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Small-angle X-ray scattering (SAXS) experiments are increasingly used toprobe RNA structure. A number of \emph{forward models} that relate measuredSAXS intensities and structural features, and that are suitable to model eitherexplicit-solvent effects or solute dynamics, have been proposed in the pastyears. Here we introduce an approach that integrates atomistic moleculardynamics simulations and SAXS experiments to reconstruct RNA structuralensembles while simultaneously accounting for both RNA conformational dynamicsand explicit-solvent effects. Our protocol exploits SAXS pure-solute forwardmodels and enhanced sampling methods to sample an heterogenous ensemble ofstructures, with no information towards the experiments provided on-the-fly.The generated structural ensemble is then reweighted through the maximumentropy principle so as to match reference SAXS experimental data at multipleionic conditions. Importantly, accurate explicit-solvent forward models areused at this reweighting stage. We apply this framework to theGTPase-associated center, a relevant RNA molecule involved in proteintranslation, in order to elucidate its ion-dependent conformational ensembles.We show that (a) both solvent and dynamics are crucial to reproduceexperimental SAXS data and (b) the resulting dynamical ensembles contain anion-dependent fraction of extended structures.

Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles