SpaKSpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies 英文参考文献.docVIP

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SpaKSpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies 英文参考文献.doc

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SpaKSpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies 英文参考文献

SpaK/SpaRTwo-componentSystemCharacterizedbya Structure-drivenDomain-fusionMethodandinVitro PhosphorylationStudies AnuChakicherla1,CarolL.EcaleZhou1*,MarthaLigonDang2,VirginiaRodriguez3,J.NormanHansen4, AdamZemla1 1ComputingApplicationsandResearchDepartment,LawrenceLivermoreNationalLaboratory,Livermore,California,UnitedStatesofAmerica,2SacredHeartsAcademy, Honolulu,Hawaii,UnitedStatesofAmerica,3GenomeTechnologyBranch,NationalHumanGenomeResearchInstitute,NationalInstitutesofHealth,Bethesda,Maryland, UnitedStatesofAmerica,4DepartmentofChemistryandBiochemistry,UniversityofMaryland,CollegePark,Maryland,UnitedStatesofAmerica Abstract Here we introduce a quantitative structure-driven computational domain-fusion method, which we used to predict the structuresofproteinsbelievedtobeinvolvedinregulationofthesubtilinpathwayinBacillussubtilis,andusedtopredicta protein-protein complex formed by interaction between the proteins. Homology modeling of SpaK and SpaR yielded preliminarystructuralmodelsbasedonabesttemplateforSpaKcomprisingadimerofahistidinekinase,andforSpaRa response regulator protein. Our LGA code was used to identify multi-domain proteins with structure homology to both modeledstructures,yieldingasetofdomain-fusiontemplatesthenusedtomodelahypotheticalSpaK/SpaRcomplex.The modelswereusedtoidentifyputativefunctionalresiduesandresiduesattheprotein-proteininterface,andbioinformatics was used to compare functionally and structurally relevant residues in corresponding positions among proteins with structuralhomologytothetemplates.Modelsofthecomplexwereevaluatedinlightofknownpropertiesofthefunctional residues within two-component systems involving His-Asp phosphorelays. Based on this analysis, a phosphotransferase complexedwithaberyllofluoridewasselectedastheoptimaltemplateformodelingaSpaK/SpaRcomplexconformation.In vitrophosphorylationstudiesperformedusingwildtypeandsite-directedSpaKmutantproteinsvalidatedthepredictions derivedfromapplicationofthestructure-drivendomain-fu