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

Mattia Bernetti,Kathleen B Hall,Giovanni Bussi

doi:10.1093/nar/gkab459

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.

Highlights

RNA molecules accomplish a plethora of functional roles in the cell, their function being dictated by their sequence and structure and, to a large extent, by their dynamical behavior [1,2]
Short plain Molecular dynamics (MD) simulations with restraints on the RNA molecule, lasting 10 ns, were performed with varying ionic conditions on GTPase-associated center (GAC) RNA starting from the crystal structure, where GAC is in its folded state
small-angle X-ray scattering (SAXS) spectra were computed from the MD sampled structure through different available software, namely PLUMED [13,63], Crysol [24], WAXSiS [29]

Summary

Introduction

RNA molecules accomplish a plethora of functional roles in the cell, their function being dictated by their sequence and structure and, to a large extent, by their dynamical behavior [1,2]. MD simulations can be seen as a powerful tool that complements experimental data making it possible to add dynamical information to experiments that report ensemble averages This can be even more important when using lowresolution experiments such as small-angle X-ray scattering (SAXS) [16,17]. Methods have been devised that allow computing SAXS spectra including the solvent contribution through relatively efficient implementations, aiming at predicting SAXS spectra as accurately as possible [18,20,27,28,29,30] This can be critical when dealing with highly charged biomolecules, such as RNA, whose effect on the surrounding solvent and on the ionic cloud can be sizable up to a distance of several nanometers [31,32]. A possible route to combine MD and experimental data is to enforce the refer-

Methods

Results

Conclusion