Biomolecular Interactions and Enzymatic Processes

描述(由申请人提供)：一个多方面的研究项目旨在对水溶液中的酶过程进行计算研究。理论方法以酶的分子动力学自由能模拟为中心，利用量子力学和分子力学(QM/MM)相结合的方法。一个主要的目标是提高QM/MM方法的能力，并实现比传统方法更高的精度。我们建议进一步改进混合分子轨道和价键(MOVB)理论，结合自洽电荷紧键密度泛函理论(SCC-DFTB)，并用从头算和密度泛函方法对CHARMM程序进行扩展，以便实验生物化学家可以方便地校准、检验和使用理论模型作为解释实验结果的研究工具。MOVB方法是在理论水平上发展起来的，包括从头算、半经验分子轨道和密度泛函理论。本研究的一个目标是将该过程结合到分子动力学模拟程序中，以有效地模拟酶反应。这个项目的一个主要目的是提供对酶反应的基本原理和机制的更深层次的理解。在这一资助期间，我们重点研究了组蛋白赖氨酸去甲基酶的催化机制，重点是含有Jumonji C结构域的酶，它属于一大类利用非血红素高价铁氧中间体的酶。组蛋白赖氨酸去甲基酶和其他组蛋白修饰酶在表观遗传调控中发挥关键作用，并已被发现与癌症的发生和进展有关。此外，我们试图解决酶质子耦合电子转移反应的一般性质，以及蛋白质动力学和酶重组能量对这些过程的影响。MOVB方法为研究这些问题提供了一个重要的研究工具，其结果将对蛋白质工程和抑制剂设计具有普遍意义。PHS 398/2590(06/09版)页面续格式页面

DESCRIPTION (provided by applicant): A multi-faceted research project is directed aimed at computational studies of enzymatic processes in aqueous solution. The theoretical approach centers on molecular dynamics free energy simulations of enzymes, making use of combined quantum mechanical and molecular mechanical (QM/MM) methods. A major goal is to increase the capability of QM/MM methods and to achieve greater accuracy than conventional approaches. We propose to further improve the mixed molecular orbital and valence bond (MOVB) theory, coupled with the self-consistent charge tight-bonding density functional theory (SCC-DFTB) and extension to the CHARMM program with ab initio and DFT methods, such that the theoretical model can be conveniently calibrated, tested and used by experimental biochemists as a research tool to help interpret experiment findings. The MOVB method has been developed at theoretical levels that include ab initio and semiempirical molecular orbital and density functional theory. One goal of the present study is to incorporate the procedure into molecular dynamics simulation programs for effectively modeling enzymatic reactions. A major thrust of this project is to provide a deeper understanding of the underlying principles and mechanisms of enzymatic reactions. During this grant period, we focus on the catalytic mechanism of histone lysine demethylases with emphasis on the Jumonji C domain containing enzymes, which belong to a large class of enzymes that utilize a non-heme high- valent iron-oxo intermediate. Histone lysine demethylases along with other histone protein modifying enzymes play a critical role in epigenetic regulation and have been found to be associated with cancer development and progress. In addition, we seek to address the general properties of enzymatic proton-coupled electron transfer reactions and the effects of protein dynamics and enzyme reorganization energies on these processes. The MOVB method provides an important research tool to study these questions, and the results will be of general importance to protein engineering and inhibitor design. PHS 398/2590 (Rev. 06/09) Page Continuation Format Page