Eur. Phys. J. D 51, 15-23 (2009)
https://doi.org/10.1140/epjd/e2008-00096-0

Transitions between secondary structures in isolated polyalanines

¹ Université Claude Bernard Lyon 1 and CNRS, LASIM, Bât. A. Kastler, 43 bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
² EBGM, Inserm UMR-S 726, Université Paris Diderot - Paris 7, 2 place Jussieu, Case 7113, 75251 Paris Cedex 05, France

Corresponding author: ^a fcalvo@lasim.univ-lyon1.fr

Received: 20 December 2007
Revised: 7 April 2008
Published online: 16 May 2008

Abstract

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 connecting 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 R_g. By performing series of shooting trajectories, the committor probabilities 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.