Ab initio conformational analysis of N- and C-terminally-protected valyl-alanine dipeptide model

Ab initio conformational analysis of the dipeptide Ac-Valine-Alanine-NHMe was performed and optimized at the RHF/3-21g level of theory in an attempt to characterize the folding of short peptides. A topological scan of alanine's (Ala) psi and phi rotors was carried out with valine (Val) in the beta(L) geometry to construct a Ramachandran surface in two- and three-dimensions. It was observed that Val sterically dominates the conformations of Ala. Of the 243 possible conformers in this study, 202 were found. Those that were not found had converged to a different geometry of lower energy and greater stability. The gamma(L) and epsilon(L) conformers of Ala were favoured, and 47 of the found conformers can be classified as potential beta-turns according to the traditional backbone torsional definitions. However, the potentially, most stable conformer, alpha(D)(a)gamma(L), was not in one of these regions of the Ramachandran surface. Thus, beta-turns may not be inherent conformations of the Val-Ala dipeptide, but may arise preferentially within protein structures due to certain steric effects from the surrounding environment. (c) 2005 Elsevier B.V. All rights reserved.