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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Giese, Timothy J; York, Darrin M (2018) A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method. J Chem Theory Comput 14:1564-1582
Lee, Tai-Sung; Cerutti, David S; Mermelstein, Dan et al. (2018) GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features. J Chem Inf Model 58:2043-2050
Gaines, Colin S; York, Darrin M (2017) Model for the Functional Active State of the TS Ribozyme from Molecular Simulation. Angew Chem Int Ed Engl 56:13392-13395
Chen, Haoyuan; Giese, Timothy J; Golden, Barbara L et al. (2017) Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations. Biochemistry 56:2985-2994
Lee, Tai-Sung; Radak, Brian K; Harris, Michael E et al. (2016) A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation. ACS Catal 6:1853-1869
Sengupta, Raghuvir N; Van Schie, Sabine N S; Giamba?u, George et al. (2016) An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. RNA 22:32-48
Zhang, Shuming; Gu, Hong; Chen, Haoyuan et al. (2016) Isotope effect analyses provide evidence for an altered transition state for RNA 2'-O-transphosphorylation catalyzed by Zn(2+). Chem Commun (Camb) 52:4462-5
Gaines, Colin S; York, Darrin M (2016) Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation. J Am Chem Soc 138:3058-65
Giamba?u, George M; York, Darrin M; Case, David A (2015) Structural fidelity and NMR relaxation analysis in a prototype RNA hairpin. RNA 21:963-74
Weissman, Benjamin P; Li, Nan-Sheng; York, Darrin et al. (2015) Heavy atom labeled nucleotides for measurement of kinetic isotope effects. Biochim Biophys Acta 1854:1737-45

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