AUTHORS: Li Zhang and Jan Hermans
REFERENCE: Proteins: Structure, Function and Genetics 24: 433-438, 1996.
Department of Biochemistry and
Water molecules inside cavities in proteins constitute integral parts of the structure. We have sought a quantitative measure of the hydrophilicity of the cavities by calculating energies and free energies of introducing a water molecule into these cavities. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. It follows that buried waters have entropy comparable to that of liquid water or ice. A simple consistent picture of the energetics of the buried waters provided by this study enabled us to address the reliability of buried waters assigned in experiments.
See elsewhere for a description of the DOWSER program, which is based on this paper, and which implements a search for cavities inside a protein and an assessment of their hydrophilicity, given a set of coordinates.