Basics of Protein Structure: Short Introduction to Molecular Structures

Transcription

1 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: 11Jan2006 ShortIntroductionto MolecularStructures Introductionto ProteinStructure Chapters1to5 CarlBranden& JohnTooze ISBN: (recommended) 1

2 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: Thebuildingblocks(Ch.1) Motifsofproteinstructure(Ch.2) Alphadomainstructures(Ch.3) Alpha/Betastructures(Ch.4) Betastructures(Ch.5) 11Jan2006 2

3 Prelude:molecularstructures JohnDalton(1810) Anewsystemofchemistry Elements,butnostructuresyet Mendeljev(1869) 11Jan2006 3

4 Johannesvan thoff Chimiedansl Espace Proposalforthedevelopment ofthree dimensionalchemical structuralformulae (1875) Tetraedricalcarbonatom 11Jan2006 4

5 LinusPauling(1951) AtomicCoordinatesand StructureFactorsforTwo HelicalConfigurationsof PolypeptideChains Alpha helix 11Jan2006 5

6 JamesWatson&FrancisCrick(1953) Molecularstructureofnucleicacids 11Jan2006 6

7 JamesWatson&FrancisCrick(1953) Molecularstructureofnucleicacids 11Jan2006 7

8 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: Thebuildingblocks(Ch.1) Motifsofproteinstructure(Ch.2) Alphadomainstructures(Ch.3) Chainsofaminoacids Three dimensional Structures Fourlevelsofprotein architecture Aminoacids:classes Disulphidebridges Histidine Proline Ramachandranplot Alpha/Betastructures(Ch.4) Betastructures(Ch.5) 11Jan2006 8

9 TheBuildingBlocks(proteins) 11Jan2006 Proteinsconsistofchainsofaminoacids Boundtogetherthroughthepeptidebond Specialfoldingofthechainyieldsstructure Structuredeterminesthefunction 9

10 Chainsofaminoacids 11Jan

11 Three dimensionalstructures Fourlevelsofproteinarchitecture 11Jan

12 Aminoacids:klassen Hydrophobicaminoacids Alanine Phenylalanine Leucine Methionine Ala Phe Leu Met A F L M Valine Isoleucine Proline Val Ile Pro V I P Aspartate( ) Lysine(+) Asp Lys D K Glutamate( ) Arginine(+) Glu Arg E R Serine Tyrosine Asparagine Histidine Ser Tyr Asn His S Y N H Threonine Cysteine Glutamine Tryptophane Thr Cys Gln Trp T C Q W Glycine Gly G Chargedaminoacids Polaraminoacids Glycine(sidechainisonlyahydrogen) 11Jan

13 Disulphidebridges Twocysteinescanformdisulphidebridges Anchoringofsecundarystructureelements 11Jan

14 Histidine HistidinehasapKvalue~6.5 Alsodifferentformspossible ImportantforformationofH bondnetworks 11Jan

15 Proline Restrictsflexibilityofthebackbone Misses thebackbonehydrogen(n H): Structure breaker 11Jan

16 Ramachandranplot Onlycertaincombinationsof valuesofphi(φ) andpsi (ψ) anglesareobserved 11Jan2006 psi psi phi omega phi 16

17 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: Thebuildingblocks(Ch.1) Secundarystructure elements Renderingsofproteins Motifsofproteinstructure(Ch.2) Alphahelix Alphadomainstructures(Ch.3) Turnsandmotifs Alpha/Betastructures(Ch.4) Beta strands&sheets Domainsformedby motifs Betastructures(Ch.5) 11Jan

18 Motifsofproteinstructure Globalstructuralcharacteristics: Outsidehydrophylic,insidehydrophobic(unless ) Oftenglobularform(unless ) 11Jan2006 Artymiuketal,StructureofHenEggWhiteLysozyme(1981) 18

