amino acids and proteins · 2010. 4. 28. · amino acids and proteins hleeyu jsuico junsay...

AMINOACIDSANDPROTEINS

HLeeYuJsuicoJunsay

DepartmentofChemistry

SchoolofScienceandEngineering

AteneodeManilaUniversity1

Proteinsservesasthecell’smachineryaswellasanorganism’sotherstructuralfeatures.

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DNA Polymerase Catalase CK2 Kinase

Hemoglobin Ovalbumin Casein

Serum albumin Ion channels

1.Enzymes

2.StorageandTransport


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Collagen Keratin Silk Fibroin

Actin Myosin 4

3.StructureandMovement


Insulin Lac repressor

5Immunoglobulin Thrombin and Fibrinogen

Ricin Venom Proteins

4.RegulaEon

5.ProtecEon


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6.Signalling

Proteinsaremadeupofaminoacids.

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Carboxylgroup

R‐grouporside‐chain

α‐aminogroup

α-carbon

Thesidechain(Rgroup)canhavevaryinggroups.

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Thesidechain(Rgroup)canhavevaryinggroups.

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AAwithAliphaEcsidechains

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AAwithAromaEcsidechains

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AAwithAromaEcsidechainsareUVacUve.

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AAwithPolarsidechains.

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AAwithPolarsidechains.

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AAwithBasicsidechains.

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AAwithAcidicsidechainsandtheircorrespondingAmides.

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Aminoacidshavespecificstereochemistry.

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AtphysiologicalpH,acidic(andbasic)groupsareeitherprotonatedordeprotonated.

AminoacidshaveIONICgroups.

ZwiLerionsareionswithaposiUveandnegaUvechargeonthesamemolecule.

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AminoacidsarepolyproUcacids.

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Netcharge:+1 Netcharge:0 Netcharge:‐1

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Theisoelectricpointofanaminoacidiswhenithaszero[0]netcharge.

Recall:thisistheequivalencepointfromthespeciesbefore(netcharge+1)andthezwiaerionicspecies(netcharge0)

€

pH =pKa1 + pKa2

2=pK1 + pKR

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TwoormoreaminoacidsmaybejoinedtogethertoformpepEdes.

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+H2O


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ThepepUdebondisessenUallyanamidebond.

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RECALL:Amidebondscanbecleavedbyacid,basesorenzymes(peEdase)

ThepepUdebondisplanar.

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N‐TerminalEnd

C‐TerminalEnd


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=≠


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=≠


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≠

≠

NamingofpepUdes

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Useofprefixes:di‐,tri‐,tetra‐,penta‐,hexa‐,hepta‐,octa‐,nona‐,deca‐

10‐100AA=polypepUdes

Morethan100AA=proteins

ThereareshortpepUdesequencesthatarebiologicallyimportant

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ThereareshortpepUdesequencesthatarebiologicallyimportant

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PROTEINSTRUCTURE

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Proteinshaveseverallevelsofstructure

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1. PrimaryStructure–sequenceororderofthemonomers(inthiscase,AA)

2. SecondaryStructure–Localizedregionsoftheprimarysequencefoldedintoaregular,repeaUngstructuralelement

3. TerEaryStructure–InteracUngsecondarystructurestoformmoreintricate3Dshapes

4. QuaternaryStructure–associaUonofoneormorechainstoformacomplex


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TheprimarystructureisthesequenceororderofAAfromN‐terminustotheC‐terminus.

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•  Eg.Insulin(AAA40590)

•  Theinfoneededforfurtherfoldingiscontainedinthe1ostructure.

MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLEAGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP

RegularlocalstructurebasedonthehydrogenbondingpaaernofthepolypepUdebackbonegivestheprotein’ssecondarystructure.

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WHYwilltherebelocalizedfoldingandtwisEng?AreallconformaEonspossible?

NotallconformaUonispossiblebecauseoftheprotein’splanarbackbone

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Twodegreesoffreedomperresidueforthepep1dechain

•  AngleabouttheC(alpha)‐Nbondisdenotedphi

•  AngleabouttheC(alpha)‐Cbondisdenotedpsi

•  TheenUrepathofthepepUdebackboneisknownifallphiandpsianglesarespecified

•  Somevaluesofphiandpsiaremorelikelythanothers.

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• G.N.Ramachandranwasthefirsttodemonstratetheconvenienceofplohngphi,psicombinaUonsfromknownproteinstructures

•  ThestericallyfavorablecombinaUonsarethebasisforpreferredsecondarystructures

Sasisekharan

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OnefavorableconformaUonformsastructurecalledalphahelix.

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AlphahelicesarestabilizedbyH‐bondsbetweentheC=OandtheN‐HofthepepUdebackbone

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Residues(sidechains)arepoinUngoutwards.

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AnotherfavorableconformaUonformspleatedsheetscalledbetasheets.βsheetsareformedbylinking2ormorestrandsbyH‐bonding

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StrandscanbeparalleloranE‐paralleltoeachother

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StrandscanbeparalleloranE‐paralleltoeachother

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Sidechainisplacedontopandattheboaomofthesheet(alternately).

