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第一章:蛋白质的结构层次本文档共86页;当前第1页;编辑于星期二\3点16分1,thesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins本文档共86页;当前第2页;编辑于星期二\3点16分ProteinSecondaryStructure■Secondarystructureistheregulararrangementofaminoacidresiduesinasegmentofapolypeptidechain,inwhicheachresidueisspatiallyrelatedtoitsneighborsinthesameway.■Themostcommonsecondarystructuresaretheαhelix,theβ

conformation,andβ

turns.■Thesecondarystructureofapolypeptidesegmentcanbecompletelydefinediftheφand

ψanglesareknownforallaminoacidresiduesinthatsegment.本文档共86页;当前第3页;编辑于星期二\3点16分10papersfromLinusPaulingandcolleaguespublishedinPNAS,1951本文档共86页;当前第4页;编辑于星期二\3点16分αhelix310helixπ

helix:theoreticallypossible,butneverfoundintheproteins?sheet:parallelandanti-parallel本文档共86页;当前第5页;编辑于星期二\3点16分αhelix?sheet3.613helix本文档共86页;当前第6页;编辑于星期二\3点16分Parametersoffiveactualortheoreticalsecondarystructures:本文档共86页;当前第7页;编辑于星期二\3点16分αhelix:

thebackboneofthepolypeptidechainisextendedintohelicalstructureWhichIsbuiltupfromonecontinuousregion.αhelix本文档共86页;当前第8页;编辑于星期二\3点16分φ,ψanglepairapproximately-60°and-50°.Thelengthrangfrom4or5to44residues.Theaveragelengthisaround10residues

本文档共86页;当前第9页;编辑于星期二\3点16分3.6residuesperturnwithhydrogenbondsbetweenC’=OofresiduesnandNHofresiduesn+4.Theendofαhelicesarepolarandarealmostatthesurfaceofproteinmolecules本文档共86页;当前第10页;编辑于星期二\3点16分310helixπ

helix4.416helixN+53residuesperturnanda10atomsbetweenthehydrogenbonddonorandacceptor,N+3本文档共86页;当前第11页;编辑于星期二\3点16分Idealizedhelices:本文档共86页;当前第12页;编辑于星期二\3点16分Hydrogenbondingpatternsforfourhelices

273103.6134.414本文档共86页;当前第13页;编辑于星期二\3点16分本文档共86页;当前第14页;编辑于星期二\3点16分Theαhelixhasadipolemoment1.Theoveralleffectisasignificantnetdipolefortheαhelix.Thatgivesapartialpositivechargeattheaminoend

apartialnegativechargeattheCarboxylend(0.5-0.7unitcharge)2.Unitchargeateachendattractligandsofoppositecharge.PhosphategroupsfrequentlybindattheN-terminalofαhelix.Incontrast,positivechargeligandsrarelybindatC-teminal.本文档共86页;当前第15页;编辑于星期二\3点16分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本文档共86页;当前第16页;编辑于星期二\3点16分本文档共86页;当前第17页;编辑于星期二\3点16分本文档共86页;当前第18页;编辑于星期二\3点16分Saccharomycescerevisiaemitochondrialthioredoxin3Baoetal.本文档共86页;当前第19页;编辑于星期二\3点16分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.本文档共86页;当前第20页;编辑于星期二\3点16分1)βsheet:

thebackboneofthepolypeptidechainisextendedintoa

zigzagstructure.2)

βsheet

isbuiltupfromacombinationofseveralregionsofthepolypeptidechain.3)Thelengthrangfrom5to10residues.β

sheet本文档共86页;当前第21页;编辑于星期二\3点16分本文档共86页;当前第22页;编辑于星期二\3点16分Theaminoacidecanallruninthesamebiochemicaldirection,amioterminaltocarboxyterminalTheaminoacidcanhavealternatingdirections,theN-terminaltoC-terminalfollowbyC-terminaltoN-terminal本文档共86页;当前第23页;编辑于星期二\3点16分Twoformshaveadistinctivepatternofhydrogen-bondingParallelAntiparallelTheβsheetthatareformedfromseveralβstrandsare