19 Secundarystructureelements 11Jan2006 Alpha helix Beta strand 19

20 Renderingsofproteins IrvingGeis: 11Jan

21 Renderingsofproteins JaneRichardson: 11Jan

22 Alphahelix Hydrogenbond: fromn Hatpositionn,toC=Oatpositionn 4( n n+4 ) 11Jan

23 Otherhelices Alternativehelicesarealsopossible 11Jan helix:hydrogenbondfromn Hatpositionn,to C=Oatpositionn 3 Biggerchanceofbadcontacts α helix:hydrogenbondfromn Hatpositionn,to C=Oatpositionn 4 π helix:hydrogenbondfromn Hatpositionn,to C=Oatpositionn 5 structuremoreopen:nocontacts Hollowinthemiddletoosmallfore.g.water AttheedgeoftheRamachandranplot 23

24 Helices Backbonehydrogenbridgesformthestructure Directedthroughhydrophobiccenterofprotein Sidechainspointoutwards Possibly:onesidehydrophobic,oneside hydrophylic 11Jan

25 Beta strands:beta sheets Beta strandsnexttoeachother formhydrogenbridges 11Jan

26 ParallelorAntiparallelsheets Anti parallel Parallel Usuallyonlyparallelor anti parallel Occasionallymixed Sidechainsalternating 11Jan

27 Turnsandmotifs Betweenthesecundarystructureelementsareloops Veryshortloopsbetweentweeβ strands:turn Differentsecundarystructureelementenoftenappear together:motifs Helix turn helix Calciumbindingmotif Hairpin Greekkeymotif β α β motif 11Jan

28 Helix turn helixmotif Helix turn helix importantfordna recognitionbyproteins EF hand: calciumbindingmotif 11Jan

29 Hairpin/Greekkeymotif Differentpossible hairpins:typei/ii Greekkey: anti parallelbeta sheets 11Jan

30 β α βmotif Mostcommonwaytoobtain parallelβ sheets Usuallythemotifis right handed 11Jan

31 Domainsformedbymotifs Withinproteindifferentdomainscanbeidentified Forexample: ligandbindingdomain DNAbindingdomain Catalyticdomain Domainsarebuiltfrommotifsofsecondarystructure elements 11Jan

32 Summary Aminoacidsformpolypeptidechains Chainsfoldintothree dimensionalstructure Specificbackboneanglesarepermittedornot: Ramachandranplot Secundarystructureelements: α helix,β sheet Commonstructuralmotifs: Helix turn helix,calciumbindingmotif,hairpin, Greekkeymotif,β α β motif Combinationofelementsandmotifs: tertiarystructure Manyproteinstructuresavailable:PDB 11Jan

33 11Jan2006 Pauze 33

34 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: Thebuildingblocks(Ch.1) Motifsofproteinstructure(Ch.2) Alphadomainstructures(Ch.3) Coiledcoil Fourhelixbundle Globinfold Alpha/Betastructures(Ch.4) Betastructures(Ch.5) 11Jan

35 α domains Commonα domains Coiledcoil 11Jan2006 Fourhelixbundle Globinfold 35

36 Coiledcoil Twohelicestwistedaroundeachother residuesperturn heptadrepeata b c d e f g hydrophobiccenterlined withionicinteractions 11Jan

37 Coiledcoil:knobsinholes 11Jan2006 backboneoftwohelicesparallel put d residuessidebyside residues a and d ofhelix1fitintohollowsinhelix2 resultsin~18degreeangle (calculate!) 37

38 Fourhelixbundle hydrophobicresiduespackedclosetogether sequentialhelicesagainsteachother sometimestwocoiledcoils:knobs in holes 11Jan

39 Fourhelixbundle:ridgesingrooves Groupaminoacidsandrecognizelines Fittheselinesontoeachother resultsin60or20degreeangle(calculate) Dependsstronglyonhelicalparameters 11Jan2006 n,n+4 n,n+3 39

