MC-PHS: a Monte Carlo implementation of the primary hydration shell for protein folding and design.
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, nonspherical, 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 beta-hairpin pentapeptide YPGDV. This method, termed MC-PHS, appears to provide efficient representation of dominant solvation effects and should prove useful in the study of protein folding and design.
Kentsis
Alex
A
Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029, USA.
Mezei
Mihaly
M
Osman
Roman
R
D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D046911:Macromolecular Substances; D008958:Models, Molecular; D008970:Molecular Weight; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012996:Solutions / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D014867:Water / Q000737:chemistry*
D000596:Amino Acids; D046911:Macromolecular Substances; D009842:Oligopeptides; D011506:Proteins; D012996:Solutions; D012997:Solvents; D014867:Water