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Research Abstracts Online
January - December 2011

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University of Minnesota Twin Cities
College of Science and Engineering
Department of Chemistry

PI: Darrin M. York, Fellow

Multiscale Quantum Models for RNA Catalysis

The York group’s research is focused on the development and application of multi-scale modeling techniques to study the detailed mechanisms of RNA catalysis. The objective of this research 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 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 such as the ribosome and spliceosome. Projects include: the study of the L1 ligase riboswitch; the series of prototype RNA enzymes including the hammerhead, hairpin and HDV ribozymes; non-enzymatic models in solution; and the protein analog RNase A. The calculations involve long-time molecular dynamics (MD) simulations of large-scale conformational events, free energy simulations of metal ion binding and pKa shifts in ribozyme active sites, combined quantum mechanical/molecular mechanical simulations of chemical mechanisms of catalysis, and high-level electronic structure calculations of model systems. These calculations are used together to provide deeper insight into mechanisms and aid in the interpretation of experiments. The applications are all computationally intensive, and have varying needs from MD simulations that require a large number of compute cores with fast Infiniband interconnect, to large-scale quantum calculations that have very large memory and disk-intensive requirements. Considerable ongoing effort has been devoted to benchmark and optimize the performance of these codes on MSI’s core systems, including the new Koronis system that was funded by the PI’s NIH high-end instrumentation grant.

Group Members

Thakshila D. Dissanayake Rallage, Graduate Student
Elena Formoso, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
George Giambasu, Graduate Student
Timothy Giese, Research Associate
Francesca Guerra, Visiting Researcher
Hugh Heldenbrand, Graduate Student
Ming Huang, Graduate Student
Pawel Janowski, Rutgers University, New Brunswick, New Jersey
Erich R. Keuchler, Graduate Student
Tai-Sung Lee, Research Associate
Violeta Lopez, Collaborator
Xabier Lopez, Theoretical Chemistry Group, Kimika Teorikoa, Donostia (Euskadi), Spain
Tyler Luchko, Rutgers University, New Brunswick, New Jersey
Yun Liu, Graduate Student
Adam Moser, Graduate Student
Kwangho Nam, Graduate Student
Olalla Nieto Faza, Department of Chemistry, University of St. Thomas, St. Paul, Minnesota
Jack Orlowski-Scherer, Collaborator
Ania Pabis, Collaborator
Maria Panteva, Collaborator
Brian Radak, Graduate Student
Kevin Range, Graduate Student
Carlos Silva Lopez, Department of Chemistry, University of St. Thomas, St. Paul, Minnesota
Jason Swail, Collaborator
Ross Walker, Visiting Researcher
Kin-Yiu Wong, Graduate Student
Wei Yang, Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida