蛋白质结构与功能

Chapter4ProteinStructure

andFunctionProteinsMakeupabout15%ofthecellHavemanyfunctionsinthecellEnzymesStructuralTransportMotorStorageSignalingReceptorsGeneregulationSpecialfunctionsShape=AminoAcidSequenceProteinsaremadeof20aminoacidslinkedbypeptidebondsPolypeptidebackboneistherepeatingsequenceoftheN-C-C-N-C-C…inthepeptidebondThesidechainorRgroupisnotpartofthebackboneorthepeptidebondPolypeptideBackboneAminoAcids

NOTE:YouneedtoknowthistableHydrophilicHydrophobicProteinFoldingThepeptidebondallowsforrotationarounditandthereforetheproteincanfoldandorienttheRgroupsinfavorablepositionsWeaknon-covalentinteractionswillholdtheproteininitsfunctionalshape–theseareweakandwilltakemanytoholdtheshapeNon-covalentBondsinProteinsGlobularProteinsThesidechainswillhelpdeterminetheconformationinanaqueoussolutionHydrogenBondsinProteinsH-bondsformbetween1)atomsinvolvedinthepeptidebond;2)peptidebondatomsandRgroups;3)RgroupsProteinFoldingProteinsshapeisdeterminedbythesequenceoftheaminoacidsThefinalshapeiscalledtheconformationandhasthelowestfreeenergypossibleDenaturationistheprocessofunfoldingtheproteinCanbedownwithheat,pHorchemicalcompoundsInthechemicalcompound,canremoveandhavetheproteinrenatureorrefoldFolding@homeTheStanfordFolding@homeresearchgoalistounderstandproteinfolding,misfolding,andrelateddiseases.CalculationstocreatemodelsrequiresasupercomputerORmanysmallercomputers(distributedcomputing).Youcanparticipatebyvisiting:Fold@homewebsite:/ArticleonFolding@home:/releases/2002/10/021022070813.htmRefoldingMolecularchaperonesaresmallproteinsthathelpguidethefoldingandcanhelpkeepthenewproteinfromassociatingwiththewrongpartnerProteinFolding2regularfoldingpatternshavebeenidentified–formedbetweenthebondsofthepeptidebackbone-helix–proteinturnslikeaspiral–fibrousproteins(hair,nails,horns)-sheet–proteinfoldsbackonitselfasinaribbon–globularproteinSheetsCoreofmanyproteinsisthesheetFormrigidstructureswiththeH-bondCanbeof2typesAnti-parallel–runinanoppositedirectionofitsneighbor(A)Parallel–runinthesamedirectionwithlongerloopingsectionsbetweenthem(B)HelixFormedbyaH-bondbetweenevery4thpeptidebond–C=OtoN-HUsuallyinproteinsthatspanamembraneThehelixcaneithercoiltotherightortheleftCanalsocoilaroundeachother–coiled-coilshape–aframeworkforstructuralproteinssuchasnailsandskinCDfromTextTheCDthatisincludedonyourtextbookbackcoverhassomevideoclipsthatwillshowthehelixandsheetsaswellasotherthingsinthischapter.Youwillwanttolookatthem.LevelsofOrganizationPrimarystructureAminoacidsequenceoftheproteinSecondarystructureHbondsinthepeptidechainbackbone-helixand-sheetsTertiarystructureNon-covalentinteractionsbetweentheRgroupswithintheproteinQuanternarystructureInteractionbetween2polypeptidechainsProteinStructureDomainsAdomainisabasicstructuralunitofaproteinstructure–distinctfromthosethatmakeuptheconformationsPartofproteinthatcanfoldintoastablestructureindependentlyDifferentdomainscanimpartdifferentfunctionstoproteinsProteinscanhaveonetomanydomainsdependingonproteinsizeDomainsUsefulProteinsTherearethousandsandthousandsofdifferentcombinationsofaminoacidsthatcanmakeupproteinsandthatwouldincreaseifeachonehadmultipleshapesProteinsusuallyhaveonlyoneusefulconformationbecauseotherwiseitwouldnotbeefficientuseoftheenergyavailabletothesystemNaturalselectionhaseliminatedproteinsthatdonotperformaspecificfunctioninthecellProteinFamiliesHavesimilaritiesinaminoacidsequenceand3-DstructureHavesimilarfunctionssuchasbreakdownproteinsbutdoitdifferentlyProteins–MultiplePeptidesNon-covalentbondscanforminteractionsbetweenindividualpolypeptidechainsBindingsite–whereproteinsinteractwithoneanotherSubunit–eachpolypeptidechainoflargeproteinDimer–proteinmadeof2subunitsCanbesamesubunitordifferentsubunitsSingleSubunitProteinsDifferentSubunitProteinsHemoglobin2globinsubunits2globinsubunitsProteinAssembliesProteinscanformverylargeassembliesCanformlongchainsiftheproteinhas2bindingsites–linktogetherasahelixoraringActinfibersinmusclesandcytoskeleton–ismadefromthousandsofactinmoleculesasahelicalfiberTypesofProteinsGlobularProteins–mostofwhatwehavedealtwithsofarCompactshapelikeaballwithirregularsurfacesEnzymesareglobularFibrousProteins–usuallyspanalongdistanceinthecell3-DstructureisusuallylongandrodshapedImportantFibrousProteinsIntermediatefilamentsofthecytoskeletonStructuralscaffoldinsidethecellKeratininhair,hornsandnailsExtracellularmatrixBindcellstogethertomaketissuesSecretedfromcellsandassembleinlongfibersCollagen–fiberwithaglycineeverythirdaminoacidintheproteinElastin–unstructuredfibersthatgivestissueanelasticcharacteristicCollagenandElastinStabilizingCross-LinksCrosslinkagescanbebetween2partsofaproteinorbetween2subunitsDisulfidebonds(S-S)formbetweenadjacent-SHgroupsontheaminoacidcysteineProteinsatWorkTheconformationofaproteingivesitauniquefunctionToworkproteinsmustinteractwithothermolecules,usually1orafewmoleculesfromthethousandsto1proteinLigand–themoleculethataproteincanbindBindingsite–partoftheproteinthatinteractswiththeligandConsistsofacavityformedbyaspecificarrangementofaminoacidsLigandBindingFormationofBindingSiteThebindingsiteformswhenaminoacidsfromwithintheproteincometogetherinthefoldingTheremainingsequencesmayplayaroleinregulatingtheprotein’sactivityAntibodyFamilyAfamilyofproteinsthatcanbecreatedtobindtoalmostanymoleculeAntibodies(immunoglobulins)aremadeinresponsetoaforeignmoleculeie.bacteria,virus,pollen…calledtheantigenBindtogethertightlyandthereforeinactivatestheantigenormarksitfordestructionAntibodiesY-shapedmoleculeswith2bindingsitesattheupperendsoftheYTheloopsofpolypeptidesontheendofthebindingsitearewhatimpartstherecognitionoftheantigenChangesinthesequenceoftheloopsmaketheantibodyrecognizedifferentantigens-specificityAntibodiesBindingStrengthCanbemeasureddirectlyAntibodiesandantigensaremixingaroundinasolution,eventuallytheywillbumpintoeachotherinawaythattheantigenstickstotheantibody,eventuallytheywillseparateduetothemotioninthemoleculesThisprocesscontinuesuntiltheequilibriumisreached–numberstickingisconstantandnumberleavingisconstantThiscanbedeterminedforanyproteinanditsligandEquilibriumConstantConcentrationofantigen,antibodyandantigen/antibodycomplexatequilibriumcanbemeasured–equilibriumconstant(K)LargertheKthetighterthebindingorthemorenon-covalentbondsthatholdthe2togetherEnzymesasCatalystsEnzymesareproteinsthatbindtotheirligandasthe1ststepinaprocessAnenzyme’sligandiscalledasubstrateMaybe1ormoremoleculesOutputofthereactioniscalledtheproductEnzymescanrepeatthesestepsmanytimesandrapidly,calledcatalystsManydifferentkinds–seetable5-2,p168EnzymesatWorkLysozymeisanimportantenzymethatprotectsusfrombacteriabymakingholesinthebacterialcellwallandcausingittobreakLysozymeaddsH2OtotheglycosidicbondinthecellwallLysozymeholdsthepolysaccharideinapositionthatallowstheH2Otobreakthebond–thisisthetransitionstate

