Molecular Dynamics of a 15-Residue Poly(l-alanine) in Water: Helix Formation and Energetics

Abstract

We present a molecular dynamics study of the α-helix formation in a system consisting of a 15-residue poly(l-alanine) and surrounding water molecules. By applying a relatively high temperature, we observed the α-helix formation several times during a 17-ns run, and reversible helix−coil transitions were also observed. The α-helix formations were usually initiated by the β-turn structures. A crank-shaft-like motion of the peptide was included in the folding process. In the formed α-helical domains, substantial 310-helix formations were found especially at the termini, as observed by the NMR study. The folding time scale at room temperature estimated from our simulation was found to lie in the range of 100 ns, which is in accord with the time scale of the T-jump experiments. The total energy of the whole system was lower in the α-helix state than in the random-coil state by 20.4 ± 4.8 kcal/mol, which is consistent with the experimental value obtained by calorimetry. This energy decrease in forming the α-hel...