Williams M A, Goodfellow J M, Thornton J M
Department of Biochemistry and Molecular Biology, University College London, United Kingdom.
Protein Sci. 1994 Aug;3(8):1224-35. doi: 10.1002/pro.5560030808.
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.
我们分析了一组75个高分辨率、非同源单体蛋白质结构中的埋藏水分子和内部空洞。每个水分子与蛋白质形成的氢键数量从0到4不等，其中3个最为常见。近一半的水分子以成对或更大的簇状形式存在。通过一个名为PRO_ACT的新程序确定，大约90%的水分子与蛋白质内部的大空洞相关。蛋白质大空洞的总体积与其分子量成正比，且不依赖于结构类别。蛋白质中最大的空洞通常是细长的而非球状的。空洞中未被水合的空洞比有水合作用的空洞多得多。随着空洞大小和可用氢键伙伴数量的增加，空洞被水分子占据的可能性也会增加，每增加一个伙伴通常会使占据状态稳定0.6千卡/摩尔。
