liguofu§3ProteinStructureConjugatedprotein:consistsofAAsandothers(Native)ProteinSimpleprotein:onlyconsistsofAAsApoprotein+prostheticgroupliguofuTheseproteinsarereferredasconjugatedproteinswhiletheaminoacidpartaloneiscalledapoprotein.liguofu§3ProteinStructure§3.1PrimaryStructure§3.2SecondaryStructure§3.3Tertiary&QuaternaryStructure§3.4Folding,Unfolding&Refoldingliguofu§3.1PrimaryStructureRelatedconceptsStructuralfeaturesHomology(同源性）liguofuRelatedconceptsPeptidebond/肽鍵：～1000yearsinH2OwithoutcatalystPeptidebond/肽鍵：～1000yearsinH2OwithoutcatalystPeptidebond/肽鍵：～1000yearsinH2OwithoutcatalystSidechain側鏈C-terminalC-末端N-terminalN-末端Residue/氨基酸殘基:Itsaveragemolecularweightis110statisticallyestimatedbytheoccurrenceof20AAsinnaturalproteinsliguofuRelatedconcepts(ctnd)Oligopeptides/寡聚肽：lessthan50aaresiduesPolypeptides/多肽：btw50-10aaresiduesProtein/蛋白質：morethan100aaresiduesEachpeptidehasacharacteristictitrationcurveandan

isoelectricpoint(pI).liguofuPeptidebondisrigidandplanar1.49?1.27?1.32?Structuralfeatures(ctnd)liguofuc)=0o,=0o;itisdisallowedbythestericoverlapbetweenHandOatomsofadjacentpeptideplanes.b)=180o,=180o;thepeptideisinitsfullyextendedconformation.Structuralfeatures(ctnd)liguofuRamachandranplotforL-AlaresiduesDarkblue:nostericoverlapandfullyallowed;mediumblue:attheextremelimitsforunfavorableatomiccontacts;lightestblue:permissibleifalittleflexibilityisallowedStructuralfeatures(ctnd)liguofuHomologyHomologousproteins:evolutionarilyrelated;performthesamefunctionindifferentspeciesInvariantresidues:Manypositionsinprimarystructureareoccupiedbythesameaaresiduesinallspecies.

Variableresidues:OtherpositionsinprimarystructureareoccupiedbydifferentaaresiduesindifferentspeciesConservativesubstitutions:Insomepositions,allsubstitutionsinvolvesimilaraaresidues(e.g.,Arg?Lys,bothofwhicharepositivelycharged).InvariantHomology(cntd,sequenceofcytochromec)liguofu馬細胞色素c的空間結構Homology(cntd)馬與金槍魚細胞色素c的空間結構比較liguofuHomology(cntd)liguofu§3.2SecondaryStructure1.

a-helixa-chain2.

b-pleatedsheet3.

bturnLoopRandomcoilliguofu1.

a-helixproposedbyPaulingandCoreyin1951liguofuliguofuliguofu第n個氨基酸a-氨基上的H與第n+4個氨基酸上的a-羰基O形成氫鍵，使a-helix內部的氫鍵數目達到最大；a-helix只能由L氨基酸或D氨基酸構構成，天然蛋白的a-helix當然只能由L氨基酸構成；L氨基酸既可以形成右手a-helix也可形成左手a-helix，但天然a-helix全部為右手a-helix；影響a-helix穩定的因素：相鄰R基團間的靜電作用、范德瓦爾斯作用、疏水相互作用或位阻作用；Pro和Gly；a-helixN-末端和C-末端氨基酸R基團的性質Notesfora-helix

M.

