Darrin M. York
Professor, Center for Integrative Proteomics Research
BioMaPS Institute and Dept. Chemistry & Chemical Biology
Multiscale modeling methods to study RNA folding and catalysis
In this talk I will describe new multiscale modeling methods that are used to study complex biological problems involving RNA folding and catalysis, and how these processes are influenced by the ion environment. Small self-cleaving ribozyme such as the hammerhead, hairpin, and hepatitis delta virus ribozymes are excellent model systems to understand how molecules of RNA, with fairly limited diversity of functional groups to perform chemistry, can acts as efficient catalysts. The mechanism of these ribozymes have been investigated with molecular simulations and quantum chemical methods, and together with experimental data, provide new insight into the necessary and sufficient conditions whereby RNA can have catalytic activity. Finally, a summary of the most current multi-scale modeling research advances, including the development of linear-scaling quantum force fields, will be presented, as well as an outlook for the future.