Long-range electrostatic effects on peptide folding

Abstract

The reversible folding/unfolding of a short peptide in solution is studied by molecular dynamics simulations. The effects of long-range electrostatic interactions are examined and found to be important both for the equilibrium between folded and unfolded states and the dynamics of the folding process. The neglect of long-range electrostatics leads to an increased population of unfolded states and increased structural fluctuations. When such interactions are taken into account, the peptide unfolds and folds to the experimentally determined structure several times during a 25 ns trajectory, with approximately equal populations of folded and unfolded states in the neighborhood of its proposed melting temperature. The effect of using spherical boundary conditions rather than periodic ones does not appear to have any major effect on the folding dynamics.