Dynamics of a protein and water molecules surrounding the protein: Hydrogen-bonding between vibrating water molecules and a fluctuating protein

Internal and rigid‐body motions of bovine pancreatic trypsin inhibitor (BPTI) and of water molecules surrounding the BPTI are studied in a vicinity of an energy minimum using a normal mode analysis proposed as the independent molecule model. Water's rigid‐body motion is predominant in comparison to its internal motions. We have derived information about the relationship between the magnitude of a thermal ellipsoid of an H‐bonding atom and the anisotropy of its ellipsoid, and the relationship between the magnitude of the ellipsoid and the H‐bond strength. We see a relationship between vibrational frequencies (assuming rigid‐body motion of the water molecules) and the H‐bond strength of the water taking part in this H‐bonding. Analyzing the H‐bond strength, we found that a hydrogen in water is likely to H‐bond to oxygen in the protein, whereas an oxygen in water has a less strong preference to H‐bond to the protein. For water molecules acting as the hydrogen acceptor, strong H‐bonding has longer lifetimes than weak H‐bonding. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 402–413, 2002