On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family NAGK the Paradigm 英文参考文献.docVIP

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On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family NAGK the Paradigm 英文参考文献.doc

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On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family NAGK the Paradigm 英文参考文献

OntheConservationoftheSlowConformational DynamicswithintheAminoAcidKinaseFamily:NAGK theParadigm EnriqueMarcos1,RamonCrehuet1*,IvetBahar2* 1DepartmentofBiologicalChemistryandMolecularModelling,IQAC-CSIC,Barcelona,Spain,2DepartmentofComputationalBiology,SchoolofMedicine,Universityof Pittsburgh,Pittsburgh,Pennsylvania,UnitedStatesofAmerica Abstract N-Acetyl-L-GlutamateKinase (NAGK) is the structural paradigm for examining thecatalytic mechanisms anddynamics of aminoacidkinasefamilymembers.GiventhattheslowconformationaldynamicsoftheNAGK(atthemicrosecondstime scaleorslower)mayberate-limiting,itisofimportancetoassessthemechanismsofthemostcooperativemodesofmotion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network modelrepresentation,whichshowsthattheconformationalmechanismsforsubstratebindingbyNAGKstronglycorrelate withtheintrinsicdynamicsoftheenzymeintheunboundform.Wefurtheranalyzedthepotentialmechanismsofallosteric signallingwithinNAGKusingaMarkovmodelfornetworkcommunication.Comparativeanalysisofthedynamicsoffamily members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establishsignaltransductionarehighlyconservedamongfamilymembers,insupportoftheparadigmsequenceRstruc- tureRdynamicsRfunction. Citation: Marcos E, Crehuet R, Bahar I (2010) On the Conservation of the Slow Conformational Dynamics within the Amino Acid Kinase Family: NAGK the Paradigm.PLoSComputBiol6(4):e1000738.doi:10.1371/journal.pcbi.1000738 Editor:MichaelLevitt,StanfordUniversity,UnitedStatesofAmerica ReceivedNovember20,2009;AcceptedMarch5,2010;PublishedApril8,2010 Copyright: ? 2010 Marcos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkwassupportedbygrantsfromtheJAE-predocprogrammeo