“pleated”本文档共86页;当前第24页;编辑于星期二\3点16分βsheetcanalsocombineintomixedβsheet(About20%ofknownproteinstructuresaremixed)本文档共86页;当前第25页;编辑于星期二\3点16分本文档共86页;当前第26页;编辑于星期二\3点16分Almostalltheβsheethavetwiststrands.This

twisthasthesamehandedness

(right-handed)φ,ψangleswithinthebroadstructurallyallowedregion本文档共86页;当前第27页;编辑于星期二\3点16分本文档共86页;当前第28页;编辑于星期二\3点16分theDouble-headedArrowheadProteaseInhibitorA

Baoetal.本文档共86页;当前第29页;编辑于星期二\3点16分本文档共86页;当前第30页;编辑于星期二\3点16分LoopregionfrequentlyparticipateinformingbindingsitesandenzymeactivesitesLoopregionsareatthesurfaceofproteinmoleculesHairpinloops本文档共86页;当前第31页;编辑于星期二\3点16分Hydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe4thaminogroupβ-turns:

connecttheendsoftwoadjacentsegmentsofanantiparallelβsheet.本文档共86页;当前第32页;编辑于星期二\3点16分本文档共86页;当前第33页;编辑于星期二\3点16分Productsof13genesinvolvedinpeptidyl-prolylcis-transisomeraseactivitythecommonpresenceofProandGlyresiduesinβturnsβ

turns本文档共86页;当前第34页;编辑于星期二\3点16分

γ

turnHydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe3rdaminogroup本文档共86页;当前第35页;编辑于星期二\3点16分ARamachandranplot本文档共86页;当前第36页;编辑于星期二\3点16分本文档共86页;当前第37页;编辑于星期二\3点16分SchematicpicturesofproteinshighlightsecondarystructureSimplifyFacilitateseeingsimilaritybetweenproteinsHelicessometimescylinders本文档共86页;当前第38页;编辑于星期二\3点16分TopologydiagramsareusefulforclassificationofproteinstructuresShowthedirectionofeachβstrandandthewaythestrandsareconnectedtoeachotheralongthepolypeptidechain本文档共86页;当前第39页;编辑于星期二\3点16分1,Thesecondarystructures2,Supersecondarystructuresanddomains

3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins本文档共86页;当前第40页;编辑于星期二\3点16分Supersecondarystructures,alsocalledmotifsorsimplyfolds,

areparticularlystablearrangementsofseveralelementsofsecondarystructureandtheconnectionsbetweenthem.本文档共86页;当前第41页;编辑于星期二\3点16分Twoαhelicesthatareconnectedbyashortloopregion.A:helix-turn-helixmotifisspecificforDNAbindingB:thecalciumbindingmotifispresentinmanyproteinsWhosefunctionisregulatedbycalcium.本文档共86页;当前第42页;编辑于星期二\3点16分Thecalcium-bindingmotifissymbolizedbyrighthandExample:thecalciumisboundtothemotifinthetroponin-CThecalcium-bindingmotifissymbolizedbyarighthand.ThismotifiscalledanEFhandbecausethefifthandsixthhelicesfromtheaminoterminusinstructureOfparavalbumin(inmusclerelaxationfoundin1973)whichalabeledEandF,arepartsofthestructurethatwereoriginalusedtoillustratecalciumbindingbythismotif.Theloopregionbetweenthetwoahelicesbindsthecalciumatom.CarboxylsidechainsfromAspandGlu,main-chainC’=OandH2Ofromligandstometalatom.Thehelix-loop-helixmotifprovidesascaffoldThatholdsthecalciumligandinproperpositiontobendandreleasecalcium.c)Thestructureoftroponin-CisbuiltupfromfourEFmotifs.本文档共86页;当前第43页;编辑于星期二\3点16分本文档共86页;当前第44页;编辑于星期二\3点16分Hairpinβmotif(Nospecificfunction)ThestrongpreferenceforβstrandstobeadjacentinβsheetswhentheyareadjacentintheaminoacidSequenceandthustoformahairpinβmotif.Thelengthoftheloopregionbetweentheβstrandsverybutaregenerallyfrom2to5residueslong.Thereisnospecificfunctionassociatedwiththismotif.本文档共86页;当前第45页;编辑于星期二\3点16分Twoexamples:a)bovintrypsininhibitor;b)snakevenomerabutoxin本文档共86页;当前第46页;编辑于星期二\3点16分TheGreekkeymotifExample:theenzymeStaphylococcusnuclease,anenzymethatdegradesDNATheGreekkeymotifisnotassociatedwithanyspecificfunction,Butitoccursfrequentlyinproteinstructures.

