Modeling and Engineering of Phosphotriesterase (PTE)

磷酸三酯酶 (PTE) 的建模和工程

• 批准号: 6948389
• 负责人: YIRONG MO
• 金额: $ 21.9万
• 依托单位: WESTERN MICHIGAN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-08-01 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6948389
• 关键词: biotechnology; catalyst; computational biology; computer simulation; environmental contamination; enzyme activity; enzyme mechanism; enzyme model; enzyme structure; enzyme substrate; esterase; molecular dynamics; organophosphorus insecticide; protein engineering; synthetic protein

DESCRIPTION (provided by applicant): Pesticides are extensively used to control the spread of insects or unwanted weeds. Among various pesticides, organophosporus pesticides are the largest individual group of pesticides, with more than 100 compounds being marketed. Their high effectiveness has resulted in the widespread use throughout the world. Exposure to organophosporus pesticides affects the central nervous system, the autonomic nervous system and peripheral muscular pathways, though the effects associated with these chemicals may be either immediate or delayed. To remove the pesticide residues in nature, enzymatic biodegradation has been recommended in terms of safety and economy. It has been found that an enzyme known as phosphotriesterase (PTE) which is isolated from naturally soil-dwelling bacterium, Pseudomonas diminuta and Flavobacterium sp, can catalyze the hydrolysis of paraoxon to p-nitrophenol and diethyl phosphate. However, PTE does not hydrolyze all the substrates at high rates. We intend to use computational tools to understand the enzymatic mechanism of PTE and further design PTE to enhance its activity towards specific organophosphates and increase its diversity to different organophosphates. Hybrid QM/MM molecular dynamics simulations will be conducted to evaluate the roles of residues in the catalytic pocket and understand the structural origin of the enzyme activity. Further, we plan to engineer the residues in the binding pockets which are computationally redesigned to enhance the reactivity of PTE. The knowledge gained through computational studies will ultimately provide guidelines for experimental tests.

描述（由申请人提供）：杀虫剂广泛用于控制昆虫或杂草的传播。在各种农药中，有机磷农药是最大的农药个体类别，已上市的化合物超过100种。它们的高效性已在全世界得到广泛使用。接触有机磷农药会影响中枢神经系统、自主神经系统和周围肌肉通路，尽管与这些化学物质相关的影响可能是立即的或延迟的。为了去除自然界中的农药残留，从安全性和经济性角度考虑，酶生物降解法已被推荐。人们发现，从天然土壤细菌、假单胞菌和黄杆菌中分离出的一种称为磷酸三酯酶（PTE）的酶可以催化对氧磷水解为对硝基苯酚和磷酸二乙酯。然而，PTE 不会以高速率水解所有底物。我们打算利用计算工具来了解PTE的酶促机制，并进一步设计PTE以增强其对特定有机磷酸酯的活性并增加其对不同有机磷酸酯的多样性。将进行混合 QM/MM 分子动力学模拟，以评估催化袋中残基的作用并了解酶活性的结构起源。此外，我们计划对结合袋中的残基进行改造，并通过计算重新设计以增强 PTE 的反应性。通过计算研究获得的知识最终将为实验测试提供指导。

项目成果

Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesterase.

• DOI: 10.1002/jcc.21238
• 发表时间: 2009-11-30
• 期刊: JOURNAL OF COMPUTATIONAL CHEMISTRY
• 影响因子: 3
• 作者: Zhang, Xin;Wu, Ruibo;Song, Lingchun;Lin, Yuchun;Lin, Menghai;Cao, Zexing;Wu, Wei;Mo, Yirong
• 通讯作者: Mo, Yirong

Functional role of Asp160 and the deprotonation mechanism of ammonium in the Escherichia coli ammonia channel protein AmtB.

• DOI: 10.1021/jp810651m
• 发表时间: 2009-04-09
• 期刊: The journal of physical chemistry. B
• 作者: Lin Y;Cao Z;Mo Y
• 通讯作者: Mo Y