生物大分子結(jié)構(gòu)與功能第2章相互作用力第3節(jié)第4節(jié)

第一章：蛋白質(zhì)的結(jié)構(gòu)層次當(dāng)前第1頁\共有83頁\編于星期四\19點1,thesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins當(dāng)前第2頁\共有83頁\編于星期四\19點ProteinSecondaryStructure■Secondarystructureistheregulararrangementofaminoacidresiduesinasegmentofapolypeptidechain,inwhicheachresidueisspatiallyrelatedtoitsneighborsinthesameway.■Themostcommonsecondarystructuresaretheαhelix,theβ

conformation,andβ

turns.■Thesecondarystructureofapolypeptidesegmentcanbecompletelydefinediftheφand

ψanglesareknownforallaminoacidresiduesinthatsegment.當(dāng)前第3頁\共有83頁\編于星期四\19點10papersfromLinusPaulingandcolleaguespublishedinPNAS,1951當(dāng)前第4頁\共有83頁\編于星期四\19點αhelix310helixπ

helix:theoreticallypossible,butneverfoundintheproteins?sheet:parallelandanti-parallel當(dāng)前第5頁\共有83頁\編于星期四\19點αhelix?sheet3.613helix當(dāng)前第6頁\共有83頁\編于星期四\19點Parametersoffiveactualortheoreticalsecondarystructures:當(dāng)前第7頁\共有83頁\編于星期四\19點αhelix:

thebackboneofthepolypeptidechainisextendedintohelicalstructureWhichIsbuiltupfromonecontinuousregion.αhelix當(dāng)前第8頁\共有83頁\編于星期四\19點φ,ψanglepairapproximately-60°and-50°.Thelengthrangfrom4or5to44residues.Theaveragelengthisaround10residues

當(dāng)前第9頁\共有83頁\編于星期四\19點3.6residuesperturnwithhydrogenbondsbetweenC’=OofresiduesnandNHofresiduesn+4.Theendofαhelicesarepolarandarealmostatthesurfaceofproteinmolecules當(dāng)前第10頁\共有83頁\編于星期四\19點310helixπ

helix4.416helixN+53residuesperturnanda10atomsbetweenthehydrogenbonddonorandacceptor,N+3當(dāng)前第11頁\共有83頁\編于星期四\19點Idealizedhelices:當(dāng)前第12頁\共有83頁\編于星期四\19點Hydrogenbondingpatternsforfourhelices

273103.6134.414當(dāng)前第13頁\共有83頁\編于星期四\19點當(dāng)前第14頁\共有83頁\編于星期四\19點Theαhelixhasadipolemoment1.Theoveralleffectisasignificantnetdipolefortheαhelix.Thatgivesapartialpositivechargeattheaminoend

apartialnegativechargeattheCarboxylend(0.5-0.7unitcharge)2.Unitchargeateachendattractligandsofoppositecharge.PhosphategroupsfrequentlybindattheN-terminalofαhelix.Incontrast,positivechargeligandsrarelybindatC-teminal.當(dāng)前第15頁\共有83頁\編于星期四\19點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當(dāng)前第16頁\共有83頁\編于星期四\19點當(dāng)前第17頁\共有83頁\編于星期四\19點當(dāng)前第18頁\共有83頁\編于星期四\19點Saccharomycescerevisiaemitochondrialthioredoxin3Baoetal.當(dāng)前第19頁\共有83頁\編于星期四\19點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

紅假單胞菌Complex(foursubunits)solvedin1985(1PRC)NobelChemistryPrizewasawardedtoJ.Deisenhofer,R.Huber,H.Michelin1988.當(dāng)前第20頁\共有83頁\編于星期四\19點1)βsheet:

thebackboneofthepolypeptidechainisextendedintoa

zigzagstructure.2)

βsheet

isbuiltupfromacombinationofseveralregionsofthepolypeptidechain.3)Thelengthrangfrom5to10residues.β

sheet當(dāng)前第21頁\共有83頁\編于星期四\19點當(dāng)前第22頁\共有83頁\編于星期四\19點Theaminoacidecanallruninthesamebiochemicaldirection,amioterminaltocarboxyterminalTheaminoacidcanhavealternatingdirections,theN-terminaltoC-terminalfollowbyC-terminaltoN-terminal當(dāng)前第23頁\共有83頁\編于星期四\19點Twoformshaveadistinctivepatternofhydrogen-bondingParallelAntiparallelTheβsheetthatareformedfromseveralβstrandsare

