Wade R C
Laboratory of Molecular Biophysics, University of Oxford, U.K.
J Comput Aided Mol Des. 1990 Jun;4(2):199-204. doi: 10.1007/BF00125318.
Energetically favorable water binding sites in the substrate pocket of cytochrome P450-cam have been predicted by a molecular mechanics method. Binding sites corresponding to all the experimentally observed water sites in this region of the enzyme were located. The calculations also indicate the presence of two further water binding sites. One of these is located in a hydrophobic region of the protein where a water molecule would not bind tightly to the substrate-free enzyme. However, in the substrate-bound enzyme, a water molecule in this region could donate a hydrogen bond of optimum geometry to the carbonyl oxygen atom of the camphor substrate and could therefore contribute to the correct positioning of the camphor substrate for 5-exo-hydroxylation. These calculations also suggest that a steric analogue of camphor, containing an alkyl group which could prevent a water molecule from binding in this region, might inhibit cytochrome P450-cam by forming a more stable enzyme-ligand complex than camphor itself.
通过分子力学方法预测了细胞色素P450-cam底物口袋中能量有利的水结合位点。找到了与该酶这一区域所有实验观察到的水位点相对应的结合位点。计算还表明存在另外两个水结合位点。其中一个位于蛋白质的疏水区域，在无底物的酶中，水分子不会紧密结合在该区域。然而，在结合底物的酶中，该区域的水分子可以向樟脑底物的羰基氧原子提供具有最佳几何结构的氢键，因此有助于樟脑底物正确定位以进行5-外向羟基化。这些计算还表明，樟脑的一种空间类似物，含有一个可以阻止水分子在该区域结合的烷基，可能通过形成比樟脑本身更稳定的酶-配体复合物来抑制细胞色素P450-cam。
