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) ψ and φ rotors was carried out with valine (Val) in the β_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 γ_L and ε_L conformers of Ala were favoured, and 47 of the found conformers can be classified as potential β-turns according to the traditional backbone torsional definitions. However, the potentially most stable conformer, α_D^aγ_L, was not in one of these regions of the Ramachandran surface. Thus, β-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.