本文档共86页;当前第47页;编辑于星期二\3点16分The

β-α-βmotifcontainstwoparallelβstrandsThisloopisofteninvolvedinFormingthefunctionalbindingsite,oractivesite.Theloopregionscanbeofverydifferentlengths,from1or2residuestoover100.ThetwoloopshaveDifferentfunctions.Theloopthatconnectsthecarboxylendoftheβstrandwithaminoendofαhelixisofteninvolvedinformingthefunctionalbindingsite,oractivesite,ofthesestructures.Theseloopregionsthususuallyhaveconservedaminoacidsequencesinhomologousproteins.Incontrast,theotherloophasnotyetfoundtocontributetoanactivesite.本文档共86页;当前第48页;编辑于星期二\3点16分Connectionsbetweenβstrandsinlayeredβsheets本文档共86页;当前第49页;编辑于星期二\3点16分Twoarrangementsofβ

strandsstabilizedbythetendencyofthestrandstotwist.Hemolysin(apore-formingtoxinthatkillsacellbycreatingaholeinitsmembrane)fromthebacteriumStaphylococcusaureus(PDB7AHL).photolyase(aproteinthatrepairscertaintypesofDNAdamage)fromE.coli(PDB1DNP).本文档共86页;当前第50页;编辑于星期二\3点16分

氨基酸顺序相邻的花样通常在三维结构上也靠近

本文档共86页;当前第51页;编辑于星期二\3点16分RNA结合蛋白(ROP)的四个-螺旋折叠为一个四螺旋束

本文档共86页;当前第52页;编辑于星期二\3点16分

-螺旋的球状折叠

本文档共86页;当前第53页;编辑于星期二\3点16分

反平行的-链形成桶结构

本文档共86页;当前第54页;编辑于星期二\3点16分上-下--回折桶结构

本文档共86页;当前第55页;编辑于星期二\3点16分

反平行-结构中的希腊图案花样

本文档共86页;当前第56页;编辑于星期二\3点16分果冻卷饼状桶(jellyrollbarrels)

结构花样

本文档共86页;当前第57页;编辑于星期二\3点16分

/

TIM桶结构开放扭曲的/结构

本文档共86页;当前第58页;编辑于星期二\3点16分开放扭曲的α/β结构中的结合部位形成裂缝

本文档共86页;当前第59页;编辑于星期二\3点16分Proteinmoleculesareorganizedinastructuralhierarchy(等级)PrimarystructureSecondarystructureTertiarystructure(domains)Quaternarystructure本文档共86页;当前第60页;编辑于星期二\3点16分LargepolypeptidechainsfoldintoseveraldomainsEGF:domainsthatarehomologoustoepidermal(表皮细胞)growthfactor(53aminoacids)本文档共86页;当前第61页;编辑于星期二\3点16分Constructinglargemotifsfromsmallerones本文档共86页;当前第62页;编辑于星期二\3点16分1,re-visitofthesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins本文档共86页;当前第63页;编辑于星期二\3点16分Helpfulwebsites:1,PDB(ProteinDataBank)2,SCOP(StructuralClassificationofProteins)3,comparisonofproteinstructuresin3D本文档共86页;当前第64页;编辑于星期二\3点16分A,X-raycrystallographyB,NMR(nuclearmagneticresonance)C,CD(circulardichroism)D,…本文档共86页;当前第65页;编辑于星期二\3点16分Computerprograms本文档共86页;当前第66页;编辑于星期二\3点16分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"本文档共86页;当前第67页;编辑于星期二\3点16分

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

JohnB.Fenn

KoichiTanaka

KurtWüthrich

1/4oftheprize

1/4oftheprize

1/2oftheprizeUSAJapanSwitzerlandVirginiaCommonwealthUniversity

Richmond,VA,USAShimadzuCorp.

