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Protein Structure

Protein Structure

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Protein Structure

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  1. Protein Structure September 4, 2008

  2. Basics of Protein Structure • Primary structure: sequence • Secondary structure: • α-helix, -sheet, -strand, loop • Supersecondary structure, motifs • Tertiary structure: • folding into functional domains with ordered structure composed of secondary structure elements • Quaternary structure • Complexes of monomers to form active structures

  3. Amino acids and peptides

  4. 20 amino acids - the building blocks

  5. Amino acid categories • Aliphatic • Valine, Alanine, Leucine and Isoleucine • Aromatic • Phenylalanine, Tyrosine and Tryptophan • Charged • Aspartic, Glutamic, Histidine, Lysine, Arginine • Polar • Serine, Threonine, Cysteine, Methionine, Asparagine, Glutamine • Odd couple • Glycine, Proline

  6. Aliphatic residues

  7. Aromatic Residues

  8. Charged Residues • Side-chains are charged under physiological conditions • Acid are negatively charged • Basic are positively charged

  9. Polar Residues

  10. The Odd Couple

  11. Peptide-bond formation

  12. w Backbone torsion angles • f phi y psi • omega 180° trans 0° cis

  13. Ramachandran Plot

  14. Other chemical bonds • Disulfide bonds or bridges • Formed by oxidation of thiol groups of two cysteines • Form a bond about 2Å in length. • Predominant feature in many small proteins • H-bonds not truly covalent • Dipolar attraction between O and H • Complex geometry wrt distances and angles

  15. Side Chain Conformation

  16. Side Chain Torsion Angles The side chain torsion angles are named c1(chi1), c2(chi2), c3 (chi3), etc., as shown below for lysine.

  17. Hydrophilic or hydrophobic…? • Virtually all soluble proteins feature a hydrophobic core surrounded by a hydrophilic surface • Peptide backbone is inherently polar • Neutralize potential H-donors & acceptors using ordered secondary structure

  18. Alpha helix • H-bonds between N-H and C=O groups in polypeptide backbone • Compact structure • 3.6 residues • Pitch: 5.6Å/turn • Rise: 1.5Å/residue • Polar/hydrophilic residues on 1 face with nonpolar or hydrophobic residues on other face

  19. Secondary Structure: -helix • 3.6 residues / turn • Axial dipole moment • Not Proline & Glycine • Protein surfaces

  20. Beta-sheet • Extended structure • Side-chains project alternately up or down • Amphipathic is solvent exposed • polar residues on one side and non-polar on other side

  21. Secondary Structure: -sheets

  22. Secondary Structure: -sheets • Parallel or antiparallel • Alternating side-chains • No mixing • Loops often have polar amino acids

  23. Parallel -sheets:

  24. Antiparallel -sheets:

  25. Silk fibroin

  26. Supersecondary structures • Also called motifs • Simple combinations of secondary structures

  27. -hairpins

  28. Two-residue -hairpins

  29. Three-residue -hairpins

  30. -meander

  31. corners are observed to have a right-handed twist when viewed from the concave side

  32. Helix hairpins

  33. The  corner

  34. EF hand

  35.  motifs

  36. Greek Key Motif

  37. Tertiary Structure • Combinations of motifs to form domains • Three main classes • All alpha • Alpha/beta • All beta

  38. Alpha Domain Structures • Four helix bundle • Globin fold

  39. Myohemeyrthrin

  40. Cytochrome b452

  41. Ferritin

  42. Globins

  43. Packing of helices

  44. Alpha/beta • TIM barrel • Rossmann fold • Horseshoe fold

  45. TIM Barrel

  46. Horseshoe Fold