期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 58, 期 4, 页码 893-904出版社
WILEY
DOI: 10.1002/prot.20347
关键词
hydration; solvent modeling; watermediated; hydrogen bonds; free-energy function; protein design; protein-protein interactions
Water-mediated hydrogen bonds play critical roles at protein-protein and protein-nucleic acid interfaces, and the interactions formed by discrete water molecules cannot be captured using continuum solvent models. We describe a simple model for the energetics of water-mediated hydrogen bonds, and show that, together with knowledge of the positions of buried water molecules observed in X-ray crystal structures, the model improves the prediction of free-energy changes upon mutation at protein-protein interfaces, and the recovery of native amino acid sequences in protein interface design calculations. We then describe a solvated rotamer approach to efficiently predict the positions of water molecules, at protein-protein interfaces and in monomeric proteins, that is compatible with widely used rotamer-based side-chain packing and protein design algorithms. Finally, we examine the extent to which the predicted water molecules can be used to improve prediction of amino acid identities and protein-protein interface stability, and discuss avenues for overcoming current limitations of the approach. (C) 2005 Wiley-Liss, Inc.
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