EDP Sciences, European Physical Journal D, 1(51), p. 15-23
Monte Carlo simulations of gas-phase polyalanine peptides have been carried out with the Amber ff96 force field. A low-temperature structural transition takes place between the α-helix stable conformation and β-sheet structures, followed by the unfolding phase change. The transition state ensembles connect- ing the helix and sheet conformations are investigated by sampling the energy landscape along specific geometric order parameters as putative reaction coordinates, namely the electric dipole μ, the end-to-end distance d, and the gyration radius Rg . By performing series of shooting trajectories, the committor prob- abilities and their distributions are obtained, revealing that only the electric dipole provides a satisfactory transition coordinate for the α ↔ β interconversion. The nucleus at the transition is found to have a high helical content.