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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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Submitted on : Monday, May 18, 2009 - 9:07:37 AM
Last modification on : Friday, April 3, 2020 - 1:12:23 AM
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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, EDP Sciences, 2009, 51 (1), pp.15-23. ⟨10.1140/epjd/e2008-00096-0⟩. ⟨inserm-00320828⟩

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