1. Structure-Function Analysis 11 Jan 20061 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –Short Introduction to Molecular Structures –“Introduction to Protein Structure” Chapters 1 to 5 Carl Branden & John Tooze ISBN: 0-8153-2305-0 (recommended)‏

2. Structure-Function Analysis 11 Jan 20062 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏

3. Structure-Function Analysis 11 Jan 20063 Prelude: molecular structures John Dalton (1810) A new system of chemistry Elements, but no structures yet Mendeljev (1869)‏

4. Structure-Function Analysis 11 Jan 20064 Johannes van ’t Hoff Chimie dans l’Espace “Proposal for the development of three-dimensional chemical structural formulae” (1875)‏ Tetraedrical carbon atom

5. Structure-Function Analysis 11 Jan 20065 Linus Pauling (1951)‏ Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains Alpha-helix

6. Structure-Function Analysis 11 Jan 20066 James Watson & Francis Crick (1953)‏ Molecular structure of nucleic acids

7. Structure-Function Analysis 11 Jan 20067 James Watson & Francis Crick (1953)‏ Molecular structure of nucleic acids

8. Structure-Function Analysis 11 Jan 20068 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Chains of aminoacids Three-dimensional Structures Four levels of protein architecture Aminoacids: classes Disulphide bridges Histidine Proline Ramachandran plot

9. Structure-Function Analysis 11 Jan 20069 The Building Blocks (proteins) Proteins consist of chains of aminoacids Bound together through the peptide bond Special folding of the chain yields structure Structure determines the function

10. Structure-Function Analysis 11 Jan 200610 Chains of aminoacids

11. Structure-Function Analysis 11 Jan 200611 Three-dimensional Structures Four levels of protein architecture

12. Structure-Function Analysis 11 Jan 200612 Aminoacids: klassen Hydrophobic aminoacids AlanineAlaAValineValV PhenylalaninePheFIsoleucineIleI LeucineLeuLProlineProP MethionineMetM Charged aminoacids Aspartate (-)AspDGlutamate (-)GluE Lysine (+)LysKArginine (+)ArgR Polar aminoacids SerineSerSThreonineThrT TyrosineTyrYCysteineCysC AsparagineAsnNGlutamineGlnQ HistidineHisHTryptophaneTrpW Glycine (sidechain is only a hydrogen)‏ GlycineGlyG

13. Structure-Function Analysis 11 Jan 200613 Disulphide bridges Two cysteines can form disulphide bridges Anchoring of secundary structure elements

14. Structure-Function Analysis 11 Jan 200614 Histidine Histidine has a pK value ~6.5 Also different forms possible Important for formation of H-bond networks

15. Structure-Function Analysis 11 Jan 200615 Proline Restricts flexibility of the backbone “Misses” the backbone hydrogen (N-H): –Structure-breaker

16. Structure-Function Analysis 11 Jan 200616 Ramachandran plot Only certain combinations of values of phi (  and psi (  angles are observed phi psi omega

17. Structure-Function Analysis 11 Jan 200617 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Secundary structure elements Renderings of proteins Alpha helix Beta-strands & sheets Turns and motifs Domains formed by motifs

18. Structure-Function Analysis 11 Jan 200618 Motifs of protein structure Global structural characteristics: –Outside hydrophylic, inside hydrophobic (unless…)‏ –Often globular form (unless…)‏ Artymiuk et al, Structure of Hen Egg White Lysozyme (1981)‏

19. Structure-Function Analysis 11 Jan 200619 Secundary structure elements Alpha-helix Beta-strand

20. Structure-Function Analysis 11 Jan 200620 Renderings of proteins Irving Geis:

21. Structure-Function Analysis 11 Jan 200621 Renderings of proteins Jane Richardson:

22. Structure-Function Analysis 11 Jan 200622 Alpha helix Hydrogen bond: from N-H at position n, to C=O at position n-4 (‘n-n+4’)‏

