Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions
Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions
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DOI：
10.1039/c0ob00691b
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发表时间：
2011-01-01
影响因子：
3.2
通讯作者：
Mulholland, Adrian J.
中科院分区：
文献类型：
--
作者：
Claeyssens, Frederik;Ranaghan, Kara E.;Mulholland, Adrian J.
Chorismate是目前关于生物催化剂基本特征的争论的中心。最近的一些研究提出，在这种酶的催化不涉及过渡态（TS）的稳定，而是主要是由于形成的反应性构象的底物。为了理解催化的起源，有必要比较不同环境中的等效反应。在水溶液中，分支酸盐催化的分支酸盐到预苯酸盐的周环转化也发生（慢得多）。在这项研究中，我们通过比较多个量子力学/分子力学（QM/MM）反应途径，在一个可靠的，经过充分测试的理论水平（B3 LYP/6- 31 G（d）/CHARMM 27）的反应（i）在枯草芽孢杆菌分支酸盐（BsCM）和（ii）在水溶剂中的催化的起源。计算得到的反应（势能）势垒在酶中为11.3 kcal mol（-1），在水中为17.4 kcal mol（-1），这两个结果与实验结果吻合得很好。两组反应途径的比较表明，由于酶中底物的不稳定或应变，反应在酶中遵循与在溶液中略有不同的反应途径。酶内的底物应变能在整个反应过程中保持恒定。没有独特的反应性构象的底物共同的两种环境中，和过渡态结构也是不同的酶和水中。在每种环境中的势垒高度的分析表明TS稳定和势垒高度之间有明确的相关性。该酶的平均微分TS稳定性为7.3 kcal mol（-1）。这显著高于少量TS在水中的稳定性（相对于底物，平均仅1.0 kcal mol（-1））。TS主要通过与酶中活性位点残基的静电相互作用来稳定，Arg 90、Arg 7和Glu 78通常是最重要的。构象效应（e. G.酶中底物的应变）对酶中观察到的较低屏障没有显著贡献。结果表明，催化作用主要是由于酶更好的TS稳定性。
Chorismate mutase is at the centre of current controversy about fundamental features of biological catalysts. Some recent studies have proposed that catalysis in this enzyme does not involve transition state (TS) stabilization but instead is due largely to the formation of a reactive conformation of the substrate. To understand the origins of catalysis, it is necessary to compare equivalent reactions in different environments. The pericyclic conversion of chorismate to prephenate catalysed by chorismate mutase also occurs (much more slowly) in aqueous solution. In this study we analyse the origins of catalysis by comparison of multiple quantum mechanics/molecular mechanics (QM/MM) reaction pathways at a reliable, well tested level of theory (B3LYP/6-31G(d)/CHARMM27) for the reaction (i) in Bacillus subtilis chorismate mutase (BsCM) and (ii) in aqueous solvent. The average calculated reaction (potential energy) barriers are 11.3 kcal mol(-1) in the enzyme and 17.4 kcal mol(-1) in water, both of which are in good agreement with experiment. Comparison of the two sets of reaction pathways shows that the reaction follows a slightly different reaction pathway in the enzyme than in it does in solution, because of a destabilization, or strain, of the substrate in the enzyme. The substrate strain energy within the enzyme remains constant throughout the reaction. There is no unique reactive conformation of the substrate common to both environments, and the transition state structures are also different in the enzyme and in water. Analysis of the barrier heights in each environment shows a clear correlation between TS stabilization and the barrier height. The average differential TS stabilization is 7.3 kcal mol(-1) in the enzyme. This is significantly higher than the small amount of TS stabilization in water (on average only 1.0 kcal mol(-1) relative to the substrate). The TS is stabilized mainly by electrostatic interactions with active site residues in the enzyme, with Arg90, Arg7 and Glu78 generally the most important. Conformational effects (e. g. strain of the substrate in the enzyme) do not contribute significantly to the lower barrier observed in the enzyme. The results show that catalysis is mainly due to better TS stabilization by the enzyme.