The objective of this proposal is to bring to bear state of the art theoretical methods to the study of the mechanisms of ribozyme catalysis and the factors that regulate reactivity. An overarching theme in the proposal is to facilitate active collaborations with a network of experimental groups in order to progress toward a consensus view of mechanism that may, ultimately, contribute to a deeper understanding of more complex cellular catalytic RNA systems such as the ribosome and spliceosome. The proposal focuses on application to a series of archetype ribozymes that catalyze site-specific phosphodiester bond cleavage (and ligation) but that have different active site architectures and catalytic requirements. As a baseline, the same reaction will be studied in a non-enzymatic dinucleotide model in solution, and catalyzed by the protein enzyme analog, RNase A. The tandem study of alternate mechanistic strategies and the factors that govern reactivity will provide penetrating insight into the rational design of new biomedical technology. However, these applications demand new methodological advances. Of key importance are accurate and efficient quantum mechanical/molecular mechanical (QM/MM) methods for catalysis, reliable molecular simulation force fields for RNA and metal ions, and efficient methods for sampling free energy surfaces and conformational transitions. Toward this end, we propose to: 1) improve the QM, MM and QM/MM models for ribozyme catalysis, 2) develop a new QM/MM method for prediction of pKa shifts in ribozymes;3) develop a novel free energy expansion approach to extend our QM/MM methods to the ab initio level;4) develop efficient path methods to study chemical mechanisms and conformational transitions in ribozymes. In this way we hope to greatly extend the predictive capability and range of application of state of the art theoretical methods to RNA catalysis.

Public Health Relevance

The goal of this proposal is to use quantum mechanical and molecular simulations methods to study the mechanisms whereby molecules of RNA catalyze important chemical reactions. The insight gained by these studies will enhance our understanding of the fundamental role RNA plays in cells and facilitate the design of new RNA-based biomedical technology.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function D Study Section (MSFD)
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Preusch, Peter C
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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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