Computational Analysis of Enzyme Catalysis and Regulation

项目概述：了解生物体的物理学原理具有重要的基础和生物医学意义。 控制生物分子中的化学步骤和其他事件（如渗透）之间耦合的分子 水分子进入活性位点，瞬时金属离子的募集，或构象重排 无论远近这是一个具有挑战性的任务，但是，由于固有的多尺度性质的问题。作为 因此，我们对决定酶催化的效率和特异性的因素的理解仍然存在于- 完整，特别是关于活动网站以外的贡献;这种知识差距极大地限制了我们的 重新设计高效酶的能力。基于这些考虑， 我们的研究是发展和应用多尺度计算方法来揭示潜在的机制 在原子水平上的酶催化，特别强调建立在何种程度上的化学， 典型的步骤与活性位点近端或远端的其他过程耦合。具体而言，我们的目标是发展 一个有效的QM/MM框架来计算酶反应的自由能分布，具有良好的平衡， 计算速度和准确性;进一步集成增强的采样方法、机器学习 技术和现代计算硬件使我们能够深入了解耦合的本质， 化学步骤和功能周期中的其他事件之间的关系。因此，我们处于一个独特的位置， 追求几个令人兴奋的应用，其中包括瞬态金属离子的机制和影响， 招募核酸加工酶，外周膜的催化和调节机制 酶和系统分析的变构耦合的转录因子;一个新兴的研究方向 是探索在连续定向进化过程中稳定性、催化活性和变构性的相互作用。我们 该项目将计算方法的发展与最近的实验广告启发的应用程序相结合， 时间分辨晶体学、深度突变扫描和连续定向进化等。 研究工作将导致新的计算工具和机制的监管机制的见解， 酶在活性部位附近或远离活性部位的过程中的变异。因此，该项目将同时 对生物分子中催化和变构的更好设计策略的基本影响和意义。

Project Summary: It is of great fundamental and biomedical importance to understand the physical princi- ples that govern the coupling between the chemical step in a biomolecule and other events, such as penetration of water molecules into the active site, recruitment of transient metal ions, or conformational rearrangements near and afar. This is a challenging task, however, due to the intrinsic multi-scale nature of the problem. As a result, our understanding in factors that dictate the efficiency and specificity of enzyme catalysis remains in- complete, especially regarding contributions beyond the active site; this knowledge gap has greatly limited our ability to design highly efficient enzymes de novo. Motivated by these considerations, the overarching theme of our research is to develop and apply multi-scale computational methods to reveal the underlying mechanism of enzyme catalysis at an atomic level, with a particular emphasis on establishing to what degree the chem- ical step is coupled with other processes proximal or distal to the active site. Specifically, we aim to develop an efficient QM/MM framework to compute free energy profiles of enzyme reactions with a good balance of computational speed and accuracy; further integration with enhanced sampling approaches, machine learning techniques and modern computational hardwares enables us to gain insights into the nature of coupling be- tween the chemical step and other events during the functional cycle. Accordingly, we are in a unique position to pursue several lines of exciting applications, which include the mechanism and impact of transient metal ion recruiting in nucleic acid processing enzymes, the catalytic and regulatory mechanism of peripheral membrane enzymes, and systemic analysis of allosteric coupling in a transcription factor; an emerging research direction is to explore the interplay of stability, catalytic activity, and allostery during continuous directed evolution. Our project integrates computational method developments with applications inspired by recent experimental ad- vances, such as time-resolved crystallography, deep mutational scanning and continuous directed evolution. The research efforts will lead to novel computational tools and mechanistic insights into the regulatory mech- anisms of enzymes by processes either near or remote from the active site. Thus the project will have both fundamental impacts and implications for better design strategies for catalysis and allostery in biomolecules.