The functional repertoire of Ribonucleic acid (RNA) molecules has dramatically expanded in recent years with fundamental roles in many regulatory processes and emerging applications in therapeutic and engineering domains. Underlying such applications are conformational dynamics of RNA molecules that encompass a large number of modes spanning vast spatiotemporal scales. Dynamics in RNA are intimately connected to intrinsic structural features (e.g. base-pairing) as well as extrinsic factors (e.g. ligand binding). While equilibrium fluctuations in biomolecules such as RNA are inherent, it is the large-scale conformational transitions that play a dominant role in interfacial processes such as biomolecular recognition. The information on such conformational states is encoded in the physical free energy landscapes of RNA molecules, the robust sampling of which can provide key thermodynamic and kinetic information on functional conformational ensembles. In this talk, we will present applications of new and emerging enhanced sampling molecular simulation methods based upon all-atom and structure-based models of small RNA molecules that are known to undergo large-scale conformational changes. A specific example that will be highlighted is of the transactivation response element RNA (TAR-RNA) from the genome of HIV-1 virus possessing versatile conformational states that are rapidly becoming targets of novel therapeutics.<br/>

Combining structure-based models and enhanced sampling methods to probe RNA conformational dynamics

254th National Meeting (2017)

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