40 Globinfold Commontheme 8helices(ABCDEFGH),shortloops Stillmuchvariation(16 99%similarity) Helixlength Exactposition Shiftthroughtheridges 11Jan

41 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: Thebuildingblocks(Ch.1) Motifsofproteinstructure(Ch.2) Alphadomainstructures(Ch.3) Alpha/Betastructures(Ch.4) Betastructures(Ch.5) 11Jan2006 Differentα β αgroups Alpha/betabarrels Horseshoefold Twistedopen sheet structures Predictinglocationof activesite 41

42 Alpha/betastructures 11Jan2006 Barrel Opentwistedsheet Horseshoefold 42

43 Differentα β αgroups barrels/horseshoe 11Jan2006 opentwistedsheet 43

44 Alpha/betabarrels TIMbarrelaftertriosephosphateisomerase Usually8β strands,atleast200aminoacids Oftenhydrophobicinterior alternatingaminoacidsinthestrands 11Jan

45 Alpha/betabarrels Activesiteformedby(variable)loopregionsattopofthebarrel Exception: inthecoreofmethylmalonyl coenzymeamutase 11Jan

46 Horseshoefold Repetetivesequenties(20aminoacids) Leucine containing Foundinabout60proteins 11Jan

47 Twistedopen sheetstructures Helicesatbothsidesofthesheet Activesiteisusuallyfoundatjunctionofthesheet Muchvariationinstructures 11Jan

48 Predictinglocationofactivesite Whensequenceofthestrandsisbroken,usuallya crevice,whichoftencontainstheactivesite 11Jan

49 DNA/Proteinstructure function analysisandprediction BasicsofProteinStructure: 11Jan2006 Thebuildingblocks(Ch.1) Motifsofproteinstructure(Ch.2) Alphadomainstructures(Ch.3) Up and downbarrels Greekkeybarrels Alpha/Betastructures(Ch.4) Jelly rollbarrels Betastructures(Ch.5) Beta helices Propellerstructures Compareparallel sheets 49

50 Betastructures barrels up and downbarrels greekkeybarrels jellyrollbarrels propellerlikestructure betahelix 11Jan

51 Up and downbarrels Relativelysimplestructure Aminoacidsalternatinghydrophobic/hydrophilic inside outside Exampleretinolbindingprotein ButalsoOmpX P2family:10strands 11Jan

52 Greekkeybarrels Greekkeymotifoccursalsoinbarrels twogreekkeys(γcrystallin) combinationgreekkey/up and down 11Jan

53 Jelly rollbarrels Kindofmega greekkeymotif wellvaakdistortedstructuresalstweesheets 11Jan

54 Propellerstructures Differentsheetstogetherforma propellor Activesiteinthemiddletop(orbottom)ofthepropellor 11Jan

55 Beta helices Yetanotherwayofobtainingparallelbeta sheets 11Jan

56 Compareparallelsheets beta loop alpha loop betabecomesbeta loop beta loop beta Inα/β barrelhelicesat20degrees(ridges&grooves) sheetsalsoat20graden Inbeta helixstrandsreallyparallel 11Jan

57 Summary Alphadomains (knobs in holes) coiledcoil fourhelixbundle (ridges&grooves) globinfold Alpha/betastructures α/βbarrel twistedopensheet horseshoefold Betastructures β barrels:up and down,greekkey,jellyroll propellerlikestructures beta helix 11Jan

58 Overview Aminoacids Chains Structure Motifs Domains Specificbackboneanglesarepermittedornot: Ramachandranplot Secundarystructureelements:α helix,β sheet Commonstructuralmotifs: Helix turn helix,calciumbinding,β hairpin, Greekkey,β α β Combinationofelementsandmotifs:tertiarystructure Alphadomains coiledcoil,fourhelixbundle,globinfold Alpha/betastructures α/βbarrel,twistedopensheet,horseshoefold Betastructures β barrels,propeller likestructures,beta helix 11Jan

59 11Jan