Effects of side-chain charges on α-helix stability in C-peptide of ribonuclease A studied by multicanonical algorithm

We have performed multicanonical Monte Carlo simulations of C-peptide of ribonuclease A. Three analogues of the peptide with charged and neutral side chains were used to study the role of side-chain charges in the stability of the observed alpha-helix. Two dielectric functions, distance-dependent and constant, are considered to study the effects of solvent contributions. The results are found to be in accord with the implications of CD and NMR experiments of C-peptide where it was found that this peptide has high alpha-helix content in aqueous solution and that the removal of the side-chain charge of Glu-9(-) enhances helix formation. The lowest-energy conformation obtained by our simulations has an alpha-helix from Ala-4 to Gln-ll in complete agreement with the corresponding structure deduced from an X-ray crystallography experiment of ribonuclease A. The salt bridge between the side chains of Glu-2(-) and Arg-10(+), which is known to exist from both NMR and X-ray experiments, is formed only when the side chains are properly charged. Its formation is greatly enhanced when the solvation effects are taken into account.