“pleated”當(dāng)前第24頁\共有83頁\編于星期四\19點βsheetcanalsocombineintomixedβsheet(About20%ofknownproteinstructuresaremixed)當(dāng)前第25頁\共有83頁\編于星期四\19點當(dāng)前第26頁\共有83頁\編于星期四\19點Almostalltheβsheethavetwiststrands.This

twisthasthesamehandedness

(right-handed)φ,ψangleswithinthebroadstructurallyallowedregion當(dāng)前第27頁\共有83頁\編于星期四\19點當(dāng)前第28頁\共有83頁\編于星期四\19點theDouble-headedArrowheadProteaseInhibitorA

Baoetal.當(dāng)前第29頁\共有83頁\編于星期四\19點當(dāng)前第30頁\共有83頁\編于星期四\19點LoopregionfrequentlyparticipateinformingbindingsitesandenzymeactivesitesLoopregionsareatthesurfaceofproteinmoleculesHairpinloops當(dāng)前第31頁\共有83頁\編于星期四\19點Hydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe4thaminogroupβ-turns:

connecttheendsoftwoadjacentsegmentsofanantiparallelβsheet.當(dāng)前第32頁\共有83頁\編于星期四\19點當(dāng)前第33頁\共有83頁\編于星期四\19點Productsof13genesinvolvedinpeptidyl-prolylcis-transisomeraseactivitythecommonpresenceofProandGlyresiduesinβturnsβ

turns當(dāng)前第34頁\共有83頁\編于星期四\19點

γ

turnHydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe3rdaminogroup當(dāng)前第35頁\共有83頁\編于星期四\19點ARamachandranplot當(dāng)前第36頁\共有83頁\編于星期四\19點當(dāng)前第37頁\共有83頁\編于星期四\19點SchematicpicturesofproteinshighlightsecondarystructureSimplifyFacilitateseeingsimilaritybetweenproteinsHelicessometimescylinders當(dāng)前第38頁\共有83頁\編于星期四\19點TopologydiagramsareusefulforclassificationofproteinstructuresShowthedirectionofeachβstrandandthewaythestrandsareconnectedtoeachotheralongthepolypeptidechain當(dāng)前第39頁\共有83頁\編于星期四\19點1,Thesecondarystructures2,Supersecondarystructuresanddomains

3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins當(dāng)前第40頁\共有83頁\編于星期四\19點Supersecondarystructures,alsocalledmotifsorsimplyfolds,

areparticularlystablearrangementsofseveralelementsofsecondarystructureandtheconnectionsbetweenthem.當(dāng)前第41頁\共有83頁\編于星期四\19點Twoαhelicesthatareconnectedbyashortloopregion.A:helix-turn-helixmotifisspecificforDNAbindingB:thecalciumbindingmotifispresentinmanyproteinsWhosefunctionisregulatedbycalcium.當(dāng)前第42頁\共有83頁\編于星期四\19點Thecalcium-bindingmotifissymbolizedbyrighthandExample:thecalciumisboundtothemotifinthetroponin-CThecalcium-bindingmotifissymbolizedbyarighthand.ThismotifiscalledanEFhandbecausethefifthandsixthhelicesfromtheaminoterminusinstructureOfparavalbumin(inmusclerelaxationfoundin1973)whichalabeledEandF,arepartsofthestructurethatwereoriginalusedtoillustratecalciumbindingbythismotif.Theloopregionbetweenthetwoahelicesbindsthecalciumatom.CarboxylsidechainsfromAspandGlu,main-chainC’=OandH2Ofromligandstometalatom.Thehelix-loop-helixmotifprovidesascaffoldThatholdsthecalciumligandinproperpositiontobendandreleasecalcium.c)Thestructureoftroponin-CisbuiltupfromfourEFmotifs.當(dāng)前第43頁\共有83頁\編于星期四\19點當(dāng)前第44頁\共有83頁\編于星期四\19點Hairpinβmotif(Nospecificfunction)ThestrongpreferenceforβstrandstobeadjacentinβsheetswhentheyareadjacentintheaminoacidSequenceandthustoformahairpinβmotif.Thelengthoftheloopregionbetweentheβstrandsverybutaregenerallyfrom2to5residueslong.Thereisnospecificfunctionassociatedwiththismotif.當(dāng)前第45頁\共有83頁\編于星期四\19點Twoexamples:a)bovintrypsininhibitor;b)snakevenomerabutoxin當(dāng)前第46頁\共有83頁\編于星期四\19點TheGreekkeymotifExample:theenzymeStaphylococcusnuclease,anenzymethatdegradesDNATheGreekkeymotifisnotassociatedwithanyspecificfunction,Butitoccursfrequentlyinproteinstructures.

