Computational Analysis of Enzyme Catalysis and Regulation

项目总结：了解其物理原理具有重要的基础性和生物医学意义。 控制生物分子中的化学步骤与其他事件(如渗透)之间的耦合的PLE 水分子进入活性中心，瞬时金属离子的招募，或构象重排 近处和远方。然而，这是一项具有挑战性的任务，因为这一问题具有内在的多尺度性质。AS 因此，我们对决定酶催化效率和特异性的因素的认识还停留在以下几个方面：(1)酶催化的效率和特异性；(2)影响酶催化活性的因素；(2)决定酶催化效率和特异性的因素。(2)酶催化的效率和专一性(fifi) 完整，特别是关于活动站点之外的贡献；这种知识差距极大地限制了我们的 能够从新设计高效的fi酶。在这些考虑的推动下， 我们的研究是开发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，特别强调建立在什么程度的化学- 该步骤与活性部位近端或远端的其他突起相结合。特别是fi，我们的目标是开发 一个fi有效的QM/MM框架用于计算酶反应的自由能过程 计算速度和精度；与增强的采样方法、机器学习进一步集成 技术和现代计算硬件使我们能够深入了解耦合的本质-- 在功能循环中，化学步骤和其他事件之间的关系。因此，我们处于独特的地位。 追求几个令人兴奋的应用领域，其中包括瞬变金属离子的机制和影响 外周膜的催化和调节机制在核酸加工酶中的应用 酶和转录因子中变构偶联的系统分析；一个新兴的研究方向 是探索稳定性、催化活性和变构在连续定向进化过程中的相互作用。我们的 该项目将计算方法的开发与受最近实验广告启发的应用程序相结合- 例如，时间分辨结晶学、深度突变扫描和连续定向进化。 这些研究工作将带来新的计算工具和对监管机制的机械性见解- 在活性部位附近或远离活性部位的过程中酶的异常。因此，该项目将两者兼而有之 生物分子中催化和变构的更好设计策略的基本影响和启示。

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.