Position dependence of amino acid intrinsic helical propensities II: non-charged polar residues: Ser, Thr, Asn, and Gln

The assumption that the intrinsic cu-helical propensities of the amino acid s are position independent was critical in several helix/coil transition th eories. In the first paper of these series, we reported that this is not th e case for Gly and nonpolar aliphatic amino acids (Val, Leu, Met, and lie). Here we have analyzed the helical intrinsic propensities of noncharged pol ar residues (Ser, Thr, Asn, and Gin) at different positions of a model poly alanine-based peptide. We found that Thr is more favorable (by similar to 0 .3 kcal/mol) at positions N1 and N2 than in the helix center, although for Ser, Asn, and Gin the differences are smaller (+/-0.2 kcal/mol), and in man y cases within the experimental error. There is a reasonable agreement (+/- 0.2 kcal/mol) between the calculated free energies, using the ECEPP/2 force field equipped with a hydration potential, and the experimental data, exce pt at position N1.