Internal dynamics of a globular protein in water

Abstract

The frequency distributions of internal dynamics of a protein are calculated in solution using normal mode analysis. Our test case is bovine pancreatic trypsin inhibitor, consisting of 58 amino acid residues. Each water molecule surrounding the protein is treated as an internally rigid body that can move with the vibrating protein. The water molecules are redistributed around the protein, as dictated by the potential energy. It is shown that water molecules around the protein are essential for the protein to keep its tertiary structure close to the X-ray structure. The density of states calculated in this model is shifted toward high frequencies when compared with results previously obtained with a model in which the water molecules were not allowed to move with the protein. This shift toward high-frequency states originates from the stronger interactions of water molecules with the sidechain atoms in the protein. The present model is computationally demanding. So the previous (frozen water) model is suggested to be a reasonable approximation for expressing internal dynamics of a protein in solution. © 1996 by John Wiley & Sons, Inc.