當(dāng)前第47頁\共有83頁\編于星期四\19點The

β-α-βmotifcontainstwoparallelβstrandsThisloopisofteninvolvedinFormingthefunctionalbindingsite,oractivesite.Theloopregionscanbeofverydifferentlengths,from1or2residuestoover100.ThetwoloopshaveDifferentfunctions.Theloopthatconnectsthecarboxylendoftheβstrandwithaminoendofαhelixisofteninvolvedinformingthefunctionalbindingsite,oractivesite,ofthesestructures.Theseloopregionsthususuallyhaveconservedaminoacidsequencesinhomologousproteins.Incontrast,theotherloophasnotyetfoundtocontributetoanactivesite.當(dāng)前第48頁\共有83頁\編于星期四\19點Connectionsbetweenβstrandsinlayeredβsheets當(dāng)前第49頁\共有83頁\編于星期四\19點Twoarrangementsofβ

strandsstabilizedbythetendencyofthestrandstotwist.Hemolysin(apore-formingtoxinthatkillsacellbycreatingaholeinitsmembrane)fromthebacteriumStaphylococcusaureus(PDB7AHL).photolyase(aproteinthatrepairscertaintypesofDNAdamage)fromE.coli(PDB1DNP).當(dāng)前第50頁\共有83頁\編于星期四\19點

氨基酸順序相鄰的花樣通常在三維結(jié)構(gòu)上也靠近

當(dāng)前第51頁\共有83頁\編于星期四\19點RNA結(jié)合蛋白(ROP)的四個-螺旋折疊為一個四螺旋束

當(dāng)前第52頁\共有83頁\編于星期四\19點

-螺旋的球狀折疊

當(dāng)前第53頁\共有83頁\編于星期四\19點

反平行的-鏈形成桶結(jié)構(gòu)

當(dāng)前第54頁\共有83頁\編于星期四\19點上-下--回折桶結(jié)構(gòu)

當(dāng)前第55頁\共有83頁\編于星期四\19點

反平行-結(jié)構(gòu)中的希臘圖案花樣

當(dāng)前第56頁\共有83頁\編于星期四\19點果凍卷餅狀桶(jellyrollbarrels)

結(jié)構(gòu)花樣

當(dāng)前第57頁\共有83頁\編于星期四\19點

/

TIM桶結(jié)構(gòu)開放扭曲的/結(jié)構(gòu)

當(dāng)前第58頁\共有83頁\編于星期四\19點開放扭曲的α/β結(jié)構(gòu)中的結(jié)合部位形成裂縫

當(dāng)前第59頁\共有83頁\編于星期四\19點Proteinmoleculesareorganizedinastructuralhierarchy(等級）PrimarystructureSecondarystructureTertiarystructure(domains)Quaternarystructure當(dāng)前第60頁\共有83頁\編于星期四\19點LargepolypeptidechainsfoldintoseveraldomainsEGF:domainsthatarehomologoustoepidermal(表皮細胞）growthfactor(53aminoacids)當(dāng)前第61頁\共有83頁\編于星期四\19點Constructinglargemotifsfromsmallerones當(dāng)前第62頁\共有83頁\編于星期四\19點1,re-visitofthesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins當(dāng)前第63頁\共有83頁\編于星期四\19點Helpfulwebsites:1,PDB(ProteinDataBank)2,SCOP(StructuralClassificationofProteins)3,comparisonofproteinstructuresin3D當(dāng)前第64頁\共有83頁\編于星期四\19點A,X-raycrystallographyB,NMR(nuclearmagneticresonance)C,CD(circulardichroism)D,…當(dāng)前第65頁\共有83頁\編于星期四\19點Computerprograms當(dāng)前第66頁\共有83頁\編于星期四\19點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"當(dāng)前第67頁\共有83頁\編于星期四\19點

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當(dāng)前第68頁\共有83頁\編于星期四\19點當(dāng)前第69頁\共有83頁\編于星期四\19點當(dāng)前第70頁\共有83頁\編于星期四\19點3Dstructurecomparison:

當(dāng)前第71頁\共有83頁\編于星期四\19點1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteins當(dāng)前第72頁\共有83頁\編于星期四\19點Inconsideringthesehigherlevelsofstructure,itisusefultoclassifyproteinsintotwomajorgroups:fibrousproteins,havingpolypeptide