MC-PHS: A Monte Carlo implementation of the primary hydration shell for protein
Abstract:
A primary hydration shell (PHS) approach is developed for Monte Carlo simulations of
conformationally rich macromolecular systems in an environment that efficiently
captures principal solvation effects. It has been previously demonstrated that molecular
dynamics using PHS is an efficient method to study peptide structure and dynamics in
aqueous solution. Here, we extend the PHS approach to Monte Carlo simulations,
whereby a stable shell of water molecules is maintained with a flexible, non-spherical,
half-harmonic potential, tuned to maintain a constant restraining energy, with the
difference between the restraint and shell energies used to dynamically adjust the shell
radius. Examination of the shell and system size dependence of the restraining potential
reveals its robustness. Moreover, its suitability for biomolecular simulations is evaluated
using small spheres of water, hydration properties of small biological molecules, and
configurational sampling of a b-hairpin pentapeptide YPGDV.
This method, termed MCPHS,
appears to provide efficient representation of dominant solvation effects and should
prove useful in the study of protein folding and design.