生物大分子结构与功能相互作用力

第一章：蛋白质的结构层次当前第1页\共有86页\编于星期四\19点1,thesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins当前第2页\共有86页\编于星期四\19点ProteinSecondaryStructure■Secondarystructureistheregulararrangementofaminoacidresiduesinasegmentofapolypeptidechain,inwhicheachresidueisspatiallyrelatedtoitsneighborsinthesameway.■Themostcommonsecondarystructuresaretheαhelix,theβ

conformation,andβ

turns.■Thesecondarystructureofapolypeptidesegmentcanbecompletelydefinediftheφand

ψanglesareknownforallaminoacidresiduesinthatsegment.当前第3页\共有86页\编于星期四\19点10papersfromLinusPaulingandcolleaguespublishedinPNAS,1951当前第4页\共有86页\编于星期四\19点αhelix310helixπ

helix:theoreticallypossible,butneverfoundintheproteinsßsheet:parallelandanti-parallel当前第5页\共有86页\编于星期四\19点αhelixßsheet3.613helix当前第6页\共有86页\编于星期四\19点Parametersoffiveactualortheoreticalsecondarystructures:当前第7页\共有86页\编于星期四\19点αhelix:

thebackboneofthepolypeptidechainisextendedintohelicalstructureWhichIsbuiltupfromonecontinuousregion.αhelix当前第8页\共有86页\编于星期四\19点φ,ψanglepairapproximately-60°and-50°.Thelengthrangfrom4or5to44residues.Theaveragelengthisaround10residues

当前第9页\共有86页\编于星期四\19点3.6residuesperturnwithhydrogenbondsbetweenC’=OofresiduesnandNHofresiduesn+4.Theendofαhelicesarepolarandarealmostatthesurfaceofproteinmolecules当前第10页\共有86页\编于星期四\19点310helixπ

helix4.416helixN+53residuesperturnanda10atomsbetweenthehydrogenbonddonorandacceptor,N+3当前第11页\共有86页\编于星期四\19点Idealizedhelices:当前第12页\共有86页\编于星期四\19点Hydrogenbondingpatternsforfourhelices

273103.6134.414当前第13页\共有86页\编于星期四\19点当前第14页\共有86页\编于星期四\19点Theαhelixhasadipolemoment1.Theoveralleffectisasignificantnetdipolefortheαhelix.Thatgivesapartialpositivechargeattheaminoend

apartialnegativechargeattheCarboxylend(0.5-0.7unitcharge)2.Unitchargeateachendattractligandsofoppositecharge.PhosphategroupsfrequentlybindattheN-terminalofαhelix.Incontrast,positivechargeligandsrarelybindatC-teminal.当前第15页\共有86页\编于星期四\19点Someaminoacidsarepreferredinαhelix:Ala(A),Glu(E),Leu(L),andMet(M)

aregoodαhelicesformers.2)

Pro(P),Gly(G),Tyr(Y)andSer(S)

areveryPoorformers3)Themostcommonlocationforanαhelixinaproteinstructureisalongtheoutsideoftheprotein,withonesidefacingthesolutionandtheothersidefacingthehydrophobicinterioroftheprotein.4)αhelicesthatacrossmembranareinaHydrophobicenvironment,mostoftheirsideChainsarehydrophobic当前第16页\共有86页\编于星期四\19点当前第17页\共有86页\编于星期四\19点当前第18页\共有86页\编于星期四\19点Saccharomycescerevisiaemitochondrialthioredoxin3Baoetal.当前第19页\共有86页\编于星期四\19点MembraneProteinJ.Deisenhofer,H.MichelScience(245):1463,1989J.Dersenhofer,O.Epp,K.Miki,R.Huber,H.Michel,Nature(318):618,1985J.Deisenhofer,O.Epp,K.Miki,R.Huber,H.Michel,J.Mol.Biol.(180):385,1984H.MichelJ.Mol.Biol.(158):567,1982FirstMembraneProteinStructure:PhotosyntheticReactionCenterofRhodopseudomonasvirdis

