Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase 英文参考文献.docVIP

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Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase 英文参考文献.doc

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Molecular Dynamics Simulations Reveal Proton Transfer Pathways in Cytochrome C-Dependent Nitric Oxide Reductase 英文参考文献

MolecularDynamicsSimulationsRevealProtonTransfer PathwaysinCytochromeC-DependentNitricOxide Reductase AndreiV.Pisliakov1*,TomoyaHino2¤,YoshitsuguShiro2,YujiSugita1,3,4 1TheoreticalMolecularScienceLaboratory,RIKENAdvancedScienceInstitute,Wako-shi,Saitama,Japan,2RIKENSPring-8Center,Sayo,Hyogo,Japan,3Computational Biophysics Research Team, RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Japan, 4Laboratory for Biomolecular Function Simulation, RIKEN QuantitativeBiologyCenter,Chuo-ku,Kobe,Japan Abstract Nitricoxidereductases(NORs)aremembraneproteinsthatcatalyzethereductionofnitricoxide(NO)tonitrousoxide(N2O), whichisacriticalstepofthenitraterespirationprocessindenitrifyingbacteria.Usingtherecentlydeterminedfirstcrystal structureofthecytochromec-dependentNOR(cNOR)[HinoT,MatsumotoY,NaganoS,SugimotoH,FukumoriY,etal.(2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensiveall-atommoleculardynamics(MD)simulationsofcNORwithinanexplicitmembrane/solventenvironmenttofully characterizewaterdistributionanddynamicsaswellashydrogen-bondednetworksinsidetheprotein,yieldingtheatomic detailsoffunctionallyimportantprotonchannels.Simulationsrevealtwopossibleprotontransferpathwaysleadingfromthe periplasmtotheactivesite,whilenopathwaysfromthecytoplasmicsidewerefound,consistentlywiththeexperimental observationsthatcNORisnotaprotonpump.Oneofthepathways,whichwasnewlyidentifiedintheMDsimulation,is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathwayisequivalenttothefunctionalperiplasmiccavitypostulatedincbb3oxidase,whichillustratesthatthetwoenzymes sharesomeelementsoftheprotontransfermechanismsandconfirmsacloseevolutionaryrelationbetweenNORsandC-type oxidases.Severalmechanismsofthecriticalprotontransferstepsnearthecatalyticcenterareproposed. Citation:PisliakovAV,HinoT,ShiroY,SugitaY(2012)MolecularDynamicsSimulationsRevealP