A conformational study of the dehydroalanine: dipeptide and homopolypeptide

A molecular mechanics study of polydehydroalanine [poly-(delta Ala)] is presented. For this purpose the AMBER 3a program has been used to perform the calculations. With exception of the point charges, the parameters for the terminal groups were taken from AMBER 3a libraries, whereas those for the delta Ala residue from Alagona et al. [J. Comp. Chem. (1991) Vol. 12, pp. 934-942]. Charges for the residue and terminal groups have been fitted from the MNDO electrostatic potential and scaled to achieve an ab initio 6-31G* quality. Calculations have been carried out using the continuous solvent approximation with three different dielectrics epsilon = 1, 1r, and 4r. The results show that, despite the preferred structure for the isolated residue is an extended conformation, a 310-helix is the preferred conformation in the solid state (epsilon = 1 and 1r), whereas a peculiar structure with psi = 0 degree is preferred with epsilon = 4r.