Journal of the American Chemical Society
An algorithm for the systematic solvation of proteins based on the directionality of hydrogen bondsAuthors: Angelo Vedani and David W. Huhta
Journal: Journal of the American Chemical Society
Departments of Chemistry and Biochemistry, University of Kansas, Lawrence, Kansas, U.S.A.
The development of an algorithm for the systematic solvation of proteins based on the directionality of H-bonds is presented. By analyzing the distribution and environment of H-bond donors and acceptors of a protein, positions for both internal and surface water molecules are identified. The algorithm was incorporated into the program AUTOSOL which is part of the molecular mechanics software Yeti. The program was tested by reproducing experimental solvent found in the high-resolution protein crystal structures of trypsin, elastase, thermolysin, glutathione reductase, and subtilisin. Based on these five proteins, AUTOSOL is able to reproduce an average of 70% of the crystallographic solvent within 1.5 Å (half the length of a H-bond) from the experimental position. Internal protein-bound water molecules are reproduced at the 92% level.