Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation
Mobility of the active site bound paraoxon and sarin in zinc-phosphotriesterase by molecular dynamics simulation and quantum chemical calculation
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DOI：
10.1021/ja000439r
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发表时间：
2001-02-07
影响因子：
15
通讯作者：
Ornstein, RL
中科院分区：
文献类型：
--
作者：
Koca, J;Zhan, CG;Ornstein, RL
磷酸三酯酶 (PTE) 与各种络合金属的动力学数据清楚地表明，磷酸三酯和硫代磷酸三酯底物的 P=O 和 P=S 键分别被活性位点络合金属离子之一或两者强烈极化。然而，这一观察结果与活性位点结合底物类似物 4-甲基苄基膦酸二乙酯的锌取代 PTE 的三维 X 射线晶体结构不一致。在该结构中，磷酰氧和最近的锌之间的距离为 3.4 埃，这个距离太大而无法承受强极化。在本文中，通过进行分子动力学（MD）模拟和量子力学计算，研究了各种PTE活性位点-基质复合物的几何结构和迁移率，考虑了两种已知的基质，对氧磷和沙林，尽管它们的周转率相差约100倍，结果表明PTE与任一基质形成复合物，其中磷酰氧与埋藏较少的锌强配位 原子。结果表明，当蛋白质浸入水浴中并通过 MD 松弛时，活性位点的几何形状发生了变化。最显着的构象变化是在预期离去基团位置的口袋中打开了网关。对于纯酶以及酶/底物复合物观察到开口，其范围为 11 至 18 埃。还表明，底物取代基位于其中的口袋表现出不同的灵活性，并通过协调的构象调整与底物相互作用。
The kinetic data published on phosphotriesterase (PTE), with various complexed metals, clearly indicates that the P=O and P=S bonds of phosphotriester and thiophosphotriester substrates, respectively, are strongly polarized by one or both of the active site complexed metal ions. However, this observation is not consistent with the three-dimensional X-ray crystal structure of zinc-substituted PTE with active site bound substrate analogue diethyl 4-methylbenzylphosphonate. In this structure, the distance between the phosphoryl oxygen and the nearest zinc is 3.4 Angstrom, a distance too large to afford strong polarization. In the present paper, the geometry and mobility of various PTE active site-substrate complexes are examined by performing both molecular dynamics (MD) simulations and quantum mechanical calculations, Two known substrates are considered, paraoxon and sarin, although their turnover rates vary about 100-fold, The results indicate that PTE forms a complex with either substrate in which the phosphoryl oxygen becomes strongly coordinated with the less buried zinc atom. It is shown that the geometry of the active site is changed when the protein is immersed in a water bath and relaxed by MD. The most substantial conformational change is the opening of the gateway in a pocket where the location of the leaving group is expected. The opening is observed for the pure enzyme as well as for the enzyme/substrate complexes and it ranges from 11 to 18 Angstrom. It is also shown that the pockets, in which the substrate substituents are localized, exhibit different flexibility and interact with the substrate with coordinated conformational adjustments.