Multi-Scale Quantum Models for Ribozyme Catalysis

描述（由申请人提供）：我们提出了一种新的多尺度建模策略来研究RNA催化的机制和调节反应性的因素。这是一项应用驱动的提案，它开发了一种分层的方法，以建立对一系列日益复杂和生物相关性的RNA酶（核酶）的深刻机制洞察。该提案的首要主题是弥合理论与实验之间的差距，并朝着机制的共识观点前进，最终有助于更深入地了解更复杂的细胞催化RNA系统。平行研究不同的催化RNA系统，采用不同的机制策略，可以揭示导致催化的必要和充分条件。鉴定保守的机械特征以及可能耐受变异的元件构成了核酶工程指导原则的基础。希望揭示这些原理将使新的生物医学技术的合理设计和促进发现。本研究的目的是：1)通过对一系列小的自裂核酶的研究，更深入地了解支持催化的指导原则；2)研究glmS和VS核酶的催化和翻译控制机制，这为RNA复杂性提供了新的特征和第二层。3)在一个可处理的I族内含子系统：偶氮核酶中探索高阶RNA的结构和功能。这些应用需要一种创新的多尺度建模策略，该策略结合了几个新元素，包括新的量子力学/分子力学组合方法，改进的糖折叠和二价离子的分子模拟力场，用于采样和分析自由能模拟的先进计算技术，明确的溶剂恒定pH分子动力学模拟来研究pH速率分布，以及3D-RISM计算，以探测活性位点的静电环境，并深入了解可能的金属离子结合位点。通过综合实验/理论研究策略，这些创新被进一步放大，其中做出了重大努力来概括主要实验数据，以帮助解释测量结果，验证计算结果并做出实验可测试的预测。

DESCRIPTION (provided by applicant): We propose a novel multiscale modeling strategy to study of the mechanisms of RNA catalysis and the factors that regulate reactivity. This is an application-driven proposal that develops a tiered approach to build up deep mechanistic insight into a series of RNA enzymes (ribozymes) of in- creasing complexity and biological relevance. An overarching theme in the proposal is to bridge the gap between theory and experiment and progress toward a consensus view of mechanism that may, ultimately, contribute to a deeper understanding of more complex cellular catalytic RNA systems. The parallel study of different catalytic RNA systems that employ alternate mechanistic strategies allows one to unveil the necessary and sufficient conditions that lead to catalysis. Identification of conserved mechanistic features as well as elements that may tolerate variation form the foundation from which guiding principles for ribozyme engineering may emerge. It is the hope that uncovering these principles will enable the rational design of new biomedical technology and facilitate discovery. The aims of the proposal are: 1) To gain a deeper understanding of the guiding principles that underpin catalysis through the study of a series of small self-cleaving ribozymes, 2) To investigate the mechanisms of catalysis and translational control in glmS and VS ribozymes, which offer new features and a second tier of RNA complexity. 3) To explore higher-order RNA structure and function in a tractable group I intron system: the Azoarcus ribozyme. These applications demand an innovative multiscale modeling strategy that combines several novel elements, including new combined quantum mechanical/molecular mechanical methods, improved molecular simulation force fields for sugar puckering and divalent ions, advanced computational techniques for sampling and analysis of free energy simulations, explicit solvent constant pH molecular dynamics simulations to study pH-rate profiles, and 3D-RISM calculations to probe the active site electrostatic environment and provide insight into possible metal ion binding sites. These innovations are further amplified by the integrated experimental/theoretical research strategy whereby significant effort is made to recapitulate primary experimental data to aid in interpretation of measurements, validate computational results and make experimentally testable predictions.