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.

Public Health Relevance

The goal of this proposal is to use a novel integrated multiscale modeling strategy to study the mechanisms whereby molecules of RNA can catalyze important biochemical reactions. New tools and insightful guiding principles for ribozyme engineering are likely to emerge through the pro- posed work that enable the rational design of new biomedical technology and facilitate discovery.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-A (02))
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Preusch, Peter
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Rutgers University
Schools of Arts and Sciences
New Brunswick
United States
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Chen, Haoyuan; Giese, Timothy J; Huang, Ming et al. (2014) Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions. Chemistry 20:14336-43
Huang, Ming; York, Darrin M (2014) Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations. Phys Chem Chem Phys 16:15846-55
Lee, Tai-Sung; Radak, Brian K; Huang, Ming et al. (2014) Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach. J Chem Theory Comput 10:24-34
Giese, Timothy J; Huang, Ming; Chen, Haoyuan et al. (2014) Recent advances toward a general purpose linear-scaling quantum force field. Acc Chem Res 47:2812-20
Kellerman, Daniel L; York, Darrin M; Piccirilli, Joseph A et al. (2014) Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation. Curr Opin Chem Biol 21:96-102
Wong, Kin-Yiu; Xu, Yuqing; York, Darrin M (2014) Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models. J Comput Chem 35:1302-16
Heldenbrand, Hugh; Janowski, Pawel A; Giamba?u, George et al. (2014) Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path. J Am Chem Soc 136:7789-92
Kuechler, Erich R; York, Darrin M (2014) Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl. J Chem Phys 140:054109
Lee, Tai-Sung; Radak, Brian K; Pabis, Anna et al. (2013) A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations. J Chem Theory Comput 9:153-164
Lee, Tai-Sung; Wong, Kin-Yiu; Giambasu, George M et al. (2013) Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. Prog Mol Biol Transl Sci 120:25-91

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