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)層次現(xiàn)在是1頁(yè)\一共有83頁(yè)\編輯于星期三1,thesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現(xiàn)在是2頁(yè)\一共有83頁(yè)\編輯于星期三ProteinSecondaryStructure■Secondarystructureistheregulararrangementofaminoacidresiduesinasegmentofapolypeptidechain,inwhicheachresidueisspatiallyrelatedtoitsneighborsinthesameway.■Themostcommonsecondarystructuresaretheαhelix,theβ

conformation,andβ

turns.■Thesecondarystructureofapolypeptidesegmentcanbecompletelydefinediftheφand

ψanglesareknownforallaminoacidresiduesinthatsegment.現(xiàn)在是3頁(yè)\一共有83頁(yè)\編輯于星期三10papersfromLinusPaulingandcolleaguespublishedinPNAS,1951現(xiàn)在是4頁(yè)\一共有83頁(yè)\編輯于星期三αhelix310helixπ

helix:theoreticallypossible,butneverfoundintheproteins?sheet:parallelandanti-parallel現(xiàn)在是5頁(yè)\一共有83頁(yè)\編輯于星期三αhelix?sheet3.613helix現(xiàn)在是6頁(yè)\一共有83頁(yè)\編輯于星期三Parametersoffiveactualortheoreticalsecondarystructures:現(xiàn)在是7頁(yè)\一共有83頁(yè)\編輯于星期三αhelix:

thebackboneofthepolypeptidechainisextendedintohelicalstructureWhichIsbuiltupfromonecontinuousregion.αhelix現(xiàn)在是8頁(yè)\一共有83頁(yè)\編輯于星期三φ,ψanglepairapproximately-60°and-50°.Thelengthrangfrom4or5to44residues.Theaveragelengthisaround10residues

現(xiàn)在是9頁(yè)\一共有83頁(yè)\編輯于星期三3.6residuesperturnwithhydrogenbondsbetweenC’=OofresiduesnandNHofresiduesn+4.Theendofαhelicesarepolarandarealmostatthesurfaceofproteinmolecules現(xiàn)在是10頁(yè)\一共有83頁(yè)\編輯于星期三310helixπ

helix4.416helixN+53residuesperturnanda10atomsbetweenthehydrogenbonddonorandacceptor,N+3現(xiàn)在是11頁(yè)\一共有83頁(yè)\編輯于星期三Idealizedhelices:現(xiàn)在是12頁(yè)\一共有83頁(yè)\編輯于星期三Hydrogenbondingpatternsforfourhelices

273103.6134.414現(xiàn)在是13頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是14頁(yè)\一共有83頁(yè)\編輯于星期三Theαhelixhasadipolemoment1.Theoveralleffectisasignificantnetdipolefortheαhelix.Thatgivesapartialpositivechargeattheaminoend

apartialnegativechargeattheCarboxylend(0.5-0.7unitcharge)2.Unitchargeateachendattractligandsofoppositecharge.PhosphategroupsfrequentlybindattheN-terminalofαhelix.Incontrast,positivechargeligandsrarelybindatC-teminal.現(xiàn)在是15頁(yè)\一共有83頁(yè)\編輯于星期三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現(xiàn)在是16頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是17頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是18頁(yè)\一共有83頁(yè)\編輯于星期三Saccharomycescerevisiaemitochondrialthioredoxin3Baoetal.現(xiàn)在是19頁(yè)\一共有83頁(yè)\編輯于星期三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.現(xiàn)在是20頁(yè)\一共有83頁(yè)\編輯于星期三1)βsheet:

thebackboneofthepolypeptidechainisextendedintoa

zigzagstructure.2)

βsheet

isbuiltupfromacombinationofseveralregionsofthepolypeptidechain.3)Thelengthrangfrom5to10residues.β

sheet現(xiàn)在是21頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是22頁(yè)\一共有83頁(yè)\編輯于星期三Theaminoacidecanallruninthesamebiochemicaldirection,amioterminaltocarboxyterminalTheaminoacidcanhavealternatingdirections,theN-terminaltoC-terminalfollowbyC-terminaltoN-terminal現(xiàn)在是23頁(yè)\一共有83頁(yè)\編輯于星期三Twoformshaveadistinctivepatternofhydrogen-bondingParallelAntiparallelTheβsheetthatareformedfromseveralβstrandsare

“pleated”現(xiàn)在是24頁(yè)\一共有83頁(yè)\編輯于星期三βsheetcanalsocombineintomixedβsheet(About20%ofknownproteinstructuresaremixed)現(xiàn)在是25頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是26頁(yè)\一共有83頁(yè)\編輯于星期三Almostalltheβsheethavetwiststrands.This

twisthasthesamehandedness

(right-handed)φ,ψangleswithinthebroadstructurallyallowedregion現(xiàn)在是27頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是28頁(yè)\一共有83頁(yè)\編輯于星期三theDouble-headedArrowheadProteaseInhibitorA

