Bhat Nayana, Nutho Bodee, Hanpaibool Chonnikan, Hadsadee Sarinya, Vangnai Alisa, Rungrotmongkol Thanyada
Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok, Thailand.
Proteins. 2024 Jan;92(1):96-105. doi: 10.1002/prot.26579. Epub 2023 Aug 30.
Methyl parathion hydrolase (MPH) is an enzyme of the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphates (OPs). Recently, MPH has attracted attention as a promising enzymatic bioremediator. The crystal structure of MPH enzyme shows a dimeric form, with each subunit containing a binuclear metal ion center. MPH also demonstrates metal ion-dependent selectivity patterns. The origins of these patterns remain unclear but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. We aimed to investigate and compare the binding of different OP pesticides to MPH with cobalt(II) metal ions. In this study, MPH was modeled from Ochrobactrum sp. with different OP pesticides bound, including methyl paraoxon and dichlorvos and profenofos. The docked structures for each substrate optimized by DFT calculation were selected and subjected to atomistic molecular dynamics simulations for 500 ns. It was found that alpha metal ions did not coordinate with all the pesticides. Rather, the pesticides coordinated with less buried beta metal ions. It was also observed that the coordination of beta metal ions was perturbed to accommodate the pesticides. The binding free energy calculations and structure-based pharmacophore model revealed that all the three substrates could bind well at the active site. However, profenofos exhibit a stronger binding affinity to MPH in comparison to the other two substrates. Therefore, our findings provide molecular insight on the binding of different OP pesticides which could help us design the enzyme for OP pesticides degradation.
甲基对硫磷水解酶（MPH）是金属β-内酰胺酶超家族的一种酶，可水解多种有机磷酸酯（OPs）。最近，MPH作为一种有前景的酶促生物修复剂受到了关注。MPH酶的晶体结构呈二聚体形式，每个亚基包含一个双核金属离子中心。MPH还表现出金属离子依赖性的选择性模式。这些模式的起源尚不清楚，但与关于金属离子在酶超家族功能进化和分化中更普遍作用的开放性问题有关。我们旨在研究和比较不同OP农药与含钴（II）金属离子的MPH的结合情况。在本研究中，构建了来自苍白杆菌属的MPH与不同OP农药结合的模型，这些农药包括甲基对氧磷、敌敌畏和丙溴磷。选择通过密度泛函理论（DFT）计算优化的每种底物的对接结构，并进行500纳秒的原子分子动力学模拟。发现α金属离子并非与所有农药配位。相反，农药与埋藏较浅的β金属离子配位。还观察到β金属离子的配位受到扰动以容纳农药。结合自由能计算和基于结构的药效团模型表明，所有三种底物都能在活性位点良好结合。然而，与其他两种底物相比，丙溴磷对MPH表现出更强的结合亲和力。因此，我们的研究结果为不同OP农药的结合提供了分子层面的见解，这有助于我们设计用于降解OP农药的酶。
