第一章：蛋白質的結構層次現在是1頁\一共有86頁\編輯于星期三1,thesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現在是2頁\一共有86頁\編輯于星期三ProteinSecondaryStructure■Secondarystructureistheregulararrangementofaminoacidresiduesinasegmentofapolypeptidechain,inwhicheachresidueisspatiallyrelatedtoitsneighborsinthesameway.■Themostcommonsecondarystructuresaretheαhelix,theβ

conformation,andβ

turns.■Thesecondarystructureofapolypeptidesegmentcanbecompletelydefinediftheφand

ψanglesareknownforallaminoacidresiduesinthatsegment.現在是3頁\一共有86頁\編輯于星期三10papersfromLinusPaulingandcolleaguespublishedinPNAS,1951現在是4頁\一共有86頁\編輯于星期三αhelix310helixπ

helix:theoreticallypossible,butneverfoundintheproteins?sheet:parallelandanti-parallel現在是5頁\一共有86頁\編輯于星期三αhelix?sheet3.613helix現在是6頁\一共有86頁\編輯于星期三Parametersoffiveactualortheoreticalsecondarystructures:現在是7頁\一共有86頁\編輯于星期三αhelix:

thebackboneofthepolypeptidechainisextendedintohelicalstructureWhichIsbuiltupfromonecontinuousregion.αhelix現在是8頁\一共有86頁\編輯于星期三φ,ψanglepairapproximately-60°and-50°.Thelengthrangfrom4or5to44residues.Theaveragelengthisaround10residues

現在是9頁\一共有86頁\編輯于星期三3.6residuesperturnwithhydrogenbondsbetweenC’=OofresiduesnandNHofresiduesn+4.Theendofαhelicesarepolarandarealmostatthesurfaceofproteinmolecules現在是10頁\一共有86頁\編輯于星期三310helixπ

helix4.416helixN+53residuesperturnanda10atomsbetweenthehydrogenbonddonorandacceptor,N+3現在是11頁\一共有86頁\編輯于星期三Idealizedhelices:現在是12頁\一共有86頁\編輯于星期三Hydrogenbondingpatternsforfourhelices

273103.6134.414現在是13頁\一共有86頁\編輯于星期三現在是14頁\一共有86頁\編輯于星期三Theαhelixhasadipolemoment1.Theoveralleffectisasignificantnetdipolefortheαhelix.Thatgivesapartialpositivechargeattheaminoend

apartialnegativechargeattheCarboxylend(0.5-0.7unitcharge)2.Unitchargeateachendattractligandsofoppositecharge.PhosphategroupsfrequentlybindattheN-terminalofαhelix.Incontrast,positivechargeligandsrarelybindatC-teminal.現在是15頁\一共有86頁\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現在是16頁\一共有86頁\編輯于星期三現在是17頁\一共有86頁\編輯于星期三現在是18頁\一共有86頁\編輯于星期三Saccharomycescerevisiaemitochondrialthioredoxin3Baoetal.現在是19頁\一共有86頁\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.現在是20頁\一共有86頁\編輯于星期三1)βsheet:

thebackboneofthepolypeptidechainisextendedintoa

zigzagstructure.2)

βsheet

isbuiltupfromacombinationofseveralregionsofthepolypeptidechain.3)Thelengthrangfrom5to10residues.β

sheet現在是21頁\一共有86頁\編輯于星期三現在是22頁\一共有86頁\編輯于星期三Theaminoacidecanallruninthesamebiochemicaldirection,amioterminaltocarboxyterminalTheaminoacidcanhavealternatingdirections,theN-terminaltoC-terminalfollowbyC-terminaltoN-terminal現在是23頁\一共有86頁\編輯于星期三Twoformshaveadistinctivepatternofhydrogen-bondingParallelAntiparallelTheβsheetthatareformedfromseveralβstrandsare

“pleated”現在是24頁\一共有86頁\編輯于星期三βsheetcanalsocombineintomixedβsheet(About20%ofknownproteinstructuresaremixed)現在是25頁\一共有86頁\編輯于星期三現在是26頁\一共有86頁\編輯于星期三Almostalltheβsheethavetwiststrands.This

twisthasthesamehandedness

(right-handed)φ,ψangleswithinthebroadstructurallyallowedregion現在是27頁\一共有86頁\編輯于星期三現在是28頁\一共有86頁\編輯于星期三theDouble-headedArrowheadProteaseInhibitorA

