythegrowingtheoreticalandexperimentalevidenceinsupportoftheintrinsicaccessibilityof functional substates, we introduce a new method, adaptive anisotropic network model (aANM), for exploring functional transitions. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimizationalgorithm,andprevioussimulationssupporttheutilityofaANMasacomputationallyefficient,yetphysically plausible,toolforunravelingpotentialtransitionpathwayssampledbylargecomplexes/assemblies.Animportantoutcome istheassessmentofthecriticalinter-residueinteractionsformed/brokennearthetransitionstate(s),mostofwhichinvolve conservedresidues. Citation:YangZ,Ma′jek P,BaharI(2009)AllostericTransitionsofSupramolecularSystemsExploredbyNetworkModels:ApplicationtoChaperoninGroEL.PLoS ComputBiol5(4):e1000360.doi:10.1371/journal.pcbi.1000360 Editor:VijayS.Pande,StanfordUniversity,UnitedStatesofAmerica ReceivedSeptember