Predicted conformation of poly (dehydroalanine): a preference for turns

Abstract

Repetitive conformations of poly(dehydroalanine) were studied using molecular mechanics. An exhaustive search of the conformational space was carried out on a ΔAla octapeptide model, using the AMBER force field and the ΔAla parameters of Alagona et al [26], under three dielectric conditions, ε = 1 (vacuum), ε = r and ε = 4r (solvent). In all cases, two major groups of low-energy conformers were found, one corresponding to a regular 3/10 helix or type III turn, the other to an irregular conformation, Φ = -157 to -170° ψ = -1 to 15° which however can be found in the i + 2 position of gamma-turns. The data confirm that ΔAla may induce turn-like structures in peptides and also indicate that it may confer flexibility to the peptide chain.