分子生物学Chapter 2Protein Structure.docx

分子生物学Chapter 2Protein Structure.docx

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分子生物学Chapter2ProteinStructure

Chapter2ProteinStructure

Introduction

Sizesandshapesofproteins

Globlarproteins,includingmostenzymes,behaveinsolutionlikecompact,roughlysphericalparticles.Fibrousproteinshaveahighaxialratioandareoftenofstructuralimportance,forexamplefibroinandkeratin.SizesrangefromafewthousandtoseveralmillionDaltons.

Someproteinscontainboundnonproteinmaterials（prostheticgroupsorothermacromolecules）,whichaccountsfortheincreasedsizesandfunctionalitiesoftheproteincomplexs.

Shapesofproteins

Globularproteins:

enzymes

Fibrousproteins:

importantstructuralproteins（silkfibroin,keratininhairandwools）

Chapter2ProteinStructure

1.AminpAcids

R-CH（NH2）-COOH

va-carbonischiral（asymmetric）exceptinglycine（RisH）

vAminoacidscanexitinbothD-andL-stereoisomers,butonlyL-isomersarefoundinproteins

vAminoacidsaredipolarions（zwitterions）inaqueoussolutionandareamphoteric.

vThesidechains（R）differinsize,shape,chargeandchemicalreactivity

vAfewproteinscontainnonstandardaminoacidsthatareformedbypost-translationalmodificationoftheparentaminoacids.

1.1Aminoacidswithchargedsidechains

“Basic”aminoacids:

containingpositivelychargedgroups

Lysine（Lys,K）:

asecondaminogroupattachedtothee-carbonatom

Arginine（arg,R）:

aguanidinogroupattachedtothed-carbonatom

Histidine（His,H）:

aimidazolegrouphasapKanearneutrality.Thisgroupcanbereversiblyprotonatedunderphysiologicalconditions,whichcontributetothecatalyticmechanismofmanyenzymes.

1.2.Aminoacidswithpolarunchargedsidechains（hydrophilic）--containinggroupsthatformhydrogenbondswithwater

Serine（Ser,S）&threonine（Thr,T）havehydroxylgroups.

1.3.Aminoacidswithnonpolaraliphaticsidechains（hydrophobic）

Alkylsidechains

1.4.Aminoacidswitharomaticsidechains（hydrophobic）

2.Primarystructure

Aminoacidsarelinkedbypeptidebondsbetweenalpha-carboxylandalpha-aminogroups.TheresultingpolypeptidesequencehasanNterminusandaCterminus.

Polypeptidescommonlyhavebetween100and1500aminoacidslinkedinthisway

Formationofapeptidebond（shadedingray）inadipeptide.

vTheaminoacidinapeptideisalsocalledaresidue.

Thesmallestaminoacid,glycine,hasasinglehydrogenatomasitsRgroup.Itssmallsizeallowsittofitintotightspaces.Unlikeanyoftheothercommonaminoacids,prolinehasacyclicringthatisproducedbyformationofacovalentbondbetweenitsRgroupandtheaminogrouponCα.Prolineisveryrigid,anditspresencecreatesafixedkinkinaproteinchain.Prolineandglycinearesometimesfoundatpointsonaprotein'ssurfacewherethechainloopsbackintotheprotein

3.SecondaryStructure

vSecondarystructurereferstothelocalizedorganizationofpartsofapolypeptidechain,whichcanassumeseveraldifferentspatialarrangements.Asinglepolypeptidemayexhibitalltypesofsecondarystructure.Withoutanystabilizinginteractions,apolypeptideassumesarandom-coilstructure.

3.1Modeloftheahelix.

Thepolypeptidebackboneisfoldedintoaspiralthatisheldinplacebyhydrogenbonds（blackdots）betweenbackboneoxygenatomsandhydrogenatoms.Allthehydrogenbondshavethesamepolarity.Theoutersurfaceofthehelixiscoveredbytheside-chainRgroups.

a-helix

every3.6residuesmakeoneturn,

thedistancebetweentwoturnsis0.54nm,

theC=O（orN-H）ofoneturnishydrogenbondedtoN-H（orC=O）oftheneighboring

3.2BetaStrandandBetaSheet

vInaβstrand,thetorsionangleofN-Cβ-C-Ninthebackboneisabout120degrees. Thefollowingfigureshowstheconformationofanidealβstrand. Notethatthesidechainsoftwoneighboringresiduesprojectintheoppositedirectionfromthebackbone. 

Betasheet

vAβsheetconsistsoftwoormorehydrogenbondedβstrands. Thetwoneighboringβstrandsmaybeparalleliftheyarealignedinthesamedirectionfromoneterminus（NorC）totheother,oranti-paralleliftheyarealignedintheoppositedirection.

bSHEETS.（a）Asimpletwo-strandedbsheetwithantiparallelbstrands.Asheetisstabilizedbyhydrogenbonds（blackdots）betweenthebstrands.Theplanarityofthepeptidebondforcesabsheettobepleated;hence,thisstructureisalsocalledabpleatedsheet,orsimplyapleatedsheet.（b）SideviewofabsheetshowinghowtheRgroupsprotrudeaboveandbelowtheplaneofthesheet.（c）ModelofbindingsiteinclassIMHC（majorhistocompatibilitycomplex）molecules,whichareinvolvedingraftrejection.Asheetcomprisingeightantiparallelbstrands（green）formsthebottomofthebindingcleft,whichislinedbyapairofahelices（blue）.Adisulfidebondisshownastwoconnectedyellowspheres.TheMHCbindingcleftislargeenoughtobindapeptide810residueslong.

