HYDROPHILICITY OF CAVITIES IN PROTEINS. Jan Hermans, Li Zhang, Christopher VanDeusen, Xinfu Xia and Jan Hermans, Department of Biochemistry and Biophysics University of North Carolina Chapel Hill, NC 27599-7260

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. The computations required to survey the atomic coordinates of a protein molecule in terms of low-energy water positions are rapid. A proper assessment of hydration should be based on free energy, not energy; however, much lengthier dynamics simulations are required to obtain free energies of transfer of water molecules into interior sites. These methods are most direct when applied to cavities able to hold a single water molecule. A simple consistent picture of the energetics of isolated buried water molecules has emerged from this study. A threshold value of the water-protein interaction energy at -12 kcal/mol was found to be able to distinguish hydrated from empty cavities. This is nearly the same value as the energy of ice, and, since the threshold must correspond to a free energy of zero, it follows that buried waters in proteins have entropy comparable to that of ice. The results of this study have enabled us to address the reliability of buried waters assigned in experiments. We have extended this work to two instances of cavities large enough to contain several water molecules. In one case (uteroglobin; 1UTG), the computed energetics support the presence of 8 water molecules, where the x-ray structure reports 12 sites, some of them rather weak. In the other case, interleukin-1beta, the computed energies and free energies of transferring one or two water molecules into the cavity are insufficiently low, and this suggests that the cavity is not hydrated, as reported in crystallographic studies, and at odds with a report based on nmr experiments that the cavity is hydrated.

The program and instructions for rapidly locating possible water interior water positions and discriminating between these on the basis of the energy of transfer are available from the authors (request DOWSER program from xia@femto.med.unc.edu).