Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures 英文参考文献.docVIP

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Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures 英文参考文献.doc

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Applying an Empirical Hydropathic Forcefield in Refinement May Improve Low-Resolution Protein X-Ray Crystal Structures 英文参考文献

ApplyinganEmpiricalHydropathicForcefieldin RefinementMayImproveLow-ResolutionProteinX-Ray CrystalStructures VishalN.Koparde1,2,J.NeelScarsdale1,3*,GlenE.Kellogg1,2 * 1Institute of Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia, United States of America, 2Department of Medicinal Chemistry,Virginia CommonwealthUniversity, Richmond, Virginia,UnitedStates ofAmerica, 3Centerforthe StudyofBiological Complexity,VirginiaCommonwealth University,Richmond,Virginia,UnitedStatesofAmerica Abstract Background: The quality of X-ray crystallographic models for biomacromolecules refined from data obtained at high- resolutionisassuredbythedataitself.However,atlow-resolution,.3.0A,? additionalinformationissuppliedbyaforcefield coupledwithanassociatedrefinementprotocol.Theseresultingstructuresareoftenoflowerqualityandthusunsuitable fordownstreamactivitieslikestructure-baseddrugdiscovery. Methodology:AnX-raycrystallographyrefinementprotocolthatenhancesstandardmethodologybyincorporatingenergy terms from the HINT (Hydropathic INTeractions) empirical forcefield is described. This protocol was tested by refining synthetic low-resolution structural data derived from 25 diverse high-resolution structures, and referencing the resulting modelstothesestructures.Themodelswerealsoevaluatedwithglobalstructuralqualitymetrics,e.g.,Ramachandranscore andMolProbityclashscore.Threeadditionalstructures,forwhichonlylow-resolutiondataareavailable,werealsore-refined withthismethodology. Results:Theenhancedrefinementprotocolismostbeneficialforreflectiondataatresolutionsof3.0A?orworse.Atthelow- resolution limit, $4.0A,? the new protocol generated models with Ca positions that have RMSDs that are 0.18A? more similar tothe reference high-resolution structure, Ramachandran scores improved by 13%, and clashscores improved by 51%,allincomparisontomodelsgeneratedwiththestandardrefinementprotocol.Thehydropathicforcefieldtermsareat leastaseffectiveasCoulombicelect