Transitions between secondary structures in isolated polyalanines |
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Authors: | F Calvo and P Poulain |
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Institution: | (1) Université Claude Bernard Lyon 1 and CNRS, LASIM, Bat. 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 |
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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 Rg. 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. |
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Keywords: | PACS" target="_blank">PACS 64 60 Cn Order-disorder transformations statistical mechanics of model systems 02 70 Uu Applications of Monte Carlo methods 87 14 Ee Proteins |
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