Biomolecular Interactions and Enzymatic Processes

描述（由申请人提供）：一个多方面的研究项目，直接针对水溶液中酶促过程的计算研究。理论方法集中于利用量子力学和分子力学（QM/MM）方法对酶系统进行分子动力学模拟。为了获得更高的准确性，我们建议进一步发展混合分子轨道价键（MOVB）方法来模拟酶的反应并对反应途径进行采样。此外，我们计划为QM/MM组合计算实现半经验密度泛函理论，这将显著扩大QM/MM应用于酶系统的范围，包括metailo酶。一个主要的推动力是对酶的非凡催化能力提供更深入的了解。我们的方法是通过检查具有共同特征但具有不同生物学功能的单个酶系统来寻求一般催化原理。特别是，水解半胱氨酸蛋白酶、人组织蛋白酶K、丙氨酸和谷氨酸外消旋酶将被详细研究，以了解底物结合、反应机制和自由能谱。组织蛋白酶K的抑制剂可以减少骨吸收，为治疗骨质疏松症和类风湿性关节炎提供了一个有希望的治疗靶点，而氨基酸消旋酶在细菌细胞壁肽聚糖层的合成中是必不可少的，使它们成为抑制剂的有吸引力的靶点。提出的计算研究将深入了解这两类重要酶的酸/碱催化机制。此外，将研究胸苷酸合成酶（TS）的动态构象变化，这种变化发生在整个酶催化反应的许多步骤中。TS催化dTMP核苷酸的从头合成用于DNA合成，这在实验中得到了广泛的研究。本研究将对蛋白质动态构象变化在胸苷酸合成酶功能中的作用提供更深入的理解，其结果将在酶催化中具有普遍意义。

DESCRIPTION (provided by applicant): A multi-faceted research project is directly aimed at computational studies of enzymatic processes in aqueous solution. The theoretical approach centers on molecular dynamics simulations of enzymatic systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. To achieve greater accuracy, we propose to further develop a mixed molecular orbital-valence bond (MOVB) method for simulation of enzyme reactions and sampling of the reaction pathway. In addition, we plan to implement a semi-empirical density functional theory for combined QM/MM calculations, which will significantly expand the scope of QM/MM applications to enzymatic systems, including metailoenzymes. A major thrust is to provide a deeper understanding of the remarkable catalytic power of enzymes. Our approach is to seek general catalytic principles, by examining individual enzymatic systems that share common features, but have different biological functions. In particular, the hydrolytic cysteine protease, human cathepsin K, and alanine and glutamate racemases, will be investigated in detail to understand substrate binding, reaction mechanism, and free energy profiles. Inhibitors of cathepsin K can reduce bone resorption, providing a promising therapeutic target for the treatment of osteoporosis and rheumatoid arthritis, while amino acid racemases are essential in the synthesis of the peptidoglycan layer of bacteria cell walls, rendering them attractive targets for inhibitors. The proposed computational study will provide insight into the mechanism of acid/base catalysis of these two important classes of enzymes. In addition, the dynamic conformational changes in thymidylate synthase (TS), that take place throughout the many-steps of the enzymatic reaction, will be studied. TS catalyzes the de novo synthesis of dTMP nucleotide for DNA synthesis, which has been extensively investigated experimentally. The proposed study will provide a deeper understanding of the roles of protein dynamic conformation change in the function of thymidylate synthase, and the results will be of general importance in enzyme catalysis.