F.Perutz（1914-2002）J.C.Kendrew（1917-1997）W.L.Bragg(1890-1971)1962年Nobel化學獎與其父W.H.Bragg獲1915年Nobel物理獎a-helix研究的失敗者獲1954年Nobel化學獎1901-19941897-19711914-1995a-helix研究的成功者liguofuPeptidebondisrigidandplanar1.49?1.27?1.32?WhyandAnswerliguofu

2.

b-pleatedsheetTheaxialdistancebetweentheadjacentaminoacidresiduesis~3.5Angstromsliguofuliguofu

3.

bturnliguofuItoftenconnectstheendsoftwoadjacentsegmentsofanantiparallelb-pleatedsheet.

bturnsareoftenfoundnearthesurfaceofaprotein.TheessenceofthestructureisthehydrogenbondingbetweentheC=OgroupofresiduenandtheNHgroupoftheresiduen+3.GlyandProareoftenfoundinbturns.

3.

bturn(ctnd)liguofuliguofuAA’stendencyinsecondarystructureliguofuRelativeprobabilitiesthatagivenaminoacidwilloccurinthethreecommontypesofsecondarystructure.liguofu§3.3Tertiary&QuaternaryStructureFibrousproteins

areadaptedforastructuralfunctionGlobularproteinsandtheirStructruralpatternsliguofu

-KeratinCollagenSilkfibroin1.

Fibrousproteinsliguofua-keratinsliguofusimpletertiarybutcomplexquaternarystructurea-keratinsliguofua-keratins:Permanentwavingofhairliguofu

a-keratinsRichinhydrophobicresidues：Phe,Ile,Val,Met,andAla.Twoa-helixwrapinparalleltogethertoformacoiledcoilinleft-handedThehydrophobicRgroupsoftwoa-helicesmeshedtogetherinaregularinterlockingpattern.Themaincomponentsofskinandmanyskinderivativesinvertebrateanimals.Usuallyhardera-keratinscontainhighernumberofCys.canbestretched(totwiceasitsoriginallength)duetoitsstructurespringines.liguofuCollagen-chain:auniquesecondarystructureliguofuliguofuliguofu3left-handed-chainwrappedtogethertoformright-handedtriplehelixwithH-bondsininterchaibutnotinIntrachainArepeatingtripeptide:Gly-X-ProorGly-X-Hyp,Gly-Pro-Hypmorefrequent.Glycanfitintothecrowdedinteriorofthetriplehelix,whilePropermitsthesharptwistingofthecollagenhelix.About25%ofthetotalproteinmassinmammalsiscollagen:tendons,cornea,theextracellularmatrixofskinandbonematrix.Collagenfibershavesimilartensilestrengthasasteelwireofequalcrosssection.CollagenliguofuStrandsoffibroin(blue)emergefromthespinneretsofaspiderinthiscolorizedelectronmicrograph.SilkfibroinliguofuliguofuSilkfibroinFibroinisrichinAlaandGly,permittingaclosepackingofsheetsandaninterlockingarrangementsofRgroups.OverallstructureisstabilizedbyextensivehydrogenbondsandbyoptimizationofvanderWaalsinteractionsbetweensheets.Silkdoesnotstretchsinceitsconformationisalreadyhighlyextended.Structureisflexiblesincethemajorforceholdingsheetstogetherisweakinteractionsratherthandisulfidebondsasin–keratins.liguofu2.GlobularproteinsandtheirStructruralpatternsMyoglobinStructruralpatternsliguofu1.Myoglobineight-helices;hydrophobicRgroupsintheinterior;twohistidineintheinterior;polarRgroupsonthesurface;hemegroupinacrevice(pocket);ThefirstproteinwhosestructurewasdeterminedliguofuliguofuDomainMotif/supersecondarystructureStructuralClassQuaternarystructure&symmetry2.StructruralpatternsliguofuTroponin(肌鈣蛋白)C,twoseparatecalcium-bindingregionsWithinalargerpolypeptidechain

Domainsare:

compactregions/distinctstructural

unitsIndependentinthermodynamicstabilityandsometimes,haveseparatefunctions.liguofuMotifs/supersecondarystructuresarePatternsbuiltwitha-helix&/orb-sheetUnitsthatbuildaproteinMotif：模體或模序、基序liguofuliguofuGreekkeyliguofuproteinstructuralclassificationliguofuliguofuliguofuliguofuQuaternarystructures&symmetryliguofuliguofuliguofuHumanpoliovirus(脊髓灰質炎病毒)liguofu§3.4