红假单胞菌Complex(foursubunits)solvedin1985(1PRC)NobelChemistryPrizewasawardedtoJ.Deisenhofer,R.Huber,H.Michelin1988.当前第20页\共有86页\编于星期四\19点1)βsheet:

thebackboneofthepolypeptidechainisextendedintoa

zigzagstructure.2)

βsheet

isbuiltupfromacombinationofseveralregionsofthepolypeptidechain.3)Thelengthrangfrom5to10residues.β

sheet当前第21页\共有86页\编于星期四\19点当前第22页\共有86页\编于星期四\19点Theaminoacidecanallruninthesamebiochemicaldirection,amioterminaltocarboxyterminalTheaminoacidcanhavealternatingdirections,theN-terminaltoC-terminalfollowbyC-terminaltoN-terminal当前第23页\共有86页\编于星期四\19点Twoformshaveadistinctivepatternofhydrogen-bondingParallelAntiparallelTheβsheetthatareformedfromseveralβstrandsare

“pleated”当前第24页\共有86页\编于星期四\19点βsheetcanalsocombineintomixedβsheet(About20%ofknownproteinstructuresaremixed)当前第25页\共有86页\编于星期四\19点当前第26页\共有86页\编于星期四\19点Almostalltheβsheethavetwiststrands.This

twisthasthesamehandedness

(right-handed)φ,ψangleswithinthebroadstructurallyallowedregion当前第27页\共有86页\编于星期四\19点当前第28页\共有86页\编于星期四\19点theDouble-headedArrowheadProteaseInhibitorA

Baoetal.当前第29页\共有86页\编于星期四\19点当前第30页\共有86页\编于星期四\19点LoopregionfrequentlyparticipateinformingbindingsitesandenzymeactivesitesLoopregionsareatthesurfaceofproteinmoleculesHairpinloops当前第31页\共有86页\编于星期四\19点Hydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe4thaminogroupβ-turns:

connecttheendsoftwoadjacentsegmentsofanantiparallelβsheet.当前第32页\共有86页\编于星期四\19点当前第33页\共有86页\编于星期四\19点Productsof13genesinvolvedinpeptidyl-prolylcis-transisomeraseactivitythecommonpresenceofProandGlyresiduesinβturnsβ

turns当前第34页\共有86页\编于星期四\19点

γ

turnHydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe3rdaminogroup当前第35页\共有86页\编于星期四\19点ARamachandranplot当前第36页\共有86页\编于星期四\19点当前第37页\共有86页\编于星期四\19点SchematicpicturesofproteinshighlightsecondarystructureSimplifyFacilitateseeingsimilaritybetweenproteinsHelicessometimescylinders当前第38页\共有86页\编于星期四\19点TopologydiagramsareusefulforclassificationofproteinstructuresShowthedirectionofeachβstrandandthewaythestrandsareconnectedtoeachotheralongthepolypeptidechain当前第39页\共有86页\编于星期四\19点1,Thesecondarystructures2,Supersecondarystructuresanddomains

3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins当前第40页\共有86页\编于星期四\19点Supersecondarystructures,alsocalledmotifsorsimplyfolds,