23. Structure-Function Analysis 11 Jan 200623 Other helices Alternative helices are also possible –3 10 -helix: hydrogen bond from N-H at position n, to C=O at position n-3 Bigger chance of bad contacts –  -helix: hydrogen bond from N-H at position n, to C=O at position n-4 –  -helix: hydrogen bond from N-H at position n, to C=O at position n-5 structure more open: no contacts Hollow in the middle too small for e.g. water At the edge of the Ramachandran plot

24. Structure-Function Analysis 11 Jan 200624 Helices Backbone hydrogenbridges form the structure –Directed through hydrophobic center of protein Sidechains point outwards –Possibly: one side hydrophobic, one side hydrophylic

25. Structure-Function Analysis 11 Jan 200625 Beta-strands: beta-sheets Beta-strands next to each other form hydrogen bridges

26. Structure-Function Analysis 11 Jan 200626 Parallel or Antiparallel sheets Anti-parallel Parallel Usually only parallel or anti-parallel Occasionally mixed Sidechains alternating

27. Structure-Function Analysis 11 Jan 200627 Turns and motifs Between the secundary structure elements are loops Very short loops between twee  -strands: turn Different secundary structure elementen often appear together: motifs –Helix-turn-helix –Calcium binding motif –Hairpin –Greek key motif –  -motif

28. Structure-Function Analysis 11 Jan 200628 Helix-turn-helix motif Helix-turn-helix important for DNA recognition by proteins EF-hand: calcium binding motif

29. Structure-Function Analysis 11 Jan 200629 Hairpin / Greek key motif Different possible hairpins : type I/II Greek key: anti-parallel beta-sheets

30. Structure-Function Analysis 11 Jan 200630  motif Most common way to obtain parallel  -sheets Usually the motif is ‘right- handed’

31. Structure-Function Analysis 11 Jan 200631 Domains formed by motifs Within protein different domains can be identified –For example: ligand binding domain DNA binding domain Catalytic domain Domains are built from motifs of secondary structure elements

32. Structure-Function Analysis 11 Jan 200632 Summary Aminoacids form polypeptide chains Chains fold into three-dimensional structure Specific backbone angles are permitted or not: Ramachandran plot Secundary structure elements:  -helix,  -sheet Common structural motifs: Helix-turn-helix, Calcium binding motif, Hairpin, Greek key motif,  -motif Combination of elements and motifs: tertiary structure Many protein structures available: PDB

33. Structure-Function Analysis 11 Jan 200633 Pauze

34. Structure-Function Analysis 11 Jan 200634 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Coiled coil Four helix bundle Globin fold

35. Structure-Function Analysis 11 Jan 200635  -domains Common  -domains Coiled coil Four helix bundleGlobin fold

36. Structure-Function Analysis 11 Jan 200636 Coiled coil Two helices twisted around each other –residues per turn 3.6  3.5 –heptad repeat a-b-c-d-e-f-g –hydrophobic center lined with ionic interactions

37. Structure-Function Analysis 11 Jan 200637 Coiled coil: knobs in holes backbone of two helices parallel put ‘d’ residues side by side residues ‘a’ and ‘d’ of helix 1 fit into hollows in helix 2 results in ~18 degree angle(calculate!)‏

38. Structure-Function Analysis 11 Jan 200638 Four helix bundle hydrophobic residues packed close together sequential helices against each other sometimes two coiled coils: knobs-in-holes

39. Structure-Function Analysis 11 Jan 200639 Four helix bundle: ridges in grooves Group aminoacids and recognize lines Fit these lines onto each other results in 60 or 20 degree angle (calculate)‏ –Depends strongly on helical parameters n,n+4n,n+3

40. Structure-Function Analysis 11 Jan 200640 Globin fold Common theme 8 helices (ABCDEFGH), short loops Still much variation (16 – 99 % similarity)‏ –Helix length –Exact position –Shift through the ridges

41. Structure-Function Analysis 11 Jan 200641 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Different  -  -  groups Alpha/beta barrels Horseshoe fold Twisted open-sheet structures Predicting location of active site

