Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study,Journal of Chemical Information and Modeling

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Molecular Basis of the Substrate Specificity of Phosphotriesterase from Pseudomonas diminuta: A Combined QM/MM MD and Electron Density Study
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2024-09-10 , DOI: 10.1021/acs.jcim.4c00425
Tatiana I Mulashkina _{1,

2} , Anna M Kulakova _{1,

2} , Maria G Khrenova _{1,

2,

3}

Affiliation

The occurrence of organophosphorus compounds, pesticides, and flame-retardants in wastes is an emerging ecological problem. Bacterial phosphotriesterases are capable of hydrolyzing some of them. We utilize modern molecular modeling tools to study the hydrolysis mechanism of organophosphorus compounds with good and poor leaving groups by phosphotriesterase from Pseudomonas diminuta (Pd-PTE). We compute Gibbs energy profiles for enzymes with different cations in the active site: native Zn²⁺cations and Co²⁺cations, which increase the steady-state rate constant. Hydrolysis occurs in two elementary steps via an associative mechanism and formation of the pentacoordinated intermediate. The first step, a nucleophilic attack, occurs with a low energy barrier independently of the substrate. The second step has a low energy barrier and considerable stabilization of products for substrates with good leaving groups. For substrates with poor leaving groups, the reaction products are destabilized relative to the ES complex that suppresses the reaction. The reaction proceeds with low energy barriers for substrates with good leaving groups with both Zn²⁺and Co²⁺cations in the active site; thus, the product release is likely to be a limiting step. Electron density and geometry analysis of the QM/MM MD trajectories of the intermediate states with all considered compounds allow us to discriminate substrates by their ability to be hydrolyzed by the Pd-PTE. For hydrolyzable substrates, the cleaving bond between a phosphorus atom and a leaving group is elongated, and electron density depletion is observed on the Laplacian of electron density maps.

中文翻译：

假单胞菌磷酸三酯酶底物特异性的分子基础：QM/MM MD 和电子密度联合研究

废物中有机磷化合物、农药和阻燃剂的出现是一个新出现的生态问题。细菌磷酸三酯酶能够水解其中一些。我们利用现代分子建模工具研究了假单胞菌磷酸三酯酶（Pd-PTE）对具有良好和不良离去基团的有机磷化合物的水解机制。我们计算了活性位点具有不同阳离子的酶的吉布斯能量分布：天然 Zn ²⁺阳离子和 Co ²⁺阳离子，这增加了稳态速率常数。水解通过缔合机制分两个基本步骤发生并形成五配位中间体。第一步是亲核攻击，在低能垒下发生，与基材无关。对于具有良好离去基团的底物，第二步具有低能垒和相当稳定的产物。对于离去基团较差的底物，反应产物相对于抑制反应的 ES 复合物来说不稳定。对于具有良好离去基团且活性位点同时具有 Zn ²⁺和 Co ²⁺阳离子的底物，反应以低能垒进行；因此，产品发布可能是一个限制步骤。对所有考虑的化合物的中间态 QM/MM MD 轨迹的电子密度和几何分析使我们能够通过 Pd-PTE 水解的能力来区分底物。对于可水解底物，磷原子和离去基团之间的裂解键被拉长，并且在电子密度拉普拉斯图上观察到电子密度耗尽。

更新日期：2024-09-10

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