areparticularlystablearrangementsofseveralelementsofsecondarystructureandtheconnectionsbetweenthem.当前第41页\共有86页\编于星期四\19点Twoαhelicesthatareconnectedbyashortloopregion.A:helix-turn-helixmotifisspecificforDNAbindingB:thecalciumbindingmotifispresentinmanyproteinsWhosefunctionisregulatedbycalcium.当前第42页\共有86页\编于星期四\19点Thecalcium-bindingmotifissymbolizedbyrighthandExample:thecalciumisboundtothemotifinthetroponin-CThecalcium-bindingmotifissymbolizedbyarighthand.ThismotifiscalledanEFhandbecausethefifthandsixthhelicesfromtheaminoterminusinstructureOfparavalbumin(inmusclerelaxationfoundin1973)whichalabeledEandF,arepartsofthestructurethatwereoriginalusedtoillustratecalciumbindingbythismotif.Theloopregionbetweenthetwoahelicesbindsthecalciumatom.CarboxylsidechainsfromAspandGlu,main-chainC’=OandH2Ofromligandstometalatom.Thehelix-loop-helixmotifprovidesascaffoldThatholdsthecalciumligandinproperpositiontobendandreleasecalcium.c)Thestructureoftroponin-CisbuiltupfromfourEFmotifs.当前第43页\共有86页\编于星期四\19点当前第44页\共有86页\编于星期四\19点Hairpinβmotif(Nospecificfunction)ThestrongpreferenceforβstrandstobeadjacentinβsheetswhentheyareadjacentintheaminoacidSequenceandthustoformahairpinβmotif.Thelengthoftheloopregionbetweentheβstrandsverybutaregenerallyfrom2to5residueslong.Thereisnospecificfunctionassociatedwiththismotif.当前第45页\共有86页\编于星期四\19点Twoexamples:a)bovintrypsininhibitor;b)snakevenomerabutoxin当前第46页\共有86页\编于星期四\19点TheGreekkeymotifExample:theenzymeStaphylococcusnuclease,anenzymethatdegradesDNATheGreekkeymotifisnotassociatedwithanyspecificfunction,Butitoccursfrequentlyinproteinstructures.

当前第47页\共有86页\编于星期四\19点The

β-α-βmotifcontainstwoparallelβstrandsThisloopisofteninvolvedinFormingthefunctionalbindingsite,oractivesite.Theloopregionscanbeofverydifferentlengths,from1or2residuestoover100.ThetwoloopshaveDifferentfunctions.Theloopthatconnectsthecarboxylendoftheβstrandwithaminoendofαhelixisofteninvolvedinformingthefunctionalbindingsite,oractivesite,ofthesestructures.Theseloopregionsthususuallyhaveconservedaminoacidsequencesinhomologousproteins.Incontrast,theotherloophasnotyetfoundtocontributetoanactivesite.当前第48页\共有86页\编于星期四\19点Connectionsbetweenβstrandsinlayeredβsheets当前第49页\共有86页\编于星期四\19点Twoarrangementsofβ

strandsstabilizedbythetendencyofthestrandstotwist.Hemolysin(apore-formingtoxinthatkillsacellbycreatingaholeinitsmembrane)fromthebacteriumStaphylococcusaureus(PDB7AHL).photolyase(aproteinthatrepairscertaintypesofDNAdamage)fromE.coli(PDB1DNP).当前第50页\共有86页\编于星期四\19点

氨基酸顺序相邻的花样通常在三维结构上也靠近

当前第51页\共有86页\编于星期四\19点RNA结合蛋白(ROP)的四个-螺旋折叠为一个四螺旋束

当前第52页\共有86页\编于星期四\19点

-螺旋的球状折叠

当前第53页\共有86页\编于星期四\19点

反平行的-链形成桶结构

当前第54页\共有86页\编于星期四\19点上-下--回折桶结构

当前第55页\共有86页\编于星期四\19点

反平行-结构中的希腊图案花样

当前第56页\共有86页\编于星期四\19点果冻卷饼状桶(jellyrollbarrels)

