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 solution at high temperatures (e.g., in simulated annealing protocols) is complicated 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 performance 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 kcal/mol Å 2 ) were applied to 5‐Å water shells surrounding the primary water sphere constructed to accommodate the solute and water at the appropriate density. With an atom‐based 14‐Å cut‐off this solvation model reproduces structural and dynamic properties of water in the range of temperatures tested here. Thus, the internal pressure is very well maintained during cooling in simulated annealing protocols, and the small force constants eliminate the potential artifacts of the surface effects and prevent the water molecules from evaporating in simulations at high temperature. The restrained water droplet model described here is computationally more economical than periodic boundary conditions (PBC) and is preferable to the PBC method in which the size of the box has to be adjusted to maintain the experimental density if simulations are performed at different temperatures. Its application is illustrated in the study of the extracellular domain of the receptor protein for the gonadotropin releasing hormone (GnRH). This receptor belongs to the family of seven transmembrane domain proteins involved in signal transduction from the extracellular environment into the cell. 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 annealing 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 only in an appropriate representation of the solvent but cannot be obtained from the commonly used simulations in vacuum with the solvent modeled solely through a dielectric constant. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 174–186, 2000