Hydration and its hydrogen bonding state on a protein surface in the crystalline state as revealed by molecular dynamics simulation

Nakagawa, Hiroshi   ; Tamada, Taro*

Protein hydration is crucial for the stability and molecular recognition of a protein. Water molecules interact with a protein surface via hydrogen bonding. Here, we examined the hydration structure and hydrogen bonding state of a globular protein, staphylococcal nuclease, at various hydration levels in a crystalline state by all-atom molecular dynamics simulation. The hydrophobic residue surface was found to be more hydrated than the hydrophilic residue surface, but both were uniformly hydrated in response to increased water content. In addition, the hydrogen bonds in hydrated water have a tetrahedral structure, which is not much different from the structure of bulk water. The hydrogen bonding structure is compatible with the results of neutron crystallography. The simulations are useful for analyzing the hydration structure and hydrogen bonding state in the crystalline state, and will greatly assist in the further analysis of the information obtained from crystal structure analysis.