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Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation英文文献资料.doc

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Biological Applications of Hybrid Quantum MechanicsMolecular Mechanics Calculation英文文献资料

HindawiPublishingCorporation JournalofBiomedicineandBiotechnology Volume2012,ArticleID236157,11pages doi:10.1155/2012/236157 ReviewArticle BiologicalApplicationsofHybridQuantumMechanics/Molecular MechanicsCalculation JiyoungKang, YohsukeHagiwara, andMasaruTateno 1 1 2 1 2 GraduateSchoolofPureandAppliedSciences,UniversityofTsukuba,TsukubaScienceCity,Tsukuba305-857,Japan GraduateSchoolofLifeScience,UniversityofHyogo,3-2-1Koto,Kamigori-cho,Ako-gun,Hyogo678-1297,Japan CorrespondenceshouldbeaddressedtoMasaruTateno,tateno@sci.u-hyogo.ac.jp Received15July2011;Revised27October2011;Accepted11November2011 AcademicEditor:SergioPantano Copyright?2012JiyoungKangetal.ThisisanopenaccessarticledistributedundertheCreativeCommonsAttributionLicense, whichpermitsunrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalworkisproperlycited. Sinceinmostcasesbiologicalmacromolecularsystemsincludingsolventwatermoleculesareremarkablylarge,thecomputational costsofperformingabinitiocalculationsfortheentirestructuresareprohibitive.Accordingly,QMcalculationsthatarejointed withMMcalculationsarecrucialtoevaluatethelong-rangeelectrostaticinteractions,whichsigni?cantlya?ecttheelectronic structuresofbiologicalmacromolecules.AUNIX-shell-basedinterfaceprogramconnectingthequantummechanics(QMs)and molecularmechanics(MMs)calculationengines,GAMESSandAMBER,wasdevelopedinourlab.Thesystemwasappliedtoa metalloenzyme,azurin,andPU.1-DNAcomplex;thereby,thesigni?canceoftheenvironmentale?ectsontheelectronicstructures ofthesiteofinterestwaselucidated.Subsequently,hybridQM/MMmoleculardynamics(MD)simulationusingthecalculation systemwasemployedforinvestigationofmechanismsofhydrolysis(editingreaction)inleucyl-tRNAsynthetasecomplexedwith themisaminoacylatedtRNA Leu ,andanovelmechanismoftheenzymaticreactionwasrevealed.Thus,ourinterfaceprogramcan playacriticalroleasapowerfultoolforstate-of-the-artsophisticatedhybridabinitioQM/MMMDsimulationsoflargesystems, suchasbi