–statebetweensubstrateandproductActivesiteisaspecialbindingsiteinenzymeswherethechemicalreactiontakesplaceLysozymeNon-covalentbondsholdthepolysaccharideintheactivesiteuntilthereactionoccursFeaturesofEnzymeCatalysisEnzymePerformanceE+SESEPE+PStep1–bindingofthesubstrateLimitingstepdependingon[S]and/or[E]Vmax–maximumrateofthereactionTurnovernumberdetermineshowfastthesubstratecanbeprocessed=rateofrxn

[E]Step2–stabilizethetransitionstateStateofsubstratepriortobecomingproductEnzymeslowerstheenergyoftransitionstateandthereforeacceleratesthereactionReactionRatesKM–[S]thatallowsrxntoproceedat½itmaximumrateProstheticGroupsOccasionallythesequenceoftheproteinisnotenoughforthefunctionoftheproteinSomeproteinsrequireanon-proteinmoleculetoenhancetheperformanceoftheproteinHemoglobinrequiresheme(ironcontainingcompound)tocarrytheO2Whenaprostheticgroupisrequiredbyanenzymeitiscalledaco-enzymeUsuallyametalorvitaminThesegroupsmaybecovalentlyornon-covalentlylinkedtotheproteinRegulationofEnzymesRegulationofenzymaticpathwayspreventthedeletionofsubstrateRegulationhappensattheleveloftheenzymeinapathwayFeedbackinhibitioniswhentheendproductregulatestheenzymeearlyinthepathwayFeedbackRegulationNegativefeedback–pathwayisinhibitedbyaccumulationoffinalproductPositivefeedback–aregulatorymoleculestimulatestheactivityoftheenzyme,usuallybetween2pathwaysADPlevelscausetheactivationoftheglycolysispathwaytomakemoreATPAllosteryConformationalcouplingof2widelyseparatedbindingsitesmustberesponsibleforregulation–activesiterecognizessubstrateand2ndsiterecognizestheregulatorymoleculeProteinregulatedthiswayundergoesallosterictransitionoraconformationalchangeProteinregulatedinthismannerisanallostericproteinAllostericRegulationMethodofregulationisalsousedinotherproteinsbesidesenzymesReceptors,structuralandmotorproteinsAllostericRegulationEnzymeisonlypartiallyactivewithsugaronlybutmuchmoreactivewithsugarandADPpresentPhosphorylationSomeproteinsareregulatedbytheadditionofaPO4groupthatallowsfortheattractionof+chargedsidechainscausingaconformationchangeReversibleproteinphosphorylationsregulatemanyeukaryoticcellfunctionsturningthingsonandoffProteinkinasesaddthePO4andproteinph