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Helix-Coil Transition Theory: from biophysics to biochemistry via probability ~ Lauraine Dalton

Helix-Coil Transition Theory: from biophysics to biochemistry via probability ~ Lauraine Dalton. Protein primary, secondary, tertiary structure. Alpha helix secondary structure properties.

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Helix-Coil Transition Theory: from biophysics to biochemistry via probability ~ Lauraine Dalton

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  1. Helix-Coil Transition Theory: from biophysics to biochemistry via probability~ Lauraine Dalton • Protein primary, secondary, tertiary structure. • Alpha helix secondary structure properties. • Historical development of helix-coil transition theory (HCTT); from chemical physics to empirical biochemistry. • Helices at work; selected examples.

  2. The peptide bond has partial pi character; its geometry is planar. Ca is a member of two planes.

  3. Rotation about Ca sigma bonds: dihedral angles phi and psipsiphipsiphi(yellow arcs)

  4. Ramachandran plot of allowed dihedral angles.Steric clashes of side chains limit rotation.

  5. Hydrogen bond network of the alpha helix

  6. Helix-coil transition, a disruptive view of unraveling

  7. Nucleation involves adjustment of 6 dihedral angles; elongation, 2

  8. Nucleation (difficult) & Propagation (facile) The equilibrium constant for nucleation (sigma) is typically 1000 times lower than for propagation (s). (…cccchhhcccc….)  s = (…ccccccccccc….) and the equilibrium constant (statistical weight) for adding another helical segment at the end of a stretch of helical residues is (….ccchhhhhhhhccc…) s = (….ccchhhhhhhcccc…)

  9. Typical values of s and s s is approx 0. 001 * s

  10. Helix macro dipole increases stability for long helices (supports elongation s)

  11. Zimm-Bragg and Lifson-Roig concepts of weighting

  12. Sharpness of the transition, as calculated by Schellman in 1958A = coexistence of hhh and ccc intermediate states;B = h or c all or noneC = infinitely long helix

  13. Chou-Fasman “rules” of biochemistry (probabilities)

  14. Helix initation and termination in proteins • J & D Richardson focused on Ncap and Ccap in analysis of 215 helical segment in known structures. • Current view is that Ncap motif consists of four residues S(T)XXE(D) = hydroxyl-XX-carboxylate. • Carboxylate (-) interacts favorably with helix macro dipole (+) • Ccap contributors are misfits; P (bulky ring) and G (no side chain; 2 H; very flexible)

  15. Helices at work; stable structures perform mechanical tasks in lipid bilayer

  16. Biotin (+Avidin) measurement tool

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