QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.
QM/MM calculations of kinetic isotope effects in the chorismate mutase active site.
复制标题
分支酸变位酶活性位点的动力学同位素效应的 QM/MM 计算。
DOI：
10.1039/b210508j
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发表时间：
2003
影响因子：
3.2
通讯作者：
I. H. Williams
中科院分区：
文献类型：
--
作者：
S. Martí;V. Moliner;I. Tuñón;I. H. Williams
已经计算了水溶液中分支酸到预苯化物的克莱森重排以及枯草芽孢杆菌分支酸变位酶活性位点的动力学同位素效应。这些包括主要 13C 和 18O 以及次要 3H 效应，用于在成键和断键位置进行取代。使用 CAMVIB/CAMISO 程序计算同位素效应所需的势能面上假定驻点的初始结构是从使用 DYNAMO 程序的混合 QM/MM 分子动力学模拟中选择的。反应物复合物和过渡态结构的细化是通过使用 GRACE 程序的 AM1/CHARMM24/TIP3P 计算进行的，在酶模拟中对 > 5200 个原子的位置进行完全梯度弛豫，并使用包含 711 个水分子的盒子在水溶液中进行相应的反应。这些结果以及气相计算结果与实验数据的比较表明，化学重排在很大程度上决定了酶机制的速率。在建模的动力学方案中包含分支酸构象预平衡步骤可以使最近的实验数据和理论预测之间更好地吻合。这些结果提供了有关重要酶促转化的新信息，并阐明了影响其分子机制动力学的关键因素。通过大型且灵活的模型处理酶和/或溶剂环境对于预测动力学同位素效应是绝对必要的。
Kinetic isotope effects have been computed for the Claisen rearrangement of chorismate to prephenate in aqueous solution and in the active site of chorismate mutase from B. subtilus. These included primary 13C and 18O and secondary 3H effects for substitutions at the bond-making and bond-breaking positions. The initial structures of the putative stationary points on the potential energy surface, required for the calculations of isotope effects using the CAMVIB/CAMISO programs, have been selected from hybrid QM/MM molecular dynamical simulations using the DYNAMO program. Refinement of the reactant complex and transition-state structures has been carried out by means of AM1/CHARMM24/TIP3P calculations using the GRACE program, with full gradient relaxation of the position of > 5200 atoms for the enzymic simulations, and with a box containing 711 water molecules for the corresponding reaction in aqueous solution. Comparison of these results, and of gas phase calculations, with experimental data has shown that the chemical rearrangement is largely rate-determining for the enzyme mechanism. Inclusion of the chorismate conformational pre-equilibrium step in the modelled kinetic scheme leads to better agreement between recent experimental data and theoretical predictions. These results provide new information on an important enzymatic transformation, and the key factors responsible for the kinetics of its molecular mechanism are clarified. Treatment of the enzyme and/or solvent environment by means of a large and flexible model is absolutely essential for prediction of kinetic isotope effects.