Ab initio calculations on blocked Pro-Ala dipeptides

Abstract

Listen

Translate article

The effect of the chirality of the amino acid at position i + 2 on a β-turn was investigated by a grid scan ab initio calculation on the Ac- l-Pro- l-Ala-NH 2 and Ac- l-Pro- d-Ala-NH 2 blocked dipeptides. Th6–31G basis set was used to estimate the effect of the alanyl side chain on the conformation of the peptide backbone in a blocked dipeptide as a simple, but complete model for a reverse turn. This study provides a quantum mechanical evaluation of the ability of the NH at the i + 3 residue to form the Hbond that closes the 10 membered ring which stabilizes the turn. The lowest energy of all 64 probed conformations of the D-Ala containing peptide corresponded to a good type II β-turn with a hydrogen bond distance between the acetyl oxygen and the amide terminal hydrogen of 2.21 Å. A comparison with the nonblocked dipeptide ab initio study indicates that the presence of the end blocks enhances the propensity of the d-Ala-containing dipeptide for a type II β-turn, but does not seem to enhance the propensity of the l-Ala-containing dipeptide for a type I β-turn. The energies and geometric parameters for the lowest four optimized conformations identified by the grid scan search for each molecule have been calculated.