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。这是一个应用驱动的建议，开发了一个分层的方法，以建立深入的机制洞察到一系列的RNA酶（核酶）的增加的复杂性和生物相关性。该提案的一个首要主题是弥合理论和实验之间的差距，并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。采用交替机制策略的不同催化RNA系统的平行研究允许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以容忍变异的元件形成核酶工程的指导原则可能出现的基础。人们希望，揭示这些原则将使新的生物医学技术的合理设计和促进发现。该提案的目的是：1）通过对一系列小的自切割核酶的研究，更深入地了解支持催化的指导原则，2）研究glmS和VS核酶中的催化和翻译控制机制，这提供了新的特征和RNA复杂性的第二层。3)目的探讨一种易处理的Ⅰ类内含子系统Azoarcus核酶的高级RNA结构和功能。这些应用需要一种创新的多尺度建模策略，该策略结合了几种新颖的元素，包括新的组合量子力学/分子力学方法，用于糖起皱和二价离子的改进的分子模拟力场，用于自由能模拟的采样和分析的先进计算技术，用于研究pH速率分布的显式溶剂恒定pH分子动力学模拟，和3D-RISM计算来探测活性位点静电环境，并提供对可能的金属离子结合位点的洞察。这些创新进一步放大的综合实验/理论研究策略，从而作出重大努力，概括主要的实验数据，以帮助解释测量，验证计算结果，并进行实验可检验的预测。

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.