Multi-scale Quantum Models for Ribozyme Catalysis

描述（由申请人提供）：这是一个应用驱动的提案，重点是通过使用最先进的理论方法，为RNA催化的分子机制提供新的见解。为了实现这一目标，采用了多方面的方法，将量子化学、分子模拟和统计力学方法相结合，其中许多方法一直是NIH最初资助期的发展重点。这些方法统称为RNA催化的“多尺度”模型：综合方法，当集体使用时，能够同时跨越广泛的空间和时间域，以提供对核酶分子机制的更深入了解。这些方法的持续发展和扩展在这一更新建议中发挥了重要作用，包括设计新的磷酰转移反应的半经验量子模型，扩展和增强QM/MM模拟的线性缩放静电和电子结构方法，以及改进的处理溶剂化和广义大分子溶剂边界势和响应的模型。尽管如此，主要的优先事项是应用最近发展的方法已经可用的磷酰转移反应的问题，发生在溶液和核酶。为此，我们建议针对实验研究的重要非酶反应校准和验证新的多尺度模型，然后将其应用于一组重点的3种原型核酶系统：锤头核酶、发夹核酶和丁型肝炎病毒核酶。这些核酶已经通过实验（包括不同催化阶段的结构信息）进行了广泛的研究，并在其替代催化机制方面提供了高度互补的特征。对这些系统的协同研究可以更深入地了解哪些特征是保守的，哪些特征可以在生物医学研究、治疗方法设计或新生物/纳米技术开发中具有相当大前景的新核酶工程中被利用。

DESCRIPTION (provided by applicant): This is an application-driven proposal that focuses on providing new insight into the molecular mechanisms of RNA catalysis through use of state-of-the-art theoretical methods. To achieve this goal, a multi-faceted approach is taken that combines quantum chemistry, molecular simulation and statistical mechanical methods, many of which have been the development focus of the initial NIH funding period. These methods are collectively referred to as "multi-scale" models for RNA catalysis: integrated methods that, when used collectively, are able to simultaneously span the broad range of spatial and temporal domains required to provide a deeper understanding of the molecular mechanisms of ribozymes. Continued development and extension of these methods plays a strong role in this renewal proposal, including the design of new semiempirical quantum models for phosphoryl transfer reactions, extension and enhancement of linear-scaling electrostatic and electronic structure methods for QM/MM simulations, and improved models for treatment of solvation and generalized macromolecular solvent boundary potential and response. Nonetheless, the main priority is to apply the recently developed methods already available to problems of phosphoryl transfer reactions that occur in solution and in ribozymes. For this purpose, we propose to calibrate and validate the new multi-scale models against important non-enzymatic reactions that have been studied experimentally, and then apply them to a focused set of 3 prototype ribozyme systems: the hammerhead, hairpin and hepatitis delta virus ribozymes. These ribozymes have been extensively studied by experiment (including structural information at different stages of catalysis), and offer highly complementary features in terms of their alternate catalytic mechanisms. Study of these systems in concert allows deeper insight into which features are conserved and which features might be exploited in the engineering of new ribozymes that may have considerable promise in biomedical research, the design of therapeutics, or development of new bio/nanotechnology.