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Journal Articles The European Physical Journal D : Atomic, molecular, optical and plasma physics Year : 2009

Transitions between secondary structures in isolated polyalanines

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 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.
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Dates and versions

inserm-00320828 , version 1 (18-05-2009)

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Florent Calvo, Pierre Poulain. Transitions between secondary structures in isolated polyalanines. The European Physical Journal D : Atomic, molecular, optical and plasma physics, 2009, 51 (1), pp.15-23. ⟨10.1140/epjd/e2008-00096-0⟩. ⟨inserm-00320828⟩
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