Effective water model for Monte Carlo simulations of proteins.
We present an effective theory for water. Our goal is to formulate an accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self-interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvation energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the nonelectrostatic contributions with estimates of hydrophobic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations. We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydrogen-bonding terms.
Banks
J
J
Department of Biomedical Engineering, Boston University, MA 02215.
Brower
R C
RC
Ma
J
J
D008958:Models, Molecular; D008962:Models, Theoretical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water
D011506:Proteins; D014867:Water