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1、ISSN00268933,MolecularBiology,2010,Vol.44,No.6,pp.958–967.?PleiadesPublishing,Inc.,2010.OriginalRussianText?A.N.Istrate,A.B.Mantsyzov,S.A.Kozin,V.I.Polshakov,2010,publishedinMolekulyarnayaBiologiya,2010,Vol.44,No.6,pp.1075–1085.STRUCTURAL–FUNCTIONALANALYSISOFBIOPOLYMERSANDTHEIRCOMPLEXESU
2、DC577.322.53;531.395OptimizationoftheMethodsforSmallPeptideSolutionStructureDeterminationbyNMRSpectroscopyA.N.Istratea,A.B.Mantsyzova,S.A.Kozinb,c,andV.I.PolshakovdaChemicalDepartment,MoscowStateUniversity,Moscow,119991RussiabResearchInstituteforBiomedicalChemistry,RussianAcademyofMedical
3、Sciences,Moscow,119121RussiacEngelhardtInstituteofMolecularBiology,RussianAcademyofSciences,Moscow,119991RussiadCenterforMagneticTomographyandSpectroscopy,FacultyofFundamentalMedicine,MoscowStateUniversity,Moscow,119991Russia;email:vpolsha@mail.ruReceivedJune29,2010PresentedbyA.A.Makarov
4、Abstract—NMRspectroscopywasrecognizedasamethodofproteinstructuredeterminationinsolution.However,determinationoftheconformationofsmallpeptides,whichundergofastmolecularmotions,remainsachallenge.Thisismainlycausedbytheimpossibilitytocollecttherequiredquantityofthedistanceanddihedralangleres
5、traintsfromNMRspectra.Atthesametime,shortchargedpeptidesplayanimportantroleinanumberofbiologicalprocesses,inparticularinpathogenesisofneurodegenerativediseasesincludingAlzheimer’sdisease.Therefore,developmentofamethodforstructuresimulationofsmallpeptidesinaqueousenvironmentusingthemostre
6、alisticforcefieldsseemstobeofcurrentimportance.SuchalgorithmhasbeendevelopedusingtheAmber03forcefieldandGromacsprogramaftermodificationofitscode.Calculationalgorithmhasbeenverifiedonamodelpeptidewithaknownsolutionstructureandametalbindingfragmentofratβamyloid,whosestructurehasbeendete
7、rminedbyalternativemethods.Thedevelopedalgorithmsubstantiallyincreasesstructurequality,inparticularRamachandranplotstatistics,anddecreasesRMSDofatomiccoordinatesinsidethecalculatedfamily.Thedescribedprotocolcanbeusedfordeterminationofconformationofshortpeptides,an