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Secondary structure of proteins : sheets supersecondary structure

Secondary structure of proteins : sheets supersecondary structure. Levels of protein structure organization. Peptide bond geometry. Hybrid of two canonical structures. 60% 40%. Dihedrals with which to describe polypeptide geometry. side chain. main chain.

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Secondary structure of proteins : sheets supersecondary structure

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  1. Secondarystructure of proteins: sheetssupersecondarystructure

  2. Levels of protein structure organization

  3. Peptide bond geometry Hybrid of two canonical structures 60% 40%

  4. Dihedrals with which to describe polypeptide geometry side chain main chain

  5. Because of peptide group planarity, main chain conformation is effectively defined by the f and y angles.

  6. The Ramachandran map

  7. Conformations of a terminally-blocked amino-acid residue E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977) C7eq C7ax

  8. A Ramachandran plot for BPTI(M6.10)

  9. Energy maps of Ac-Ala-NHMe and Ac-Gly-AHMe obtained with the ECEPP/2 force field

  10. Energy curve of Ac-Pro-NHMe obtained with the ECEPP/2 force field fL-Pro»-68o

  11. Dominant b-turns

  12. Types of b-turns in proteins Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)

  13. Older classification Lewis, Momany, Scheraga, Biochim. Biophys. Acta, 303, 211-229 (1973)

  14. fi+1=-60o, yi+1=-30o, fi+2=-90o, yi+2=0o fi+1=60o, yi+1=30o, fi+2=90o, yi+2=0o fi+1=-60o, yi+1=-30o, fi+2=-60o, yi+2=-30o fi+1=60o, yi+1=30o, fi+2=60o, yi+2=30o

  15. fi+1=-60o, yi+1=120o, fi+2=80o, yi+1=0o fi+1=60o, yi+1=-120o, fi+2=-80o, yi+1=0o

  16. fi+1=-80o, yi+1=80o, fi+2=80o, yi+2=-80o

  17. cis-proline |yi+1|»80o, |fi+2|<60o |yi+1|»60o, |fi+2|»180o

  18. Hydrogen bond geometry in b-turns Type of structure Average for b-turns g-turn Asx-type b-turns

  19. Helical structures a-helical structure predicted by L. Pauling; the name was given after classification of X-ray diagrams. Helices do have handedness.

  20. Geometrical parameters of helices Average parameters of helical structures Turns closed by H-bond H-bond radius Type

  21. Idealized hydrogen-bonded helical structures: 310-helix (left), a-helix (middle), p-helix (right)

  22. Schematic representation a-helices: helical wheel 3.6 residues per turn = a residue every 100o.

  23. Examples of helical wheels

  24. Amphipatic (or amphiphilic) helices One side contains hydrophobic amino-acids, the other one hydrophilic ones. In globular proteins, the hydrophilic side is exposed to the solvent and the hydrophobic side is packed against the inside of the globule Hydrophobic Hydrophilic Amphipatic helices often interact with lipid membranes hydrophilic head group aliphatic carbon chain lipid bilayer

  25. download cytochrome B562

  26. Length of a-helices in proteins 10-17 amino acids on average (3-5 turns); however much longer helices occur in muscle proteins (myosin, actin)

  27. Proline helices (without H-bonds) Polyproline helices I, II, and III (PI, PII, and PIII): contain proline and glycine residues and are left-handed. PII is the building block of collagen; has also been postulated as the conformation of polypeptide chains at initial folding stages.

  28. Structure F Y w turns/residue residues/turn a-helix -57 -47 180 +3.6 1.5 310-helix -49 -26 180 +3.0 2.0 p-helix -57 -70 180 +4.4 1.15 Polyproline I -83 +158 0 +3.33 1.9 Polyproline II -78 +149 180 -3.0 3.12 Polyproline III -80 +150 180 +3.0 3.1 f and y angles of regular and polyproline helices

  29. Deca-glycine in PPII and PPI without hydrogen atoms, spacefill modells, CPK colouring Poly-L-proline in PPII conformation, viewed parallel to the helix axis, presented as sticks, without H-atoms. (PDB)It can be seen, that the PPII helix has a 3-fold symmetry, and every 4th residue is in the same position (at a distance of 9.3 Å from each other). PPI-PRO.PDB PPII-PRO.PDB

  30. The b-helix

  31. Comparison of a-helical and b-sheet structure

  32. b-sheet structures Pauling and Corey continued thinking about periodic structures that could satisfy the hydrogen bonding potential of the peptide backbone. They proposed that two extended peptide chains could bond together through alternating hydrogen bonds. Alpha, Beta, … I got ALL the letters up here, baby!

  33. A single b-strand

  34. An example of b-sheet

  35. Antiparallel sheet (L6-7) The side chains have alternating arrangement; usually hydrophobic on one and hydrophilic on the opposite site resulting in a bilayer 2TRX.PDB

  36. Parallel sheet (L6-7) The amino acid R groups face up & down from a beta sheet 2TRX.PDB

  37. Residues/turn Structure F Y w Distance along axis/turn Antiparallel b -139 +135 -178 2.0 3.4 Parallel b -119 +113 180 2.0 3.2 a-helix -57 -47 180 3.6 1.5 310-helix -49 -26 180 3.0 2.0 p-helix -57 -70 180 4.4 1.15 Polyproline I -83 +158 0 3.33 1.9 Polyproline II -78 +149 180 3.0 3.12 Polyproline III -80 +150 180 3.0 3.1 A diagram showing the dihedral bond angles for regular polypeptide conformations.Note: omega = 0º is a cis peptide bond and omega = 180º is a trans peptide bond.

  38. Schemes for antiparallel (a) and parallel (b) b-sheets

  39. Dipole moment of b-sheets • 1/3 peptide-bond dipole is parallel to strand direction for parallel b-sheets • 1/15 peptide-bond dipole is parallel to strand direction for antiparallel b-sheets

  40. The b-sheets are stabilized by long-range hydrogen bonds and side chain contacts

  41. b-sheets are pleated

  42. And the ruffles add flavor! • Backbone hydrogen bonds in b-sheets are by about 0.1 Å shorter from those in a-helices and more linear (160o) od helikalnych (157o) • b-sheets are not initiated by any specific residue types • Pro residues are rare inside b-strands; one exception is dendrotoxin K (1DTK)

  43. b-sheet chirality Because of interactions between the side chains of the neighboring strands, the b-strands have left-handed chirality which results in the right twist of the b-sheets N-end C-end

  44. The degree of twist is determined by the tendency to save the intrachain hydrogen bonds in the presence of side-chain crowding

  45. The geometry of twisted b-sheets parallel ‘twisted’ anti-parallel

  46. The geometry of parallel­­ twistedb -sheets thioredoxin trioseposphate isomerase

  47. Parallel b-structures occur mostly in a/b proteins where the b-sheet is covered by a-helical helices

  48. Geometry of antiparallel­¯b-sheets (mostly outside proteins and between domains) twisted (coiled) Multistrand twisted Cyllinders Threestrand with a b-bulge Three strand helicoidal Cupola (dome)

  49. Example of a coiled two-strand antiparallel b-sheet TERMOLIZYNA-RASMOL

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