Solvation in simulated annealing and high-temperature molecular dynamics of proteins: A restrained water droplet model

The use of explicit water molecules in simulations of protein systems in so lution at high temperatures (e.g., in simulated annealing protocols) is com plicated by the temperature-dependent changes in the physical properties of water. We propose a new protocol for such simulations based on a solvation model in which a spherical harmonic restraint is applied to a water shell surrounding the primary solvent sphere containing the polypeptide. The perf ormance of different force constants, applied in water shells of different widths, was tested in simulations at temperatures ranging from 300 to 500 K . The best results were obtained when small force constants (0.0007-0.002 k cal/mol Angstrom(2)) were applied to 5-Angstrom water shells surrounding th e primary water sphere constructed to accommodate the solute and water at t he appropriate density. With an atom-based 14-Angstrom cut-off this solvati on model reproduces structural and dynamic properties of water in the range of temperatures tested here. Thus, the internal pressure is very well main tained during cooling in simulated annealing protocols, and the small force constants eliminate the potential artifacts of the surface effects and pre vent the water molecules from evaporating in simulations at high temperatur e. The restrained water droplet model described here is computationally mor e economical than periodic boundary conditions (PBC) and is preferable to t he PBC method in which the size of the box has to be adjusted to maintain t he experimental density if simulations are performed at different temperatu res. Its application is illustrated in the study of the extracellular domai n of the receptor protein for the gonadotropin releasing hormone (GnRH). Th is receptor belongs to the family of seven transmembrane domain proteins in volved in signal transduction from the extracellular environment into the c ell. The extracellular loops (ECLs) connecting the seven transmembrane (TM) domains are exposed to aqueous solvent and play a key role in binding GnRH to its receptor. The solvation model was used in a successful simulated an nealing protocol that explored the conformational space of the interacting ECLs. We show that the resulting secondary structure of ECL 3 is supported by experimental data and depends on hydrophobic interactions that appear on ly in an appropriate representation of the solvent but cannot be obtained f rom the commonly used simulations in vacuum with the solvent modeled solely through a dielectric constant. (C) 2000 John Wiley & Sons, Inc.