ArticleJournal of the American Chemical Society2012
Magnesium fluctuations modulate RNA dynamics in the SAM-I riboswitch.
Article in Journal of the American Chemical Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers, 1 of them a synthesis that pooled it.
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Who cites it
57 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Exploring the interactions of antihistamine with retinoic acid receptor beta (RARB) by molecular dynamics simulations and genome-wide meta-analysis.Journal of molecular graphics & modelling · 2023Pooled it
- Article
- A cooperative effect of ligands, MgThe Journal of biological chemistry · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- Human lncRNAProceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Conformational heterogeneity in the dGsw purine riboswitch: role of MgRNA (New York, N.Y.) · 2025Article
- Evaluation of Pregabalin bioadhesive multilayered microemulsion IOP-lowering eye drops.Journal of controlled release : official journal of the Controlled Release Society · 2024Article
- Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.RNA (New York, N.Y.) · 2024Article
- AAp-MSMD: Amino Acid Preference Mapping on Protein-Protein Interaction Surfaces Using Mixed-Solvent Molecular Dynamics.Journal of chemical information and modeling · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.Communications biology · 2023Article
- Pressure pushes tRNAProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Magnesium ions mediate ligand binding and conformational transition of the SAM/SAH riboswitch.bioRxiv : the preprint server for biology · 2023Article
- Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch.Communications biology · 2022Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Dynamics of Cations around DNA and Protein as Revealed byAnalytical chemistry · 2022Article
- Visualizing RNA Structures by SAXS-Driven MD Simulations.Frontiers in bioinformatics · 2022Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.The journal of physical chemistry. B · 2021Article
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Authors and funding
7 authors.
Funding
Abstract
Experiments demonstrate that Mg(2+) is crucial for structure and function of RNA systems, yet the detailed molecular mechanism of Mg(2+) action on RNA is not well understood. We investigate the interplay between RNA and Mg(2+) at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations. The structure, including three stemloops, is very stable on this time scale. Simulations reveal that outer-sphere coordinated Mg(2+) ions fluctuate on the same time scale as the RNA, and that their dynamics couple. Locally, Mg(2+) association affects RNA conformation through tertiary bridging interactions; globally, increasing Mg(2+) concentration slows RNA fluctuations. Outer-sphere Mg(2+) ions responsible for these effects account for 80% of Mg(2+) in our simulations. These ions are transiently bound to the RNA, maintaining interactions, but shuttled from site to site. Outer-sphere Mg(2+) are separated from the RNA by a single hydration shell, occupying a thin layer 3-5 Å from the RNA. Distribution functions reveal that outer-sphere Mg(2+) are positioned by electronegative atoms, hydration layers, and a preference for the major groove. Diffusion analysis suggests transient outer-sphere Mg(2+) dynamics are glassy. Since outer-sphere Mg(2+) ions account for most of the Mg(2+) in our simulations, these ions may change the paradigm of Mg(2+)-RNA interactions. Rather than a few inner-sphere ions anchoring the RNA structure surrounded by a continuum of diffuse ions, we observe a layer of outer-sphere coordinated Mg(2+) that is transiently bound but strongly coupled to the RNA.
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