Kríz Zdenek, Otyepka Michal, Bártová Iveta, Koca Jaroslav
National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
Proteins. 2004 May 1;55(2):258-74. doi: 10.1002/prot.20026.
The interactions between the protein and the solvent were analyzed, and protein regions with a high density of water molecules, as well as structural water molecules, were determined by using molecular dynamics (MD) simulations. A number of water molecules that were in contact with the protein for the whole trajectory were determined. Their interaction energies and hydrogen bonds with protein residues were analyzed. Altogether, 39, 27, 49, and 32 water molecules bound to the protein were found for trajectories of the free CDK2, CDK2/ATP, CDK2/roscovitine, and CDK2/isopentenyladenine complexes, respectively. Positions of observed water molecules were compared with X-ray crystallography data. Special attention was paid to water molecules in the active site of the enzyme, and especially to the deep pocket, where the N9 roscovitine side-chain is buried. Exchange of active-site water molecules with bulk water through the tunnel from the pocket was observed. In the CDK2/isopentenyladenine complex simulation, two water molecules that arrange interaction between the inhibitor and the enzyme via an H-bond were observed. Two stable water molecules in the trajectory of the free CDK2 were found that occupy the same position as the nitrogens N3 and N9 of the isopentenyladenine or N1 and N6 nitrogens of the adenosine triphosphate (ATP). The positions of structural water molecules were compared with the positions of substrate polar groups and crystallographic water molecules found in the Brookhaven Protein Data Bank for various CDK2 complexes. It was concluded that tracing tightly bound water molecules may substantially help in designing new inhibitors.
分析了蛋白质与溶剂之间的相互作用，并通过分子动力学（MD）模拟确定了水分子密度高的蛋白质区域以及结构水分子。确定了在整个轨迹中与蛋白质接触的大量水分子。分析了它们与蛋白质残基的相互作用能和氢键。分别在游离CDK2、CDK2/ATP、CDK2/罗斯考维汀和CDK2/异戊烯基腺嘌呤复合物的轨迹中发现，与蛋白质结合的水分子总数分别为39、27、49和32个。将观察到的水分子位置与X射线晶体学数据进行了比较。特别关注了酶活性位点中的水分子，尤其是N9罗斯考维汀侧链所在的深口袋中的水分子。观察到活性位点水分子通过口袋中的通道与大量水进行交换。在CDK2/异戊烯基腺嘌呤复合物模拟中，观察到两个通过氢键在抑制剂和酶之间形成相互作用的水分子。在游离CDK2的轨迹中发现了两个稳定的水分子，它们占据的位置与异戊烯基腺嘌呤的N3和N9氮原子或三磷酸腺苷（ATP）的N1和N6氮原子相同。将结构水分子的位置与布鲁克海文蛋白质数据库中各种CDK2复合物中底物极性基团和晶体学水分子的位置进行了比较。得出的结论是，追踪紧密结合的水分子可能对设计新的抑制剂有很大帮助。
