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. C  is a member of two planes.

3. Rotation about Ca sigma bonds: dihedral angles phi and psi psi phi psi phi (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  and 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 1958 A = coexistence of hhh and ccc intermediate states; B = h or c all or none C = 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