Theory of protein molecule self-organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments

Constants of the helix–coil transition for all natural amino acid residues are evaluated on the basis of thermodynamic parameters obtained in paper I of this series. The specific effects at the termini of the helices are also considered as well as the parameters controlling the formation of β-bends in the unfolded protein chain. Evaluated s constants of the helix–coil transition agree with the experimental data on helix–coil transitions of synthetic polypeptides in water. Only a very qualitative correlation exists between s constants (both experimental and theoretical) and the occurrence of corresponding residues in internal turns of α-helices in globular proteins: residues with s > 1 occur in helices as a rule more often than residues with s < 1. At the same time a direct correlation is demonstrated between theoretical parameters of residue incorporation into α-helical termini and β-bends in an unfolded polypeptide chain and the occurrence of residues in corresponding positions of the globular protein secondary structures.