Baoetal.現在是29頁\一共有86頁\編輯于星期三現在是30頁\一共有86頁\編輯于星期三LoopregionfrequentlyparticipateinformingbindingsitesandenzymeactivesitesLoopregionsareatthesurfaceofproteinmoleculesHairpinloops現在是31頁\一共有86頁\編輯于星期三Hydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe4thaminogroupβ-turns:

connecttheendsoftwoadjacentsegmentsofanantiparallelβsheet.現在是32頁\一共有86頁\編輯于星期三現在是33頁\一共有86頁\編輯于星期三Productsof13genesinvolvedinpeptidyl-prolylcis-transisomeraseactivitythecommonpresenceofProandGlyresiduesinβturnsβ

turns現在是34頁\一共有86頁\編輯于星期三

γ

turnHydrogenbondbetweentheoxygenof1stcarboxylgroupandhydrogenofthe3rdaminogroup現在是35頁\一共有86頁\編輯于星期三ARamachandranplot現在是36頁\一共有86頁\編輯于星期三現在是37頁\一共有86頁\編輯于星期三SchematicpicturesofproteinshighlightsecondarystructureSimplifyFacilitateseeingsimilaritybetweenproteinsHelicessometimescylinders現在是38頁\一共有86頁\編輯于星期三TopologydiagramsareusefulforclassificationofproteinstructuresShowthedirectionofeachβstrandandthewaythestrandsareconnectedtoeachotheralongthepolypeptidechain現在是39頁\一共有86頁\編輯于星期三1,Thesecondarystructures2,Supersecondarystructuresanddomains

3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現在是40頁\一共有86頁\編輯于星期三Supersecondarystructures,alsocalledmotifsorsimplyfolds,

areparticularlystablearrangementsofseveralelementsofsecondarystructureandtheconnectionsbetweenthem.現在是41頁\一共有86頁\編輯于星期三Twoαhelicesthatareconnectedbyashortloopregion.A:helix-turn-helixmotifisspecificforDNAbindingB:thecalciumbindingmotifispresentinmanyproteinsWhosefunctionisregulatedbycalcium.現在是42頁\一共有86頁\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.現在是43頁\一共有86頁\編輯于星期三現在是44頁\一共有86頁\編輯于星期三Hairpinβmotif(Nospecificfunction)ThestrongpreferenceforβstrandstobeadjacentinβsheetswhentheyareadjacentintheaminoacidSequenceandthustoformahairpinβmotif.Thelengthoftheloopregionbetweentheβstrandsverybutaregenerallyfrom2to5residueslong.Thereisnospecificfunctionassociatedwiththismotif.現在是45頁\一共有86頁\編輯于星期三Twoexamples:a)bovintrypsininhibitor;b)snakevenomerabutoxin現在是46頁\一共有86頁\編輯于星期三TheGreekkeymotifExample:theenzymeStaphylococcusnuclease,anenzymethatdegradesDNATheGreekkeymotifisnotassociatedwithanyspecificfunction,Butitoccursfrequentlyinproteinstructures.

現在是47頁\一共有86頁\編輯于星期三The

β-α-βmotifcontainstwoparallelβstrandsThisloopisofteninvolvedinFormingthefunctionalbindingsite,oractivesite.Theloopregionscanbeofverydifferentlengths,from1or2residuestoover100.ThetwoloopshaveDifferentfunctions.Theloopthatconnectsthecarboxylendoftheβstrandwithaminoendofαhelixisofteninvolvedinformingthefunctionalbindingsite,oractivesite,ofthesestructures.Theseloopregionsthususuallyhaveconservedaminoacidsequencesinhomologousproteins.Incontrast,theotherloophasnotyetfoundtocontributetoanactivesite.現在是48頁\一共有86頁\編輯于星期三Connectionsbetweenβstrandsinlayeredβsheets現在是49頁\一共有86頁\編輯于星期三Twoarrangementsofβ

strandsstabilizedbythetendencyofthestrandstotwist.Hemolysin(apore-formingtoxinthatkillsacellbycreatingaholeinitsmembrane)fromthebacteriumStaphylococcusaureus(PDB7AHL).photolyase(aproteinthatrepairscertaintypesofDNAdamage)fromE.coli(PDB1DNP).現在是50頁\一共有86頁\編輯于星期三

