Biochem 4000 - Lecture 2 PI

  1. Image Upload 1
    What is angle A?
    ω - Omega
  2. Image Upload 2
    What is angle B?
    φ - Phi
  3. Image Upload 3
    What is angle C?
    Ψ - Psi
  4. What torsion angle does omega like?
    ~180 degrees
  5. Conformational propensity
    Frequency in which a residue adopts a given conformation
  6. Does conformational propensity apply to main chain atoms?
  7. What does conformational propensity depend upon?
    • Residue physiochemical properties
    • Sequence context (flanking residues) [Lesser extent]
  8. Outline hou-Fasman method
    Calculate single propensity for each residue type and secondary structure.
  9. Problems with the Chou-fasman model
    • Based solely on physiochemical properties
    • Does not account for sequence context
  10. Cho fasman formula
    P[Secondary structure]= (%Residue[Secondary structure]/%All Residues[Secondary structure])
  11. GOR Method
    • Select a residue for propensity examination
    • Examine the eight residues to either side (17 residue total window)
    • Use the Chou-fasman formula
  12. Glutamate has an α-helix propensity of 1.51. What does this mean?
    Glu is in an α-helix ~50% more than not
  13. What direction do R-groups lean on α-helices?
    Toward the N-terminus
  14. Why do branched residues dislike helices?
    Their large R-groups cause steric clashes
  15. Which secondary structure favours large R-groups?
  16. Two types of helix cap (N and C)
    • Glu (N) - Uses side chain for hydrogen bonding
    • Ala (C) - Uses main chain NH3 for bidentate H-bonds (310)
  17. Why is helix capping important?
    To satisfy hydrogen bonding on the ends of an α-helix.
  18. Residues preferring α-helices
    • Glutamate (N-cap)
    • Alanine (C-cap)
    • Methionine
  19. Residues preferring sheets
    • β-branched residues and Tyrosine
    • Tyrosine, valine , isoleucine and threonine
  20. Residues preferring turns
    • Proline, glycine and small polar charged residues
    • Proline, glycine, aspartate, asparagine and serine
  21. Residues generally preferring nonspecific secondary structures over turns
    • Leucine, phenylalanine and tryptophan
    • Nonpolar
  22. Residues with no real preference
    • Arginine
    • Cysteine
    • Glutamate
    • Histidine
    • Lysine
  23. Residue sequence preceding a helix
    ...-Pro-Gly-Pro-Gly-... (Helix whithin twelve residues)
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Biochem 4000 - Lecture 2 PI