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分子生物物理学.ppt

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2024/10/21分子水平Biopolymers: Nucleicacid(DNA,RNA) ProteinPROTEINSTRUCTURESecondaryStructureChiralzwitterionClassificatoryofaminoacid basedsidechains(Rgroups)ProteinPrimaryStructurePeptidebondphi(F),psi(Y),andomega(W)H-bonddefinition,H-bondlocationO….H-XProteinSecondaryStructureHelices repetitivesecondarystructurea-helixintroductiona-heliceshave3.6aminoacidresiduesperturn,i.e.ahelix36aminoacidslongwouldform10turns.thephiandpsianglesofthealphahelixlieinthecenterofanallowed,minimumenergyregionoftheRamachandran(phi,psi)map.thedipolesofhydrogenbondingbackboneatomsareinnearperfectalignment.theradius(2.3angstrom)ofthehelixallowsforfavorablevanderWaalsinteractionsacrossthehelicalaxisCOgrouptowardcarboxylterminus NHgrouptowardamideterminus H-bond,i-(i+4) Sidechain:i-(i+3);i-(i+4) interactionsbetweeniandi+4stabilizehelixDistortionsofa-helices310helixintroductionStandard310helixProlinehelixp-helicesintroductionthephiandpsianglesofthepurepihelix(-57.1,-69.7)lieattheveryedgeofanallowed,minimumenergyregionoftheRamachandran(phi,psi)map. thepihelixrequiresthattheangletau(N-Ca-C')belarger(114.9)thanthestandardtetrahedralangleof109.5degrees. thelargeradiusofthepihelixmeansthepolypeptidebackboneisnolongerinvanderWaalscontactacrossthehelicalaxisforminganaxialholetoosmallforsolventwatertofill. sidechainsaremorestaggeredthantheideal3.10helixbutnotaswellasthealphahelix.H-bond:1-5alpha-helix,surfaceofprotein,barrier amphiphilic proteindesignprojects byDegrado,USAHelixdipoleSheet-139and+135ParallelsheetTwistsParallelsheetsarelesstwistedthananti-parallelandarealwaysburied.BulgesTurnGamma-turnTypeIandI’turnThebackbonedihedralanglesofresidueare(-60,120)and(80,0)ofresiduesi+1andi+2,respectivelyofthetypeIIturn.thehydrogenbondbetweenCOofresidueiandNHofresiduei+3.Thisisasingleturnofright-handed(III)andleft-handed(III')3.10helix,respectively.Thebackbonedihedralanglesofresidueare(-60,-30)and(-60,-30)ofresiduesi+1andi+2,respectivelyoftheclassicaltypeIIIturn.2.3.4.OtherstructuresIdentificationofseconda