Protein Hydration

A hydration shell surrounds proteins in solution. The structures of proteins at atomic resolution presently available in the Protein Data Bank (PDB) provide detailed information on the mode of hydration and plausible roles of water molecules in protein structure and function. This article presents an analysis of water structure in proteins determined at atomic resolution. Water molecules bind to proteins by making hydrogen bonds with oxygen and nitrogen atoms with oxygen as the preferred atom. The mean length of hydrogen bonds between oxygen and water is shorter than that of nitrogen and water. However, the mean thermal parameter of water molecules hydrogenbonded to oxygen atoms is higher than that of water molecules hydrogen-bonded to nitrogen atoms. Water molecules of the first hydration shell are stabilized by hydrogen bonding with protein atoms, while the stability of the second hydration shell is derived from hydrogen bonding with molecules of the first shell. The number of molecules in the second and higher shells is less than half of that of the first shell. As could be expected, the mean thermal parameter of molecules is higher in the second shell compared to that of the first shell. The number of water molecules buried in protein interfaces increases with increasing size of protein. In several proteins, water molecules form hydrogen-bonded networks that could cover a large part of the protein surface. Pentagonal and tetrahedral arrangements of hydrogen-bonded water molecules could be observed in several structures. Strongly bound water molecules with low thermal parameters appear to be essential for maintaining the loops in appropriate positions. Tightly bound water molecules are also found at the active site of some proteins. These molecules may play important roles in protein function.