Origin of the catalytic power of acetylcholinesterase: Computer simulation studies
Origin of the catalytic power of acetylcholinesterase: Computer simulation studies
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DOI：
10.1021/ja972326m
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发表时间：
1998-01-14
影响因子：
15
通讯作者：
Warshel, A
中科院分区：
文献类型：
--
作者：
Fuxreiter, M;Warshel, A
采用分子模拟方法对乙酰胆碱酯酶（AChE）酰化反应的能量学进行了研究。这些包括通过使用经验价键（EVE）势面和全原子自由能微扰（FEP）方法的活化自由能的评价，以及通过使用半显微镜版本的蛋白质偶极Langevin偶极（PDLD/S）方法的酶的催化效果的估计。酶的作用的确定是基于使用可靠的实验信息，在水中的参考反应的能量学评估，然后使用稳健的模拟，从溶剂笼的蛋白质活性位点的反应系统的移动的效果的评估。由于水中的能量学不是通过第一原理方法来评估的，因此该过程减少了整体分析的误差范围。两种模拟方法和不同初始条件的使用提供了一种方法来评估计算的误差范围和相应结论的有效性。EVE和PDLD/S方法均表明，相对于水中的相应参考反应，酶将酰化步骤的活化屏障降低了10-15 kcal/mol。这对应于（10（7）-10（11））倍速率加速，这与相应的实验估计很好地一致。酶的催化能力的起源似乎与过渡态的静电稳定有关。该静电效应可以被分类为带电中间体的能量的降低和重组能的降低的组合。不同的蛋白质残基的过渡态的稳定的贡献进行了估计。它表明，在一些建议相反，乙酰胆碱酯酶和其他酶不工作，提供一个疏水环境，而是一个极性环境。这项工作的结论是，最重要的催化作用与附近的残留物，而不是遥远的电离残留物。它还得出结论，酶已经进化首先优化的实际键断裂/键制作化学过程的速度，然后才微调的速度，通过优化的屏障扩散步骤。由于化学步骤的优化涉及超过10 kcal/mol，扩散步骤的优化涉及至多1或2 kcal/mol，看来扩散步骤的可能加速是二级效应。这些结论与现有的实验研究是一致的。
The energetics of the acylation step of AChE (acetylcholinesterase) is explored by using molecular simulation approaches. These include the evaluation of activation free energies by using the empirical valence bond (EVE) potential surface and an all-atom free energy perturbation (FEP) approach, as well as estimates of the catalytic effect of the enzyme by using the semimicroscopic version of the Protein Dipoles Langevin Dipoles (PDLD/S) method. The determination of the effect of the enzyme is based on the use of reliable experimental information in evaluating the energetics of the reference reaction in water and then on using robust simulations for the evaluation of the effect of moving the reacting system from a solvent cage to the protein active site. This procedure reduces the error range of the overall analysis since the energetics in water is not evaluated by a first principle approach. The use of two simulation methods and different initial conditions provide a way for assessing the error range of the calculations and the validity of the corresponding conclusions. Both the EVE and PDLD/S approaches show that the enzyme reduces the activation barrier of the acylation step by 10-15 kcal/mol relative to the corresponding reference reaction in water. This corresponds to a (10(7)-10(11))-fold rate acceleration, which is in good agreement with the corresponding experimental estimate. The origin of the catalytic power of the enzyme appears to be associated with electrostatic stabilization of the transition state. This electrostatic effect can be classified as a combination of reduction of the energy of the charged intermediate and reduction in the reorganization energy. The contributions of different protein residues to the stabilization of the transition state are estimated. It is demonstrated that, in contrast to some proposals, AChE and other enzymes do not work by providing a hydrophobic environment but rather a polar environment. This work concludes that the most important catalytic effects are associated with nearby residues rather than distant ionized residues. It is also concluded that the enzyme has evolved first to optimize the speed of the actual bond breaking/bond making chemical processes and only then to fine-tune the rate by optimizing the barrier for the diffusion step. Since the optimization of the chemical step involves more than 10 kcal/mol and the optimization of the diffusion step involves at most 1 or 2 kcal/mol, it appears that the possible acceleration of the diffusion step is a second-order effect. These conclusions are consistent with the available experimental studies.