Abstract: RNAs are notoriously flexible biomolecules, requiring an ensemble-representation of their structure. Constructing such dynamical ensembles, which comprise the set of conformations an RNA can adopt, along with their associated populations, is challenging because biophysical measurements only indirectly report on the properties of the underlying conformational (Boltzmann) distribution. In this talk, I will describe how we use statistical mechanics to model the dynamical ensembles of RNA using local solvent accessibility data. My talk will culminate with a description of how we used experimentally-derived solvent accessibility information to construct a pair of atomistic ensembles of the aptamer domain of the S-adenosylmethionine (SAM) class-I riboswitch. The differences we observed in the resulting -SAM and +SAM ensembles are consistent with a SAM-dependent reshaping of the aptamer's dynamical landscape. Interestingly, within our -SAM ensemble, we observed a transient conformational state that may be a folding intermediate and which harbors a hidden binding pocket that we predict can selectively recognize small-molecule ligands.
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