Multi-scale Quantum Models for Ribozyme Catalysis

描述（由申请人提供）：本提案的目的是将最先进的理论方法用于研究核酶催化机制和调节反应性的因素。 该提案中的一个首要主题是促进与实验组网络的积极合作，以便朝着机制的共识观点迈进，最终可能有助于更深入地了解更复杂的细胞催化RNA系统，如核糖体和剪接体。 该提案的重点是应用到一系列的原型核酶，催化位点特异性磷酸二酯键裂解（和连接），但有不同的活性位点的架构和催化的要求。 作为基线，将在溶液中的非酶二核苷酸模型中研究相同的反应，并由蛋白酶类似物RNA酶A催化。 交替机制的策略和管理反应的因素的串联研究将提供深入的洞察到新的生物医学技术的合理设计。 然而，这些应用需要新的方法进步。 关键的重要性是准确和有效的量子力学/分子力学（QM/MM）的催化方法，可靠的分子模拟力场的RNA和金属离子，和有效的方法采样的自由能表面和构象转变。 为此，我们提出：1）改进用于核酶催化的QM、MM和QM/MM模型; 2）发展一种新的预测核酶pKa位移的QM/MM方法; 3）发展一种新的自由能展开方法，将我们的QM/MM方法扩展到从头算水平; 4）发展有效的路径方法，研究核酶的化学机理和构象转变。 通过这种方式，我们希望大大扩展预测能力和应用范围的最先进的理论方法RNA催化。 公共卫生相关性：这项计划的目标是利用量子力学和分子模拟方法来研究RNA分子催化重要化学反应的机制。 通过这些研究获得的见解将增强我们对RNA在细胞中发挥的基本作用的理解，并促进新的基于RNA的生物医学技术的设计。

DESCRIPTION (provided by applicant): The objective of this proposal is to bring to bear state of the art theoretical methods to the study of the mechanisms of ribozyme catalysis and the factors that regulate reactivity. An overarching theme in the proposal is to facilitate active collaborations with a network of experimental groups in order to progress toward a consensus view of mechanism that may, ultimately, contribute to a deeper understanding of more complex cellular catalytic RNA systems such as the ribosome and spliceosome. The proposal focuses on application to a series of archetype ribozymes that catalyze site-specific phosphodiester bond cleavage (and ligation) but that have different active site architectures and catalytic requirements. As a baseline, the same reaction will be studied in a non-enzymatic dinucleotide model in solution, and catalyzed by the protein enzyme analog, RNase A. The tandem study of alternate mechanistic strategies and the factors that govern reactivity will provide penetrating insight into the rational design of new biomedical technology. However, these applications demand new methodological advances. Of key importance are accurate and efficient quantum mechanical/molecular mechanical (QM/MM) methods for catalysis, reliable molecular simulation force fields for RNA and metal ions, and efficient methods for sampling free energy surfaces and conformational transitions. Toward this end, we propose to: 1) improve the QM, MM and QM/MM models for ribozyme catalysis, 2) develop a new QM/MM method for prediction of pKa shifts in ribozymes; 3) develop a novel free energy expansion approach to extend our QM/MM methods to the ab initio level; 4) develop efficient path methods to study chemical mechanisms and conformational transitions in ribozymes. In this way we hope to greatly extend the predictive capability and range of application of state of the art theoretical methods to RNA catalysis. PUBLIC HEALTH RELEVANCE: The goal of this proposal is to use quantum mechanical and molecular simulations methods to study the mechanisms whereby molecules of RNA catalyze important chemical reactions. The insight gained by these studies will enhance our understanding of the fundamental role RNA plays in cells and facilitate the design of new RNA-based biomedical technology.