Baoetal.現(xiàn)在是29頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是30頁(yè)\一共有83頁(yè)\編輯于星期三LoopregionfrequentlyparticipateinformingbindingsitesandenzymeactivesitesLoopregionsareatthesurfaceofproteinmoleculesHairpinloops現(xiàn)在是31頁(yè)\一共有83頁(yè)\編輯于星期三Hydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe4thaminogroupβ-turns:

connecttheendsoftwoadjacentsegmentsofanantiparallelβsheet.現(xiàn)在是32頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是33頁(yè)\一共有83頁(yè)\編輯于星期三Productsof13genesinvolvedinpeptidyl-prolylcis-transisomeraseactivitythecommonpresenceofProandGlyresiduesinβturnsβ

turns現(xiàn)在是34頁(yè)\一共有83頁(yè)\編輯于星期三

γ

turnHydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe3rdaminogroup現(xiàn)在是35頁(yè)\一共有83頁(yè)\編輯于星期三ARamachandranplot現(xiàn)在是36頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是37頁(yè)\一共有83頁(yè)\編輯于星期三SchematicpicturesofproteinshighlightsecondarystructureSimplifyFacilitateseeingsimilaritybetweenproteinsHelicessometimescylinders現(xiàn)在是38頁(yè)\一共有83頁(yè)\編輯于星期三TopologydiagramsareusefulforclassificationofproteinstructuresShowthedirectionofeachβstrandandthewaythestrandsareconnectedtoeachotheralongthepolypeptidechain現(xiàn)在是39頁(yè)\一共有83頁(yè)\編輯于星期三1,Thesecondarystructures2,Supersecondarystructuresanddomains

3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現(xiàn)在是40頁(yè)\一共有83頁(yè)\編輯于星期三Supersecondarystructures,alsocalledmotifsorsimplyfolds,

areparticularlystablearrangementsofseveralelementsofsecondarystructureandtheconnectionsbetweenthem.現(xiàn)在是41頁(yè)\一共有83頁(yè)\編輯于星期三Twoαhelicesthatareconnectedbyashortloopregion.A:helix-turn-helixmotifisspecificforDNAbindingB:thecalciumbindingmotifispresentinmanyproteinsWhosefunctionisregulatedbycalcium.現(xiàn)在是42頁(yè)\一共有83頁(yè)\編輯于星期三Thecalcium-bindingmotifissymbolizedbyrighthandExample:thecalciumisboundtothemotifinthetroponin-CThecalcium-bindingmotifissymbolizedbyarighthand.ThismotifiscalledanEFhandbecausethefifthandsixthhelicesfromtheaminoterminusinstructureOfparavalbumin(inmusclerelaxationfoundin1973)whichalabeledEandF,arepartsofthestructurethatwereoriginalusedtoillustratecalciumbindingbythismotif.Theloopregionbetweenthetwoahelicesbindsthecalciumatom.CarboxylsidechainsfromAspandGlu,main-chainC’=OandH2Ofromligandstometalatom.Thehelix-loop-helixmotifprovidesascaffoldThatholdsthecalciumligandinproperpositiontobendandreleasecalcium.c)Thestructureoftroponin-CisbuiltupfromfourEFmotifs.現(xiàn)在是43頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是44頁(yè)\一共有83頁(yè)\編輯于星期三Hairpinβmotif(Nospecificfunction)ThestrongpreferenceforβstrandstobeadjacentinβsheetswhentheyareadjacentintheaminoacidSequenceandthustoformahairpinβmotif.Thelengthoftheloopregionbetweentheβstrandsverybutaregenerallyfrom2to5residueslong.Thereisnospecificfunctionassociatedwiththismotif.現(xiàn)在是45頁(yè)\一共有83頁(yè)\編輯于星期三Twoexamples:a)bovintrypsininhibitor;b)snakevenomerabutoxin現(xiàn)在是46頁(yè)\一共有83頁(yè)\編輯于星期三TheGreekkeymotifExample:theenzymeStaphylococcusnuclease,anenzymethatdegradesDNATheGreekkeymotifisnotassociatedwithanyspecificfunction,Butitoccursfrequentlyinproteinstructures.