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Turnsmayalsobefoundassecondarystructure(usuallyprolineandglycine).

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IndividualelementsofsecondarystructureareojencombinedintostablegeometricalarrangementscalledsupersecondarystructureormoEfs.

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Aproteindomainisapartofproteinsequenceandstructurethatcanevolve,funcUonandexistindependentlyoftherestoftheproteinchain.

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RECALL:primarystructuredeterminessecondarystructure…WHY?!

•  TheαhelixcanberegardedasthedefaultconformaUon–Aminoacidsthatfavorαhelices: Glu,Gln,Met,Ala,Leu–Aminoacidsthatdisruptαhelices: Val,Thr,Ile,Ser,Asx,Pro

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•  Branchingattheβ‐carbon,suchasinvaline,destabilizestheαhelixbecauseofstericinteracUons

•  Ser,Asp,andAsntendtodisruptαhelicesbecausetheirsidechainscompeteforH‐bondingwiththemainchainamideNHandcarbonyl

•  Prolinetendstodisruptbothαhelicesandβsheets

• GlycinereadilyfitsinallstructuresthusitdoesnotfavorαhelicesinparUcular

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SOCANYOUPREDICTthe2°structureofagivenAAsequence?

1. LAKKKKFG2. GAAGSGAPAGAASYG3. FFVMATSGPGAFTLFK4. GEDDEDF

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SOCANYOUPREDICTthe2°structureofagivenAAsequence?

•  PredicUonsofsecondarystructureofproteinsadoptedbyasequenceofsixorfewerresidueshaveprovedtobe60to70%accurate

• Manyproteinchemistshavetriedtopredictstructurebasedonsequence

•  BUTsecondarystructureisinfluencedbyterEarystructure.

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TheterEarystructureistheover‐all3DfoldofthepolypepUdechain.Governedbythe“hydrophobiceffect”–athermodynamiceffect,andstabilizedbyIMFAs

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TheterEarystructureistheover‐all3DfoldofthepolypepUdechain.Governedbythe“hydrophobiceffect”–athermodynamiceffect,andstabilizedbyIMFAs

CanbeFIBROUSorGLOBULAR

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Fibrousproteinsusuallyperformstructuralroles(mechanicallystrong),insolubleandtaketheformoftriplehelices.

•  AlphaKeraUn:hair,nails,claws,horns,beaks

•  BetaKeraUn:silkfibers(alternaUngGly‐Ala‐Ser)

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▫  NearlyoneresidueoutofthreeisGly▫  Prolinecontentisunusuallyhigh▫  Unusualaminoacidsfound:(4‐hydroxyproline,3‐hydroxyproline,5‐hydroxylysine)▫  Specialuncommontriplehelix!

COLLAGEN:

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Globularproteinsarewater‐solubleproteins.

Anamphiphilichelixinflavodoxin:

Anonpolarhelixincitratesynthase:

Apolarhelixincalmodulin:

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Globularproteinsarewater‐solubleproteins.

Anamphiphilichelixinflavodoxin:

Anonpolarhelixincitratesynthase:

Apolarhelixincalmodulin:

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DisulfidebondsarealsoimportantinmaintainingterUarystructure.

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DisulfidebondsarealsoimportantinmaintainingterUarystructure.

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FoldingofproteinsintoitsterUarystructureisusuallyspontaneous,butothersmayrequireaccessoryproteinscalledmolecularchaperones.

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Molecularchaperonesprovidea“safehaven”forsecondarystructuresandmoUfs.

(topreventunwantedaggregaUonofhydrophobicregions)

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BecauseproteinsinteractbymeansofIMFAs,thesemaybedisruptedusingdifferentagents.

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DenaturedproteinsarebiologicallyinacUve.AcUvitymaybereturned,whenpropercondiUonsaremet.

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•  Insulin(heterosubunits)

ADVANTAGESof4oStructures▫  Stability:reducUonofsurfacetovolumeraUo▫  GeneUceconomyandefficiency▫  BringingcatalyUcsitestogether▫  CooperaUvity

QuaternarystructureinvolvesthespaUalarrangementsofmulU‐subunitsofaproteinmolecule.Mayhaveheteroorhomosubunits.

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1. PrimaryStructure–sequenceororderofthemonomers(inthiscase,AA)

2. SecondaryStructure–Localizedregionsoftheprimarysequencefoldedintoaregular,repeaUngstructuralelement

3. TerEaryStructure–InteracUngsecondarystructurestoformmoreintricate3Dshapes

4. QuaternaryStructure–associaUonofoneormorechainstoformacomplex

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Proteinshaveseverallevelsofstructureanditdeterminestheprotein’sfuncEon

amino acids and proteins · 2010. 4. 28. · amino acids and proteins hleeyu jsuico junsay...

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