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

Abstract

Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of forward models that relate measured SAXS intensities and structural features, and that are suitable to model either explicit-solvent effects or solute dynamics, have been proposed in the past years. Here, we introduce an approach that integrates atomistic molecular dynamics simulations and SAXS experiments to reconstruct RNA structural ensembles while simultaneously accounting for both RNA conformational dynamics and explicit-solvent effects. Our protocol exploits SAXS pure-solute forward models and enhanced sampling methods to sample an heterogenous ensemble of structures, with no information towards the experiments provided on-the-fly. The generated structural ensemble is then reweighted through the maximum entropy principle so as to match reference SAXS experimental data at multiple ionic conditions. Importantly, accurate explicit-solvent forward models are used at this reweighting stage. We apply this framework to the GTPase-associated center, a relevant RNA molecule involved in protein translation, in order to elucidate its ion-dependent conformational ensembles. We show that (a) both solvent and dynamics are crucial to reproduce experimental SAXS data and (b) the resulting dynamical ensembles contain an ion-dependent fraction of extended structures.

Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments

“…We find that residual discrepancies with respect to the SAXS data cannot be accounted for by systematic errors of SAXS curve prediction from the RNA coordinates, which may be reflecting a degree of imbalance between the intra-RNA and RNA-solvent interactions carried by the force fields tested here ( Salsbury and Lemkul 2021 ). More work needs to be done to correct for these effects before SAXS data can be used to reweight conformationally heterogeneous ensembles in combination with the NMR data ( Plumridge et al 2017 ; Bernetti et al 2021 ).…”

RNA triplex structures revealed by WAXS-driven MD simulations

“…26 Despite recent efforts 27, 28 it is not yet clear if current approaches provide a general framework to provide atomically detailed descriptions consistent with experiments. As an alternative approach, all atom models of RNAs are being successfully refined and tuned to come to agreement with experimental data acquired by NMR, 29–33 cryoEM 34 , solution small 35 or wide angle scattering (SWAXS). 36…”

“…Subtle variations of the structures are interpreted using correlation maps. 37 As mentioned above, similar data-guided approaches are being exploited in conjunction with other experimental measurements 29–35 .…”

Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals

“…Although RNA duplexes are highly stable thermodynamically, the higher-order folding landscape of RNA is often complex, with multiple competing minima, as well as kinetic traps [14][15][16][17]. This results in conformational heterogeneity in the solution [18]. The molecular surface of folded RNAs is dominated by a regular array of negatively charged phosphates that can lead to packing (through counterions) into crystals that are disordered at the atomic level [19][20][21].…”