CAREER: Computation-Enabled Rational Design of Cytochrome P450 for Ionic Liquid Biodegradation

职业：用于离子液体生物降解的细胞色素 P450 的计算合理设计

• 批准号: 1845143
• 负责人: Jindal Shah
• 金额: $ 51.43万
• 依托单位: Oklahoma State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1845143&HistoricalAwards=false
• 关键词: CAREER; Computation; Enabled; Rational; Design

Ionic liquids, composed of molecular cation and anion pairs, can be designed to exist as liquids under ambient conditions. Negligible volatility and ability to design ionic liquids with desired physicochemical and biological properties are the drivers for the current and emerging development of ionic liquid technologies on an industrial scale. Such advances also elevate the concerns that the release of ionic liquids into the environment from wastewater discharges, accidental spillage or a chemical plant accident, is likely to lead to aquatic and groundwater contamination due to their water solubility and limited biodegradability. The proposed research aims to generate foundational knowledge and computational methodologies that can be extended to enzyme engineering for ionic liquid biodegradation. The goal of the proposed research is to unravel the thermodynamics and kinetics of the bacterial cytochrome P450-mediated hydroxylation, the first step in the biodegradation, of imidazolium-based ionic liquids. The knowledge will then be utilized to rationally design the P450 BM3 enzyme to activate or accelerate the hydroxylation step. The research is guided by the hypothesis that the molecular level understanding of the intermediate steps leading to ionic liquid hydroxylation can be leveraged to identify amino acid residues in the enzyme binding pocket and the substrate access channel that present a thermodynamic and/or kinetic barrier to the reaction. The hypothesis will be tested by (i) characterizing the thermodynamics of the catalytic cycle of ionic liquid hydroxylation; (ii) determining kinetic aspects of the catalytic cycle of ionic liquid hydroxylation, and (iii) evaluating the influence of in silico modification of the key P450 catalytic center residues on the thermodynamics and kinetics of ionic liquid hydroxylation. Free energy-based molecular dynamics simulations will be employed to determine the thermodynamic driving force for ionic liquid binding and product release from the catalytic center. A hybrid approach involving quantum mechanical treatment of the reacting species and molecular mechanics representation of the protein environment and the solvent will be adopted for the intermediate reaction steps. Integration of research and education will be achieved by training high school chemistry and biology teachers and aspiring teachers from the OSUTeach program in using molecular editing and visualization tools, incorporating quantum calculations into a graduate level course on modeling and simulation, and teaching undergraduate students how to utilize computation and visualization in their courses.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

由分子阳离子和阴离子对组成的离子液体可以设计为在环境条件下作为液体存在。可以忽略不计的波动和设计具有所需物理化学和生物学特性的离子液体的能力，是工业规模上离子液体技术的当前和新兴开发的驱动因素。这种进步还提高了人们的担忧，即从废水排放，意外溢出或化学厂事故中释放到环境中，由于其水溶性和有限的生物降解性，可能会导致水生和地下水污染。拟议的研究旨在生成可以扩展到离子液体生物降解的酶工程的基础知识和计算方法。拟议的研究的目的是阐明细菌细胞色素P450介导的羟基化的热力学和动力学，这是咪唑基离子液体生物降解的第一步。然后，知识将用于合理设计P450 BM3酶以激活或加速羟基化步骤。这项研究的指导下是通过假设的指导：可以利用导致离子液体羟基化的中间步骤的分子水平理解，以鉴定酶结合口袋中的氨基酸残基和呈底物访问通道，这些氨基酸残基带来了对反应的热力学和/或基因障碍。该假设将通过（i）表征离子液体羟基化的催化循环的热力学来检验； （ii）确定离子液体羟基化催化循环的动力学方面，以及（iii）评估关键P450催化中心残基对离子液体液态羟基化热力学和动力学的硅酸盐修饰中的影响。将采用基于自由能的分子动力学模拟来确定离子液体结合和从催化中心释放产物的热力学驱动力。一种涉及反应物质的量子力学处理和蛋白质环境的分子力学表示的杂种方法以及中间反应步骤将采用溶剂。 Integration of research and education will be achieved by training high school chemistry and biology teachers and aspiring teachers from the OSUTeach program in using molecular editing and visualization tools, incorporating quantum calculations into a graduate level course on modeling and simulation, and teaching undergraduate students how to utilize computation and visualization in their courses.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual优点和更广泛的影响审查标准。