ArticleFrontiers in bioinformatics2022
Visualizing RNA Structures by SAXS-Driven MD Simulations.
Article in Frontiers in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed.
- pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.Nucleic acids research · 2026Article
- The Distinct Structural Propensities of Poly-C, A, and U Single-Stranded RNA.Biomacromolecules · 2026Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- Comparison of Three Computational Tools for the Prediction of RNA Tertiary Structures.Non-coding RNA · 2024Article
- A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM.Nucleic acids research · 2023Article
- Atomistic structure of the SARS-CoV-2 pseudoknot in solution from SAXS-driven molecular dynamics.Nucleic acids research · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 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
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Insights into the structural stability of major groove RNA triplexes by WAXS-guided MD simulations.Cell reports. Physical science · 2022Article
- An overview of structural approaches to study therapeutic RNAs.Frontiers in molecular biosciences · 2022Review
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3 authors.
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Abstract
The biological role of biomolecules is intimately linked to their structural dynamics. Experimental or computational techniques alone are often insufficient to determine accurate structural ensembles in atomic detail. We use all-atom molecular dynamics (MD) simulations and couple it to small-angle X-ray scattering (SAXS) experiments to resolve the structural dynamics of RNA molecules. To accomplish this task, we utilize a set of re-weighting and biasing techniques tailored for RNA molecules. To showcase our approach, we study two RNA molecules: a riboswitch that shows structural variations upon ligand binding, and a two-way junction RNA that displays structural heterogeneity and sensitivity to salt conditions. Integration of MD simulations and experiments allows the accurate construction of conformational ensembles of RNA molecules. We observe a dynamic change of the SAM-I riboswitch conformations depending on its binding partners. The binding of SAM and Mg
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