42. Structure-Function Analysis 11 Jan 200642 Alpha/beta structures BarrelOpen twisted sheet Horseshoe fold

43. Structure-Function Analysis 11 Jan 200643 Different  groups barrels / horseshoeopen twisted sheet

44. Structure-Function Analysis 11 Jan 200644 Alpha/beta barrels TIM barrel after triosephosphate isomerase Usually 8  -strands, at least 200 aminoacids Often hydrophobic interior –alternating aminoacids in the strands

45. Structure-Function Analysis 11 Jan 200645 Alpha/beta barrels Active site formed by (variable) loop regions at top of the barrel Exception: in the core of methylmalonyl-coenzyme A mutase

46. Structure-Function Analysis 11 Jan 200646 Horseshoe fold Repetetive sequenties (20 aminoacids)‏ Leucine-containing Found in about 60 proteins

47. Structure-Function Analysis 11 Jan 200647 Twisted open-sheet structures Helices at both sides of the sheet Active site is usually found at junction of the sheet Much variation in structures

48. Structure-Function Analysis 11 Jan 200648 Predicting location of active site When sequence of the strands is broken, usually a crevice, which often contains the active site

49. Structure-Function Analysis 11 Jan 200649 DNA/Protein structure-function analysis and prediction Basics of Protein Structure: –The building blocks (Ch. 1)‏ –Motifs of protein structure (Ch. 2)‏ –Alpha domain structures (Ch. 3)‏ –Alpha/Beta structures (Ch. 4)‏ –Beta structures (Ch. 5)‏ Up-and-down barrels Greek key barrels Jelly-roll barrels Propeller structures Beta-helices Compare parallel sheets

50. Structure-Function Analysis 11 Jan 200650 Beta structures barrels –up-and-down barrels –greek key barrels –jelly roll barrels propeller like structure beta helix

51. Structure-Function Analysis 11 Jan 200651 Up-and-down barrels Relatively simple structure Aminoacids alternating hydrophobic / hydrophilic –inside – outside Example retinol binding protein But also OmpX P2 family: 10 strands

52. Structure-Function Analysis 11 Jan 200652 Greek key barrels Greek key motif occurs also in barrels –two greek keys (  crystallin)‏ –combination greek key / up-and-down

53. Structure-Function Analysis 11 Jan 200653 Jelly-roll barrels Kind of mega-greek key motif well vaak distorted structures als twee sheets

54. Structure-Function Analysis 11 Jan 200654 Propeller structures Different sheets together form a ‘propellor’ Active site in the middle top (or bottom) of the propellor

55. Structure-Function Analysis 11 Jan 200655 Beta-helices Yet another way of obtaining parallel beta-sheets

56. Structure-Function Analysis 11 Jan 200656 Compare parallel sheets beta-loop-alpha-loop-beta becomes beta-loop-beta-loop-beta In  /  -barrel helices at 20 degrees (ridges & grooves)‏ –sheets also at 20 graden In beta-helix strands really parallel

57. Structure-Function Analysis 11 Jan 200657 Summary Alpha domains –coiled coil (knobs-in-holes)‏ –four helix bundle –globin fold(ridges & grooves)‏ Alpha/beta structures –  /  barrel –twisted open sheet –horseshoe fold Beta structures –  -barrels: up-and-down, greek key, jelly roll –propeller like structures –beta-helix

58. Structure-Function Analysis 11 Jan 200658 Overview Aminoacids – Chains – Structure – Motifs – Domains Specific backbone angles are permitted or not: Ramachandran plot Secundary structure elements:  -helix,  -sheet Common structural motifs: Helix-turn-helix, Calcium binding,  -hairpin, Greek key,  Combination of elements and motifs: tertiary structure Alpha domains coiled coil, four helix bundle, globin fold Alpha/beta structures  /  barrel, twisted open sheet, horseshoe fold Beta structures  -barrels, propeller-like structures, beta-helix

59. Structure-Function Analysis 11 Jan 200659