Ytreberg F Marty, Zuckerman Daniel M
Department of Computational Biology and the Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, 200 Lothrop Street, Pittsburgh, Pennsylvania 15261, USA.
J Phys Chem B. 2005 May 12;109(18):9096-103. doi: 10.1021/jp0510692.
We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dissimilar conformational states. Our results elucidate the contrasting roles of entropy in implicitly solvated leucine dipeptide and decaglycine. The method extends earlier work by Voter and overcomes the notorious "overlap" problem in free energy computations by constructing a mathematically equivalent calculation with high conformational similarity. The approach requires only equilibrium simulations of the two states of interest, without the need for sampling transition states. We discuss possible extensions and optimizations of the approach.