Folding,

Unfolding&RefoldingLossofstructureresultsinlossoffunctionDenaturationofsomeproteinsisreversiblePolypeptidesfoldrapidlybystepwiseprocessDeathbymisfolding:theprion（朊病毒）ProteinfoldinginvivoliguofuLossofstructureresultsinlossoffunctionDenaturant:Destroyhydrophobicinteraction:去垢劑，有機溶劑等DestroyHbondsDestroystaticelectricalforceTemperature尿素、胍鹽、酸、堿liguofuDenaturationofsomeproteinsisreversibleliguofuliguofuPolypeptidesfoldrapidlybystepwiseprocessliguofuliguofuliguofuDeathbymisfolding:thepriondiseases(1)NormalbraintissueSpongybraintissueTransmissibleSpongiformEncephalopathiesAnimalScrapie:羊搔癢病BSE(bovinespongiformencephalopathy)(Madcowdisease)HumanCJD:Creutzfeld-JacobDisease，克雅氏病GSS:Gerstmann-Straussler-Scheinkersyndrome，GSS綜合癥FFI:FatalfamilialInsomnia，致死性家庭失眠癥Kuru：庫魯病AlpersSyndromeliguofuDeathbymisfolding:thepriondiseases(3)1982，StanleyB.Prusinercoinedtheword“prion”referto“proteininfectiousparticle”1997，StanleyB.PrusinerwontheNobelPrizeinPhysiologyorMedicineliguofuDeathbymisfolding:thepriondiseases(4)PrPCPrPSCPrP

＝

PrionProteinC

＝

CellularSc

＝

ScrapiePrPSCfurther

inducesPrPCintoPrPSCliguofuNeed：

Proteindisulfideisomerase(PDI）

Peptidylprolylisomerases(PPIases)Molecularchaperonesareproteinsthatinteractwithpartiallyfoldedorimproperlyfoldedpolypeptides,facilitatingcorrectfoldingpathwaysorprovidingmicroenvironmentsinwhichfoldingcanoccurProteinfoldinginvivowell-studied.Hsp70family:heatshockproteinsGroEL/GroESsystemliguofuProteindisulfideisomerase(PDI）liguofuPeptidylprolylisomerases(PPIases)liguofuDnaK&andDnaJinE.colihomologsoftheeukaryoticHsp70&Hsp40liguofuGroEL/GroESsysteminE.coliliguofuliguofuTheEndliguofuliguofuHbondsBetweenneutralgroupsBetweenpeptidebondsIonicinteractionsAttractionRepulsionvanderWaalsinteractionsAnytwoatomsincloseproximityHydrophobicinteractionsFourTypesofNoncovalent(“Weak”)InteractionsamongBiomoleculesinAqueousSolventliguofu四種作用力強力弱力引力電磁力

離子鍵

共價鍵

金屬鍵

范德瓦爾斯力

氫鍵

疏水相互作用StericforceSolvationforce分子作用力(molecularforce)Intramolecularforce分子間作用力(intermolecularforce)liguofu范德瓦耳斯力(vanderWaalsforce)范德瓦耳斯力偶極靜電力：離子與偶極子間或偶極子與偶極子間的吸引力誘導偶極力：離子或偶極子與其誘導出的偶極子間的吸引力色散力：瞬時偶極子與其誘導出的偶極子間的吸引力liguofuIntermolecularforceliguofu色散力(LondonDispersion)liguofuHydrogenbondliguofuliguofu常見生物分子間的氫鍵角度與氫鍵的強弱liguofu疏水相互作用(Hydrophobicinteraction)Amongtheseforcesthehydrophobic(whichliterallymeans‘water-fearing’)force,hasattractedalotofinterestprimarilybecauseoftworeasons.Firstly,itissignificantlylongerrangedthantheothers;itsinteractionlengthcanbeaslongasabout100nanometerswhereasthatofothersnormallydoesnotexceed5nanometers.Secondly,thereisnosatisfactoryexplanationforitslongrangenature.liguofuΔG=ΔH－TΔS