Differential helix propensity of small apolar side chains studied by molecular dynamics simulations.

ABSTRACT

A series of oligoalanine molecules with single amino acid replacements in the middle of the chain has been studied by molecular dynamics simulations. Differences in stability of the alpha-helix (as free energies delta delta G degrees) were estimated for the following series of residues alpha-aminoisobutyric acid, alanine, alpha-amino-n-butyric acid, valine, glycine, D-alanine, t-leucine (= alpha-amino-beta,beta-dimethyl-n- butyric acid), and proline, arranged here in decreasing order of helix-forming potential. (The results for proline and valine had been reported earlier.) No experimental results were available for alpha-amino-n-butyric acid, D-alanine, and t-leucine at the time these calculations were done. The values of delta delta G degrees, including the three predictions, are in striking agreement with recent experimental results. A combination of free dynamics, dynamics with forced conformational change, and dynamics with forced molecular replacement was used. Conformational distributions were calculated for the peptide backbone of the dipeptides and, where appropriate, for the side chains of the dipeptide and the alpha-helix. The results demonstrate an unexpected level of accuracy for the all-atom model used to represent atomic interactions in the simulations. The simulations permit a detailed analysis of different factors responsible for conformational preferences and differences in stability. These conclusions drawn from this analysis agree with accepted qualitative explanations and allow these explanations to be quantitated to an extent not heretofore possible.