Resat H, Marrone T J, McCammon J A
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA.
Biophys J. 1997 Feb;72(2 Pt 1):522-32. doi: 10.1016/s0006-3495(97)78692-2.
Studying the thermodynamics of biochemical association reactions at the microscopic level requires efficient sampling of the configurations of the reactants and solvent as a function of the reaction pathways. In most cases, the associating ligand and receptor have complementary interlocking shapes. Upon association, loosely connected or disconnected solvent cavities at and around the binding site are formed. Disconnected solvent regions lead to severe statistical sampling problems when simulations are performed with explicit solvent. It was recently proposed that, when such limitations are encountered, they might be overcome by the use of the grand canonical ensemble. Here we investigate one such case and report the association free energy profile (potential of mean force) between trypsin and benzamidine along a chosen reaction coordinate as calculated using the grand canonical Monte Carlo method. The free energy profile is also calculated for a continuum solvent model using the Poisson equation, and the results are compared to the explicit water simulations. The comparison shows that the continuum solvent approach is surprisingly successful in reproducing the explicit solvent simulation results. The Monte Carlo results are analyzed in detail with respect to solvation structure. In the binding site channel there are waters bridging the carbonyl oxygen groups of Asp189 with the NH2 groups of benzamidine, which are displaced upon inhibitor binding. A similar solvent-bridging configuration has been seen in the crystal structure of trypsin complexed with bovine pancreatic trypsin inhibitor. The predicted locations of other internal waters are in very good agreement with the positions found in the crystal structures, which supports the accuracy of the simulations.
在微观层面研究生化缔合反应的热力学，需要根据反应路径对反应物和溶剂的构型进行高效采样。在大多数情况下，缔合配体和受体具有互补的互锁形状。缔合时，在结合位点及其周围会形成松散连接或断开的溶剂腔。当使用显式溶剂进行模拟时，断开的溶剂区域会导致严重的统计采样问题。最近有人提出，当遇到此类限制时，可以通过使用巨正则系综来克服。在此，我们研究了这样一个案例，并报告了使用巨正则蒙特卡罗方法计算得到的胰蛋白酶和苯甲脒之间沿选定反应坐标的缔合自由能分布（平均力势）。还使用泊松方程为连续介质溶剂模型计算了自由能分布，并将结果与显式水模拟进行了比较。比较结果表明，连续介质溶剂方法在重现显式溶剂模拟结果方面出奇地成功。我们对蒙特卡罗结果的溶剂化结构进行了详细分析。在结合位点通道中，有水分子桥接天冬氨酸189的羰基氧基团和苯甲脒的氨基，这些水分子在抑制剂结合时会被取代。在与牛胰蛋白酶抑制剂复合的胰蛋白酶晶体结构中也观察到了类似的溶剂桥接构型。预测的其他内部水分子位置与晶体结构中发现的位置非常吻合，这支持了模拟的准确性。
