Molecular dynamics study of hydration of the protein interior

Molecular dynamics (MD) simulations were performed to study the patterns of hydration of cavities in the interior of staphylococcal nuclease (SN) and of the variants V66E and V66K. In these variants the polar groups of Glu and Lys are internal, and they affect the polarity and size of a small internal cavity. Internal water molecules were identified in the simulations based on their coordination state. They were characterized in terms of their residence times, average locations, dipole moment fluctuations, hydrogen bonding interactions, and interaction energies. The best agreement in the locations of MD and crystallographically determined water molecules was found for molecules that have residence times of several ns, and which display small mean square displacements in the MD simulations. In the simulations the hydrophobic cavity near Val-66 in the wild type contains a relatively disordered water molecule that has never been seen crystallographically. Consideration of the protein dynamics was found to be important when studying hydration in the protein interior: inside the protein the interaction energies of water molecules fluctuate less than in bulk water, giving rise to a favorable contribution to the chemical potential. The analysis of the MD trajectories revealed that the fluctuations in the protein structure (especially the loop elements) can strongly influence protein hydration by changing the patterns or strengths of hydrogen bonding interactions between water molecules and the protein, or by providing potential energy barriers for water penetration.