氨基酸順序相鄰的花樣通常在三維結構上也靠近

現在是51頁\一共有86頁\編輯于星期三RNA結合蛋白(ROP)的四個-螺旋折疊為一個四螺旋束

現在是52頁\一共有86頁\編輯于星期三

-螺旋的球狀折疊

現在是53頁\一共有86頁\編輯于星期三

反平行的-鏈形成桶結構

現在是54頁\一共有86頁\編輯于星期三上-下--回折桶結構

現在是55頁\一共有86頁\編輯于星期三

反平行-結構中的希臘圖案花樣

現在是56頁\一共有86頁\編輯于星期三果凍卷餅狀桶(jellyrollbarrels)

結構花樣

現在是57頁\一共有86頁\編輯于星期三

/

TIM桶結構開放扭曲的/結構

現在是58頁\一共有86頁\編輯于星期三開放扭曲的α/β結構中的結合部位形成裂縫

現在是59頁\一共有86頁\編輯于星期三Proteinmoleculesareorganizedinastructuralhierarchy(等級）PrimarystructureSecondarystructureTertiarystructure(domains)Quaternarystructure現在是60頁\一共有86頁\編輯于星期三LargepolypeptidechainsfoldintoseveraldomainsEGF:domainsthatarehomologoustoepidermal(表皮細胞）growthfactor(53aminoacids)現在是61頁\一共有86頁\編輯于星期三Constructinglargemotifsfromsmallerones現在是62頁\一共有86頁\編輯于星期三1,re-visitofthesecondarystructures2,Supersecondarystructuresanddomains3,Toolstoinvestigatetheproteinconformation4,globularproteinsandSCOP5,fibrousproteins現在是63頁\一共有86頁\編輯于星期三Helpfulwebsites:1,PDB(ProteinDataBank)2,SCOP(StructuralClassificationofProteins)3,comparisonofproteinstructuresin3D現在是64頁\一共有86頁\編輯于星期三A,X-raycrystallographyB,NMR(nuclearmagneticresonance)C,CD(circulardichroism)D,…現在是65頁\一共有86頁\編輯于星期三Computerprograms現在是66頁\一共有86頁\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"現在是67頁\一共有86頁\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現在是68頁\一共有86頁\編輯于星期三現在是69頁\一共有86頁\編輯于星期三現在是70頁\一共有86頁\編輯于星期三3Dstructurecomparison:

現在是71頁\一共有86頁\編輯于星期三1,re-visitofthesecondarystructures2,Toolstoinvestigatetheproteinconformation3,Supersecondarystructuresanddomains4,globularproteinsandSCOP5,fibrousproteins現在是72頁\一共有86頁\編輯于星期三Inconsideringthesehigherlevelsofstructure,itisusefultoclassifyproteinsintotwomajorgroups:fibrousproteins,havingpolypeptidechainsarrangedinlongstrandsorsheets,andglobularproteins,havingpolypeptidechainsfoldedintoasphericalorglobularshape.現在是73頁\一共有86頁\編輯于星期三Thetwogroupsdifferfunctionallyfromeachother:fibrousproteinsprovidesupport,shape,andexternalprotectiontovertebratesglobularproteins:mostenzymesandregulatoryproteinsThetwogroupsarestructurallydistinct:

fibrousproteinsusuallyconsistlargelyofasingletypeofsecondarystructure;globularproteinsoftencontainseveraltypesofsecondarystructure.現在是74頁\一共有86頁\編輯于星期三StructuralClassificationofProteins(SCOP)(globularproteins)1,Allα2,Allβ3,α/β4,α+β現在是75頁\一共有86頁\編輯于星期三Proteinfamilyandsuperfamily現在是76頁\一共有86頁\編輯于星期三現在是77頁\一共有86頁\編輯于星期三現在是78頁\一共有86頁\編輯于星期