3.3Turns

Composedofthreeorfourresidues,turnsarecompact,U-shapedsecondarystructuresstabilizedbyahydrogenbondbetweentheirendresidues.Theyarelocatedonthesurfaceofaprotein,formingasharpbendthatredirectsthepolypeptidebackbonebacktowardtheinterior.Glycineandprolinearecommonlypresentinturns.

4.TertiaryStructure

vTertiarystructure,thenext-higherlevelofstructure,referstotheoverallconformationofapolypeptidechain,thatis,thethree-dimensionalarrangementofalltheaminoacidsresidues.Incontrasttosecondarystructure,whichisstabilizedbyhydrogenbonds,tertiarystructureisstabilizedbyhydrophobicinteractionsbetweenthenonpolarsidechainsand,insomeproteins,bydisulfidebonds.Thesestabilizingforcesholdtheαhelices,βstrands,turns,andrandomcoilsinacompactinternalscaffold

Theribbonrepresentationofthe3DstructureofRNaseA. 

vNoncovalentinteractionbetweensidechainsthatholdthetertiarystructuretogether:

vanderWaalsforces,hydrogenbonds,electrostaticsaltbridges,hydrophobicinteractions

vCovalentinteraction:

disulfidebonds

vDenaturationofproteinbydisruptionofits2oand3ostructurewillleadtoarandomcoilconformation

5.Quaternarystructure

Manyproteinsarecomposedoftwoormorepolypeptidechains（subunits）.Thesesubunitsmaybeidenticalordifferent.Thesameforceswhichstabilizetertiarystructureholdthesesubunitstogether.Thisleveloforganizationcalledquaternarystructure.

Prostheticgroups

vProstheticgroupscovalentlyornoncovalentlyattachedtomanyconjugatedproteins,andgivetheproteinschemicalfunctionality.Manyareco-factorsinenzymereactions.

vExamples:

hemegroupsinhemogobin

Organizationofthecataboliteactivator

protein（CAP）

6.Domains,motifsandfamilies

6.1ProteinMotifs

vAmotifisacharacteristicdomainstructureconsistingoftwoormoreαhelicesorβstrands.  

vCommonexamplesincludecoiledcoil,helix-turn-helixhelix-loop-helix,zincfinger,leucinezipperetc.

vManyproteinscontainoneormoremotifsbuiltfromparticularcombinationsofsecondarystructures.

vAmotifisdefinedbyaspecificcombinationofsecondarystructuresthathasaparticulartopologyandisorganizedintoacharacteristicthree-dimensionalstructure.

Structuralmotifs:

•Groupingsofsecondarystructuralelementsthatfrequentlyoccuringlobularproteins

•Oftenhavefunctionalsignificanceandrepresenttheessentialpartsofbindingorcatalyticsitesconservedamongaproteinfamily

•Representthebestsolutiontoastructural-functionalrequirement

βαβmotif

6.2Domains:

Structurallyindependentunitsofmanyproteins,connectedbysectionswithlimitedhigherorderstructurewithinthesamepolypeptide.

Theycanalsohavespecificfunctionsuchassubstratebinding

FunctionalDomains

vDomainssometimesaredefinedinfunctionaltermsbasedonobservationsthattheactivityofaproteinislocalizedtoasmallregionalongitslength.Forinstance,aparticularregionorregionsofaproteinmayberesponsibleforitscatalyticactivity（e.g.,akinasedomain）orbindingability（e.g.,aDNA-bindingdomain,membrane-bindingdomain）.

Modules:

vTheorganizationoftertiarystructureintodomainsfurtherillustratestheprinciplethatcomplexmoleculesarebuiltfromsimplercomponents.Likesecondary-structuremotifs,tertiary-structuredomainsareincorporatedasmodulesintodifferentproteins,therebymodifyingtheirfunctionalactivities.Themodularapproachtoproteinarchitectureisparticularlyeasytorecognizeinlargeproteins,whichtendtobeamosaicofdifferentdomainsandthuscanperformdifferentfunctionssimultaneously

Schematicdiagramsofvariousproteins,illustratingtheirmodularnature.

vEpidermalgrowthfactor（EGF）isgeneratedbyproteolyticcleavageofaprecursorproteincontainingmultipleEGFdomains（orange）.TheEGFdomainalsooccursinNeuproteinandintissueplasminogenactivator（TPA）.Otherdomains,ormodules,intheseproteinsincludeachymotrypticdomain（purple）,animmunoglobulindomain（green）,afibronectindomain（yellow）,amembrane-spanningdomain（pink）,andakringledomain（blue）.

6.3Proteinfamilies:

Structurallyandfunctionallyrelatedproteinsfromdifferentsources

Evolutionarytreeshowinghowtheglobinproteinfamilyarose,startingfromthemostprimitiveoxygen-bindingproteins,leghemoglobins,inplants.Sequencecomparisonshaverevealedthatevolutionoftheglobinproteinsparallelstheevolutionofvertebrates.Majorjunctionsoccurredwiththedivergenceofmyoglobinfromhemoglobinandthelaterdivergenceofhemoglobinintotheaandbsubunits.

Domains,motif