現(xiàn)在是47頁(yè)\一共有83頁(yè)\編輯于星期三The

β-α-βmotifcontainstwoparallelβstrandsThisloopisofteninvolvedinFormingthefunctionalbindingsite,oractivesite.Theloopregionscanbeofverydifferentlengths,from1or2residuestoover100.ThetwoloopshaveDifferentfunctions.Theloopthatconnectsthecarboxylendoftheβstrandwithaminoendofαhelixisofteninvolvedinformingthefunctionalbindingsite,oractivesite,ofthesestructures.Theseloopregionsthususuallyhaveconservedaminoacidsequencesinhomologousproteins.Incontrast,theotherloophasnotyetfoundtocontributetoanactivesite.現(xiàn)在是48頁(yè)\一共有83頁(yè)\編輯于星期三Connectionsbetweenβstrandsinlayeredβsheets現(xiàn)在是49頁(yè)\一共有83頁(yè)\編輯于星期三Twoarrangementsofβ

strandsstabilizedbythetendencyofthestrandstotwist.Hemolysin(apore-formingtoxinthatkillsacellbycreatingaholeinitsmembrane)fromthebacteriumStaphylococcusaureus(PDB7AHL).photolyase(aproteinthatrepairscertaintypesofDNAdamage)fromE.coli(PDB1DNP).現(xiàn)在是50頁(yè)\一共有83頁(yè)\編輯于星期三

氨基酸順序相鄰的花樣通常在三維結(jié)構(gòu)上也靠近

現(xiàn)在是51頁(yè)\一共有83頁(yè)\編輯于星期三RNA結(jié)合蛋白(ROP)的四個(gè)-螺旋折疊為一個(gè)四螺旋束

現(xiàn)在是52頁(yè)\一共有83頁(yè)\編輯于星期三

-螺旋的球狀折疊

現(xiàn)在是53頁(yè)\一共有83頁(yè)\編輯于星期三

反平行的-鏈形成桶結(jié)構(gòu)

現(xiàn)在是54頁(yè)\一共有83頁(yè)\編輯于星期三上-下--回折桶結(jié)構(gòu)

現(xiàn)在是55頁(yè)\一共有83頁(yè)\編輯于星期三

反平行-結(jié)構(gòu)中的希臘圖案花樣

現(xiàn)在是56頁(yè)\一共有83頁(yè)\編輯于星期三果凍卷餅狀桶(jellyrollbarrels)

結(jié)構(gòu)花樣

現(xiàn)在是57頁(yè)\一共有83頁(yè)\編輯于星期三

/

TIM桶結(jié)構(gòu)開放扭曲的/結(jié)構(gòu)

現(xiàn)在是58頁(yè)\一共有83頁(yè)\編輯于星期三開放扭曲的α/β結(jié)構(gòu)中的結(jié)合部位形成裂縫

現(xiàn)在是59頁(yè)\一共有83頁(yè)\編輯于星期三Proteinmoleculesareorganizedinastructuralhierarchy(等級(jí)）PrimarystructureSecondarystructureTertiarystructure(domains)Quaternarystructure現(xiàn)在是60頁(yè)\一共有83頁(yè)\編輯于星期三LargepolypeptidechainsfoldintoseveraldomainsEGF:domainsthatarehomologoustoepidermal(表皮細(xì)胞）growthfactor(53aminoacids)現(xiàn)在是61頁(yè)\一共有83頁(yè)\編輯于星期三Constructinglargemotifsfromsmallerones現(xiàn)在是62頁(yè)\一共有83頁(yè)\編輯于星期三1,re-visitofthesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現(xiàn)在是63頁(yè)\一共有83頁(yè)\編輯于星期三Helpfulwebsites:1,PDB(ProteinDataBank)2,SCOP(StructuralClassificationofProteins)3,comparisonofproteinstructuresin3D現(xiàn)在是64頁(yè)\一共有83頁(yè)\編輯于星期三A,X-raycrystallographyB,NMR(nuclearmagneticresonance)C,CD(circulardichroism)D,…現(xiàn)在是65頁(yè)\一共有83頁(yè)\編輯于星期三Computerprograms現(xiàn)在是66頁(yè)\一共有83頁(yè)\編輯于星期三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"現(xiàn)在是67頁(yè)\一共有83頁(yè)\編輯于星期三

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現(xiàn)在是68頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是69頁(yè)\一共有83頁(yè)\編輯于星期三現(xiàn)在是70頁(yè)\一共有83頁(yè)\編輯于星期三3Dstructurecomparison:

現(xiàn)在是71頁(yè)\一共有83頁(yè)\編輯于星期三1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteins現(xiàn)在是72頁(yè)\一共有83頁(yè)\編輯于星期三Inconsideringthesehigherlevelsofstructure,itisusefultoclassifyproteinsintotwomajorgroups:fibrousproteins,havingpolypep