ArticleNucleic acids research2021
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 37 citations in OpenAlex.
- IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.Journal of molecular biology · 2026Article
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- Phosphorylation toggles the SARS-CoV-2 nucleocapsid protein between two membrane-associated condensate states.Nature communications · 2025Article
- Article
- RNA ensembles from in vitro to in vivo: Toward predictive models of RNA cellular function.Current opinion in structural biology · 2024Review
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints.Bioinformatics (Oxford, England) · 2023Article
- Recognizing the power of machine learning and other computational methods to accelerate progress in small molecule targeting of RNA.RNA (New York, N.Y.) · 2023Article
- The promise of cryo-EM to explore RNA structural dynamics.Journal of molecular biology · 2022Review
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.RNA (New York, N.Y.) · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
- Biomotors, viral assembly, and RNA nanobiotechnology: Current achievements and future directions.Computational and structural biotechnology journal · 2022Review
- Computational drug discovery under RNA times.QRB discovery · 2022Review
- The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer.Molecular therapy. Nucleic acids · 2021Article
- Engineering Crystal Packing in RNA Structures I: Past and Future Strategies for Engineering RNA Packing in Crystals.Crystals · 2021Article
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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