Computer Simulations of Enzymes

描述(申请人提供)：基于X射线和核磁共振实验的结构信息，使用分子动力学和量子力学/分子力学(QM/MM)方法进行的计算模拟能够描述酶催化的化学反应机理。从头算QM/MM方法利用了相关量子力学方法的准确性和可靠性，但与相应的半经验量子力学方法相比，计算成本要高得多。因此，基于从头算QM/MM方法的反应路径和活化自由能计算在模拟时间尺度和相空间采样方面遇到了独特的挑战。这一建议旨在进一步发展从头算QM/MM方法，并将其应用于研究重要酶的化学反应机理。其长期目标是发展和建立基于密度泛函理论的QM/MM模拟，作为研究酶的结构和化学反应的实验的平等伙伴，并提供对生物体系中化学反应机理的详细见解。最近发展了从头算QM/MM-MFEP方法，以克服以前从头算QM/MM方法中遇到的一些困难，以获得最小能量的反应路径。以前基于总能量的方法依赖于蛋白质/溶剂环境的局部构象。在QM/MM-MFEP方法中，反应体系通过活性中心的QM子系统的平均力势(PMF)表面来描述，而描述其余蛋白质和溶剂的大量MM自由度被统计平均。这一建议旨在进一步发展QM/MM-MFEP方法，使之成为一种全面和准确的方法，用于从头算QM/MM方法模拟溶液和酶中的反应过程。QM/MM方法将被用来研究几种重要酶的反应机制：(1)色氨酰-tRNA合成酶，它催化氨基酸的激活过程；(2)索尔特酶，它识别和裂解多肽，然后与革兰氏阳性病原菌结合，将多肽共价连接到细胞壁；以及(3)革兰氏阳性细菌菌毛，它在许多细菌的生物学功能中发挥重要作用。这项工作将有助于理论方法论的进步和对重要酶反应机理的理解。此外，它还将有助于新药和酶抑制剂的设计。 与公众健康相关：这项建议旨在开发模拟酶催化的化学过程的方法，并研究某些重要酶的催化机制。拟议的工作将导致在研究酶的研究工具方面取得重大进展。由于酶催化了生物体中的大部分化学过程，它将有助于理解生命过程，并有助于抑制剂和药物的设计。

DESCRIPTION (provided by applicant): Based on structural information from X-ray and NMR experiments, computational simulations performed using molecular dynamics and the quantum mechanical/molecular mechanical (QM/MM) approach are able to describe the mechanisms of chemical reactions catalyzed by enzymes. Ab initio QM/MM methods capitalize on the accuracy and reliability of the associated quantum mechanical approaches, however at a much higher computational cost compared with corresponding semiempirical quantum mechanical approaches. Thus reaction path and activation free energy calculations based on ab initio QM/MM methods encounter unique challenges in simulation timescales and phase space sampling. This proposal aims to develop further the ab initio QM/MM methodology and its application to the investigation of the mechanisms of chemical reactions in important enzymes. The long-term goal is to develop and establish density functional theory-based QM/MM simulation as an equal partner with experiments for the study of the structure and chemical reactions of enzymes and to provide detailed insight into chemical reaction mechanisms in biological systems. The ab initio QM/MM-MFEP method has been developed recently to overcome some of the difficulties encountered in previous ab initio QM/MM approaches for obtaining minimum energy reaction paths. Previous total energy-based methods suffer from a dependence on the local conformations of the protein/solvent environment. In the QM/MM-MFEP method, the reaction system is described via the potential of mean force (PMF) surface of the QM subsystem in the active site, while the large number of MM degrees of freedom describing the rest of the protein and solvent are statistically averaged. This proposal aims to develop the QM/MM-MFEP method further into a comprehensive and accurate method for the simulation of reaction processes in solution and in enzymes using ab initio QM/MM methods. The QM/MM methodology will be used to investigate the reaction mechanism of several important enzymes: (1) Tryptophanyl-tRNA synthetase, which catalyzes the amino acid activation process; (2) Sortase, which recognizes and cleaves peptides, and then covalently links the peptides to cell walls, in association with Gram-positive pathogenic bacteria; and (3) Gram-positive bacterial pili, which play important roles in the biological functions of many bacteria. The proposed work will lead to the advancement of theoretical methodology and the understanding of important enzyme reaction mechanisms. In addition, it will also serve to aid in the design of new drugs and enzyme inhibitors. PUBLIC HEALTH RELEVANCE: This proposal aims at developing methods for simulating chemical processes catalyzed by enzymes, and investigating the catalytic mechanisms of certain important enzymes. The proposed work will lead to significant advances in research tools for studying enzymes. Because enzymes catalyze most of the chemical processes in living organisms, it will contribute to the understanding of life processes, as well as aiding in the design of inhibitors and drugs.