Theoretical modeling of enzyme catalytic power: Analysis of "cratic" and electrostatic factors in catechol O-methyltransferase
Theoretical modeling of enzyme catalytic power: Analysis of "cratic" and electrostatic factors in catechol O-methyltransferase
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DOI：
10.1021/ja0299497
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发表时间：
2003-06-25
影响因子：
15
通讯作者：
Williams, IH
中科院分区：
文献类型：
--
作者：
Roca, M;Martí, S;Williams, IH
采用统计模拟和内能最小化两种混合QM/MM技术，对水溶液中邻苯二酚O-甲基转移酶(COMT)催化的双分子反应进行了比较理论研究。与其他工作人员以前的研究不同，我们定位并表征了酶活性部位、水中和真空中反应的过渡结构，我们的平均作用力计算潜力是基于从凝聚介质中的势能面特征获得的反应坐标，而不是从气相。用AM1/CHARMM方法计算的S-腺苷甲硫氨酸与邻苯二酚反应的自由能为15kcal mol(-1)，降低了300K下三甲基硫正离子与邻苯二酚阴离子反应的AM1/TIP3P自由能垒，与已有的估算结果一致.在水中的非催化模型反应中，反应物的热力学优先形式是溶剂分离离子对(SSIP)。将SSIP转化为接触离子对，其结构类似于COMT活性中心反应的米氏络合物(MC)，不利于7kcal摩尔(-1)，这主要是由于溶剂的重组。我们考虑了其他方法来估计所谓的“临界”自由能，以使反应物物种沿着正确的方向反应，但我们得出的结论是，通过简单的标准态修正通过分子动力学模拟直接估计缔合自由能可能是最好的方法。后一种修正允许这样一个事实，即周期性边界模拟所采用的晶胞大小并不对应于1M的标准状态浓度。考虑MC类物种允许将催化效应分解为预组织和重组阶段。在前组织阶段，底物在水中或在酶活性部位被聚集成类似MC的物种。在重组阶段，可以直接比较酶环境和水环境的作用，因为底物的重组在两种情况下几乎是相同的。沿反应坐标的电场分析表明，在水中，TS相对于类MC物种是不稳定的，这是因为溶质的极性减小，从而导致反应场也减小。在酶中，电场主要是一个恒定的电场，因此只有很小的环境重组。因此，TS的失稳程度低于溶液，活化势垒较小。
A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.