Woda J, Schneider B, Patel K, Mistry K, Berman H M
Department of Chemistry, Rutgers University, Piscataway, New Jersey 08854-8087, USA.
Biophys J. 1998 Nov;75(5):2170-7. doi: 10.1016/S0006-3495(98)77660-X.
Eleven protein-DNA crystal structures were analyzed to test the hypothesis that hydration sites predicted in the first hydration shell of DNA mark the positions where protein residues hydrogen-bond to DNA. For nine of those structures, protein atoms, which form hydrogen bonds to DNA bases, were found within 1.5 A of the predicted hydration positions in 86% of the interactions. The correspondence of the predicted hydration sites with the hydrogen-bonded protein side chains was significantly higher for bases inside the conserved DNA recognition sequences than outside those regions. In two CAP-DNA complexes, predicted base hydration sites correctly marked 71% (within 1.5 A) of protein atoms, which form hydrogen bonds to DNA bases. Phosphate hydration was compared to actual protein binding sites in one CAP-DNA complex with 78% marked contacts within 2.0 A. These data suggest that hydration sites mark the binding sites at protein-DNA interfaces.
分析了11个蛋白质-DNA晶体结构，以检验以下假设：在DNA的第一水化层中预测的水化位点标记了蛋白质残基与DNA形成氢键的位置。对于其中9个结构，在86%的相互作用中，与DNA碱基形成氢键的蛋白质原子位于预测水化位置的1.5埃范围内。保守DNA识别序列内的碱基与形成氢键的蛋白质侧链的预测水化位点的对应性明显高于这些区域之外的碱基。在两个CAP-DNA复合物中，预测的碱基水化位点正确标记了71%（在1.5埃范围内）与DNA碱基形成氢键的蛋白质原子。在一个CAP-DNA复合物中，将磷酸根水化与实际蛋白质结合位点进行比较，2.0埃范围内标记的接触点占78%。这些数据表明，水化位点标记了蛋白质-DNA界面处的结合位点。
