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Protein Science, Vol 3, Issue 8 1224-1235, Copyright © 1994 by Cold Spring Harbor Laboratory Press

ARTICLE

Buried waters and internal cavities in monomeric proteins

M. A. WILLIAMS, J. M. GOODFELLOW and J. M. THORNTON
Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom Laboratory of Molecular Biology, Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom

We have analyzed the buried water molecules and internal cavities in a set of 75 high-resolution, nonhomologous, monomeric protein structures. The number of hydrogen bonds formed between each water molecule and the protein varies from 0 to 4, with 3 being most common. Nearly half of the water molecules are found in pairs or larger clusters. Approximately 90% are shown to be associated with large cavities within the protein, as determined by a novel program, PRO_ACT. The total volume of a protein's large cavities is proportional to its molecular weight and is not dependent on structural class. The largest cavities in proteins are generally elongated rather than globular. There are many more empty cavities than hydrated cavities. The likelihood of a cavity being occupied by a water molecule increases with cavity size and the number of available hydrogen bond partners, with each additional partner typically stabilizing the occupied state by 0.6 kcal/mol.
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