Biochem 4000 - Lecture 4 PII

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  1. What do loops do?
    Connect secondary structures (helices, sheets etc)
  2. Long loop β-hairpin
    • Special case of Ω-loops
    • Wide range of nonspecific conformations (random coil)
  3. β-meander
    • Consecutive antiparallel β-strands connected by long loop β-hairpin
    • Supersecondary stucture
  4. β-corner alternative definition
    • β-hairpin with two-residue β-bulge
    • Supersecondary structure
  5. Long loop conformations
    Large variety/many possibilities
  6. αα-hairpin
    Two antiparallel α helices connected by a long loop
  7. Parallel and antiparallel helix interactions
    • Hydrophobic strip
    • One hydrophobic residue per turn
    • (Amphipathic helices possible)
  8. Shortest loops
    • Two and three residues
    • Single allowed conformation
  9. 2 Residue αα hairpin
    • Residue 1: Bridging conf. (α-β) (ignore bold)
    • Residue 2: Gly
    • (Helix perpendicular)
  10. 3 Residue αα-hairpin
    • Residue 1: Bridging conf. (α-β) [X]
    • Residue 2: Left handed helix conf. [Gly]
    • Residue 3: β-strand conf. [X]
    • (X-Gly-X)
  11. Capping αα helices
    • 2-Residue: Residue 1 caps first helix
    • 3-Residue: Residues 2 & 3 cap terminii of both helices
  12. 4 Residue helix hairpin overview
    • aka αα-hairpin
    • Two possible conformations
    • ~23° between helices
  13. 4 residue αα-hairpin conformation 1)
    • Residue 1: Bridging
    • Residue 2: Left-handed helix
    • Residue 3: β-strand
    • Residue 4: β-strand
  14. 4 residue αα-hairpin conformation 2)
    • Residue 1: β-strand
    • Residue 2: Bridging
    • Residue 3: β-strand
    • Residue 4: Bridging
  15. αα-corner
    • Two ~perpendicular α-helices connected by a short loop
    • Chiral
  16. 3 Residue αα-corner
    • Residue 1: Small (Gly, Ala; avoid steric conflict), cap first helix
    • Residue 2: Hydrophobic
    • Residue 3: Small polar (Ser, Asp), cap second helix
  17. Handedness of helices
    Right handed (left handers have steric clash)
  18. EF hand
    • Functional motif - Helix-loop-helix
    • Occur in pairs
    • Enclose calcium (carboxyl residues)
  19. Structure of an EF hand
    • 12 Residue long loop
    • Invariant Gly at position 6
    • Asp and Glu required in four positions
  20. DNA-binding protein interactions
    • Occur in pairs
    • Helix one and loop position helix 2 in major groove (B-DNA)
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Ant
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Card Set:
Biochem 4000 - Lecture 4 PII
Updated:
2016-02-20 03:34:21
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Biochem 4000
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