Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of Cα Atoms 英文参考文献.docVIP

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Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of Cα Atoms 英文参考文献.doc

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Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of Cα Atoms 英文参考文献

RecognitionofInteractionInterfaceResiduesinLow- ResolutionStructuresofProteinAssembliesSolelyfrom thePositionsofCaAtoms RupaliA.Gadkari*,DeepthiVarughese,N.Srinivasan* MolecularBiophysicsUnit,IndianInstituteofScience,Bangalore,India Abstract Background:Thenumberofavailablestructuresoflargemulti-proteinassembliesisquitesmall.Suchstructuresprovide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolutionofthesestructures.Intherecenttimesanumberofattemptsthatcombinelowresolutioncryo-EMdatawith higherresolutionstructuresdeterminedusingX-rayanalysisorNMRorgeneratedusingcomparativemodelinghavebeen reported.Eveninsuchattemptsthebestresultonearrivesatistheverycourseideaabouttheassemblystructureinterms oftraceoftheCaatomswhicharemodeledwithmodestaccuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposedandburiedresiduessolelyfromthepositionofCaatomsandaminoacidsequenceusingresiduetype-dependent thresholdsforaccessiblesurfaceareasofCa.Weextendthemethodfurthertorecognizepotentialprotein-proteininterface residues. Conclusion/ Significance: Our approach to identify buried and exposed residues solely from the positions of Ca atoms resulted in an accuracy of 84%, sensitivity of 83–89% and specificity of 67–94% while recognition of interfacial residues correspondedtoanaccuracyof94%,sensitivityof70–96%andspecificityof58–94%.Interestingly,detailedanalysisofcases ofmismatchbetweenrecognitionofinterfaceresiduesfromCapositionsandall-atommodelssuggestedthat,recognition of interfacial residues using Ca atoms only correspond better with intuitive notion of what is an interfacial residue. Our methodshouldbeusefulintheobjectiveanalysisofstructuresofproteinassemblieswhenpositionsofonlyCapositions areavailableas,forexample,inthecasesofinte