结构花样

当前第57页\共有86页\编于星期四\19点

/

TIM桶结构开放扭曲的/结构

当前第58页\共有86页\编于星期四\19点开放扭曲的α/β结构中的结合部位形成裂缝

当前第59页\共有86页\编于星期四\19点Proteinmoleculesareorganizedinastructuralhierarchy(等级）PrimarystructureSecondarystructureTertiarystructure(domains)Quaternarystructure当前第60页\共有86页\编于星期四\19点LargepolypeptidechainsfoldintoseveraldomainsEGF:domainsthatarehomologoustoepidermal(表皮细胞）growthfactor(53aminoacids)当前第61页\共有86页\编于星期四\19点Constructinglargemotifsfromsmallerones当前第62页\共有86页\编于星期四\19点1,re-visitofthesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins当前第63页\共有86页\编于星期四\19点Helpfulwebsites:1,PDB(ProteinDataBank)2,SCOP(StructuralClassificationofProteins)3,comparisonofproteinstructuresin3D当前第64页\共有86页\编于星期四\19点A,X-raycrystallographyB,NMR(nuclearmagneticresonance)C,CD(circulardichroism)D,…当前第65页\共有86页\编于星期四\19点Computerprograms当前第66页\共有86页\编于星期四\19点NMRandNobelPrice:1944:I.I.Rabi,suggeststhatinformationaboutatoms'nucleicanbeobtainedbystudyingtheinternalmagnetismofprotons.Thisformsthefundamentalbasisfortoday'sresonanceimagingtechnologies1952:

PhysicistsE.Purcell(Harvard)andF.Bloch(Stanford)discoverNuclearMagneticResonance(NMR).

1991:R.Ernst,AdvancesinNMRcouldleadtotheabilitytodirectlyobservethechemicalactionofmedicationinthebody.2002:JohnB.Fenn,KoichiTanaka,KurtWüthrichforthedevelopmentofnuclearmagneticresonancespectroscopyfordeterminingthethree-dimensionalstructureofbiologicalmacromoleculesinsolution"当前第67页\共有86页\编于星期四\19点

TheNobelPrizeinChemistry2002"forthedevelopmentofmethodsforidentificationandstructureanalysesofbiologicalmacromolecules""fortheirdevelopmentofsoftdesorptionionisationmethodsformassspectrometricanalysesofbiologicalmacromolecules""forhisdevelopmentofnuclearmagneticresonancespectroscopyfordeterminingthethree-dimensionalstructureofbiologicalmacromoleculesinsolution"

JohnB.Fenn

KoichiTanaka

KurtWüthrich

1/4oftheprize

1/4oftheprize

1/2oftheprizeUSAJapanSwitzerlandVirginiaCommonwealthUniversity

Richmond,VA,USAShimadzuCorp.

Kyoto,JapanEidgenössischeTechnischeHochschule(SwissFederalInstituteofTechnology)

Zurich,Switzerland;TheScrippsResearchInstitute

LaJolla,CA,USAb.1917b.1959b.1938当前第68页\共有86页\编于星期四\19点当前第69页\共有86页\编于星期四\19点当前第70页\共有86页\编于星期四\19点3Dstructurecomparison:

当前第71页\共有86页\编于星期四\19点1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteins当前第72页\共有86页\编于星期四\19点Inconsideringthesehigherlevelsofstructure,itisusefultoclassifyproteinsintotwomajorgroups:fibrousproteins,havingpolypeptidechainsarrangedinlongstrandsorsheets,andglobularproteins,havingpolypeptidechainsfoldedintoasphericalorglobularshape.当前第73页\共有86页\编于星期四\19点Thetwogroupsdifferfunctionallyfromeachother:fibrousproteinsprovidesupport,shape,andexternalprotectiontovertebratesglobularproteins:mostenzymesandregulatoryproteinsThetwogroupsarestructurallydistinct:

fibrousproteinsusuallyconsistlargelyofasingletypeofsecondarystructure;globularproteinsoftencontainseveraltypesofsecondarystructure.当前第74页\共有86页\编于星期四\19点StructuralClassificationofProteins(SCOP)(globularproteins)1,Allα2,Allβ3,α/β4,α+β当前第75页\共有86页\编于星期四\19点Proteinfamilyandsuperfamily当前第76页\共有86页\编于星期四\19点当前第77页\共有86页\编于星期四\19点当前第78页\共有86页\编于星期四\1