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。该提案的一个主要主题是促进与实验小组网络的积极合作，以便在机制方面取得共识，最终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。该提案侧重于应用于一系列原型核酶，这些核酶催化位点特异性磷酸二酯键的裂解（和连接），但具有不同的活性位点结构和催化要求。作为基线，同样的反应将在溶液中的非酶二核苷酸模型中进行研究，并由蛋白质酶类似物RNase a催化。交替的机制策略和控制反应性的因素的串联研究将为新生物医学技术的合理设计提供深入的见解。然而，这些应用需要新的方法进步。重要的是精确和高效的量子力学/分子力学（QM/MM）催化方法，可靠的RNA和金属离子分子模拟力场，以及有效的自由能表面和构象转变采样方法。为此，我们建议：1)改进核酶催化的QM、MM和QM/MM模型；2)开发新的QM/MM方法来预测核酶的pKa位移；3)开发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来研究核酶的化学机制和构象转变。通过这种方式，我们希望极大地扩展最先进的理论方法对RNA催化的预测能力和应用范围。

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.