ArticleBiophysical journal2014
Reduced model captures Mg(2+)-RNA interaction free energy of riboswitches.
Article in Biophysical journal, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 47 citations in OpenAlex.
- Probing Charge-Controlled Inter-Domain Flexibility: Integrating Experimental and Coarse-Grained Approaches.Journal of chemical information and modeling · 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
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Implicit Solvent with Explicit Ions Generalized Born Model in Molecular Dynamics: Application to DNA.Journal of chemical theory and computation · 2024Article
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Influence of MgACS omega · 2023Article
- Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.Journal of molecular biology · 2022Article
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Directional translocation resistance of Zika xrRNA.Nature communications · 2020Article
- MgBiophysical journal · 2020Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Quantifying MgPolymers · 2018Article
- Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing.Molecular cell · 2018Article
- Competitive Binding of MgBiophysical journal · 2018Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- MgBiophysical journal · 2017Article
- Divalent ion competition reveals reorganization of an RNA ion atmosphere upon folding.Nucleic acids research · 2017Article
- A magnesium-induced triplex pre-organizes the SAM-II riboswitch.PLoS computational biology · 2017Article
- Counting the ions surrounding nucleic acids.Nucleic acids research · 2017Article
- Theory Meets Experiment: Metal Ion Effects in HCV Genomic RNA Kissing Complex Formation.Frontiers in molecular biosciences · 2017Review
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The stability of RNA tertiary structures depends heavily on Mg(2+). The Mg(2+)-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ2+, the number of excess Mg(2+) associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg(2+) ions interact closely and strongly with the RNA, unlike monovalent ions such as K(+), suggesting that an explicit treatment of Mg(2+) is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg(2+)-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg(2+) through the explicit representation of Mg(2+) ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K(+) and models its competition with condensed Mg(2+). The model contains one fitted parameter, the number of condensed K(+) ions in the absence of Mg(2+). Values of Γ2+ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ2+ to the Mg(2+)-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg(2+) and RNA dynamics.
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