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

离子液体由分子阳离子和阴离子对组成，可以设计成在环境条件下以液体形式存在。可忽略的挥发性和设计具有理想物理化学和生物特性的离子液体的能力是离子液体技术在工业规模上当前和新兴发展的驱动力。这些进展也引起了人们的关注，即离子液体从废水排放、意外泄漏或化工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，可能导致水生和地下水污染。提出的研究旨在产生基础知识和计算方法，可以扩展到离子液体生物降解的酶工程。提出的研究目标是揭示细菌细胞色素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。然后利用这些知识来合理设计P450 BM3酶来激活或加速羟基化步骤。该研究的指导假设是，对导致离子液体羟基化的中间步骤的分子水平理解可以用来识别酶结合口袋中的氨基酸残基和底物进入通道，这些通道为反应提供了热力学和/或动力学屏障。该假设将通过(i)表征离子液体羟基化催化循环的热力学来验证；（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催化中心残基的硅改性对离子液体羟基化热力学和动力学的影响。基于自由能的分子动力学模拟将用于确定离子液体结合和产物从催化中心释放的热力学驱动力。中间反应步骤将采用一种混合方法，包括对反应物质的量子力学处理和对蛋白质环境和溶剂的分子力学表征。通过培训高中化学和生物教师以及来自OSUTeach项目的有抱负的教师使用分子编辑和可视化工具，将量子计算纳入研究生水平的建模和模拟课程，并教本科生如何在他们的课程中利用计算和可视化，将研究和教育结合起来。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

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.