Collaborative Research: CDS&E: Computational Investigation of Solvent Effects on Enzyme Catalysis

酶是一种在生物系统中催化化学反应的特殊蛋白质。温度、压力或蛋白质周围环境组成的变化，以及其他许多因素，都会对酶催化的反应产生重大影响。通过这一奖项，化学部生命过程化学计划资助了北德克萨斯大学的G.Andres Cisneros博士和德克萨斯大学奥斯汀分校的Pengyu Ren博士开发计算方法和软件，以准确预测周围溶剂中的电荷对酶催化的影响。对酶在高电荷溶剂(离子液体)中如何发挥作用的详细了解可能会导致生物技术和生物工程应用的新的生物启发催化剂的开发。本项目采用先进的计算方法研究了辣根过氧化物酶(HRP)在不同荷电溶液中的反应机理。过氧化物酶是帮助防止好氧生物体中氧化损伤的重要酶。新开发的方法和程序源代码是免费提供的，这影响了科学界预测酶在各种环境中行为的能力。此外，该项目通过两个参与机构的各种外展和指导计划，让学生和来自科学中代表性较低的少数群体的教师参与进来。该项目的主要前提是，同源酶显示最大活性的温度差异是由于对激活自由能的焓和熵贡献平衡的差异，即使这些自由能相似。这种焓-熵平衡的差异是由于表面残基的柔性不同造成的。或者，与溶剂相互作用对表面残基柔韧性的影响可能会对活性中心产生长程静电效应。因此，本研究的主要目的是应用量子力学/分子力学(QM/MM)模拟来研究高电荷态离子液体(IL)溶液对酶催化反应的热熵平衡的影响。该项目延续了阿米巴-IL(用于离子液体中生物分子应用的原子多极优化能量学)力场的开发，并在LICHEM(分层相互作用化学模型)程序包的QM/MM代码及其与TINKER-OpenMM分子力学/动力学软件包的接口中实现了增强的采样方法。这些工具被用来计算模拟辣根过氧化物酶在不同IL溶液中的反应机理。对不同的IL溶液体系计算的Arrhenius图确定了每个被测体系的焓-熵平衡，以确定不同的溶剂环境对反应路径的影响。这项工作的结果对溶剂在酶催化中的作用以及表面残基柔性在酶反应机理中的作用/影响提供了基本的见解。此外，该项目开发了阿米巴的新方法和参数，并向广大科学界提供。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

Enzymes are specialized proteins that catalyze chemical reactions in biological systems. Changes in temperature, pressure, or composition of the environment surrounding the protein, among many other factors, can have significant effects on enzyme catalyzed reactions. With this award, the Chemistry of Life Processes Program of the Chemistry Division is funding Dr. G. Andres Cisneros from the University of North Texas and Dr. Pengyu Ren from the University of Texas at Austin to develop computational methods and software to accurately predict the effects that charges in the surrounding solvent have on enzymatic catalysis. Detailed understandings for how enzymes function in highly charged solvents (ionic liquids) potentially lead to the development of new bio-inspired catalysts for biotechnology and bioengineering applications. The state-of-the-art computational methods from this project are used to investigate the reaction mechanisms of horseradish peroxidase (HRP) in different charged solutions. Peroxidases are important enzymes that help prevent oxidative damage in aerobic organisms. The newly developed methods and source codes for programs are made freely available, which impact the ability of the scientific community to predict the behavior of enzymes in a variety of environments. In addition, the project engages school students and teachers from underrepresented minority groups in the sciences through various outreach and mentoring programs at the two participating institutions.The main premise of this project is that differences in temperatures at which homologous enzymes show maximum activity arise from differences in the balance between enthalpic and entropic contributions to the free energies of activation, even when these free energies are similar. This difference in enthalpic-entropic balance is due to differences in flexibility of surface residues. Alternatively, effects on the flexibility of surface residues from interactions with the solvent may exert long range-electrostatic effects on the active sites. Therefore, the main goal of this study is to apply quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the effect of highly charged ionic liquid (IL) solutions on the enthalpic-entropic balance for enzymatic catalysis. This project continues the development of the AMOEBA-IL (atomic multipole optimized energetics for biomolecular applications in ionic liquids) force field and implements enhanced sampling methods in the QM/MM code of the LICHEM (Layered Interacting Chemical Models) package and its interface to TINKER-OpenMM molecular mechanics/dynamics sortware package. These tools are used to computationally model the reaction mechanism of horseradish peroxidase in different IL solutions. Arrhenius plots calculated for the various IL solution systems determine the enthalpic-entropic balance for each tested system to ascertain the effect of the different solvent environments on the reaction pathway. Results from this work provide fundamental insights into the role of solvents on enzyme catalysis and the role/impact of surface-residue flexibility on enzymatic reaction mechanisms. Additionally, this project develops new methods and parameters for AMOEBA, and these are made available to the broad scientific community.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.