Kyoto,JapanEidgen?ssischeTechnischeHochschule(SwissFederalInstituteofTechnology)

Zurich,Switzerland;TheScrippsResearchInstitute

LaJolla,CA,USAb.1917b.1959b.1938本文档共86页;当前第68页;编辑于星期二\3点16分本文档共86页;当前第69页;编辑于星期二\3点16分本文档共86页;当前第70页;编辑于星期二\3点16分3Dstructurecomparison:

本文档共86页;当前第71页;编辑于星期二\3点16分1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteins本文档共86页;当前第72页;编辑于星期二\3点16分Inconsideringthesehigherlevelsofstructure,itisusefultoclassifyproteinsintotwomajorgroups:fibrousproteins,havingpolypeptidechainsarrangedinlongstrandsorsheets,andglobularproteins,havingpolypeptidechainsfoldedintoasphericalorglobularshape.本文档共86页;当前第73页;编辑于星期二\3点16分Thetwogroupsdifferfunctionallyfromeachother:fibrousproteinsprovidesupport,shape,andexternalprotectiontovertebratesglobularproteins:mostenzymesandregulatoryproteinsThetwogroupsarestructurallydistinct:

fibrousproteinsusuallyconsistlargelyofasingletypeofsecondarystructure;globularproteinsoftencontainseveraltypesofsecondarystructure.本文档共86页;当前第74页;编辑于星期二\3点16分StructuralClassificationofProteins(SCOP)(globularproteins)1,Allα2,Allβ3,α/β4,α+β本文档共86页;当前第75页;编辑于星期二\3点16分Proteinfamilyandsuperfamily本文档共86页;当前第76页;编辑于星期二\3点16分本文档共86页;当前第77页;编辑于星期二\3点16分本文档共86页;当前第78页;编辑于星期二\3点16分α/β:

theα

andβ

segmentsareinterspersedoralternate本文档共86页;当前第79页;编辑于星期二\3点16分α+β:

theα

andβ

regionsaresomewhatsegregated本文档共86页;当前第80页;编辑于星期二\3点16分Typicalstructuresofglobularproteins本文档共86页;当前第81页;编辑于星期二\3点16分Thedistributionofhydrophilicandhydrophobicresiduesinglobularproteins本文档共86页;当前第82页;编辑于星期二\3点16分PDBHoldingsList:7-Sep-2004Proteins,Peptides,andVirusesProtein/NucleicAcidComplexesNucleicAcidsCarbohydratestotalX-rayDiffractionandother2135310487471423162NMR323510360843950Total24588115113551827112MoleculeType本文档共86页;当前第83页;编辑于星期二\3点16分ClassNumberoffoldsNumberofsuperfamiliesNumberoffamiliesAllalphaproteins179299480Allbetaproteins126248462Alphaandbetaproteins(a/b)121199542Alphaandbetaproteins(a+b)234349567Multi-domainproteins383853Membraneandcellsurfaceproteins366673Smallproteins6695150Total80012942327SCOPClassificationStatistics1.65release

20619PDBEntries(1August2003)本文档共86页;当前第84页;编辑于星期二\3点16分本文档共86页;当前第85页;编辑于星期二\3点16分1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteinsThefundamentalstructuralunitisasimplerepeatingelementofsecondarystructure.Allfibrousproteinsareinsolubleinwater.Ahydrophobicaminoacidresiduesbothintheinterioroftheproteinandonthesurface.本文档共86页;当前第86页;编辑于星期二\3点16分

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