ArticleRNA (New York, N.Y.)2010
Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 61 citations in OpenAlex.
- Structural basis for Mg²⁺-glycine synergy in the tandem glycine riboswitch revealed by cryo-EM.Npj structural biology · 2026Article
- Cryo-EM reveals remodeling of a tandem riboswitch at 2.9 Å resolution.Research square · 2025Article
- Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.Journal of molecular biology · 2022Review
- Measurement of the specific and non-specific binding energies of MgBiophysical journal · 2022Article
- Direct Measurement of Interhelical DNA Repulsion and Attraction by Quantitative Cross-Linking.Journal of the American Chemical Society · 2022Article
- Binding Characteristics Study of DNA based Aptamers forMolecules (Basel, Switzerland) · 2021Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology.Current opinion in structural biology · 2019Review
- Divalent ions tune the kinetics of a bacterial GTPase center rRNA folding transition from secondary to tertiary structure.RNA (New York, N.Y.) · 2018Article
- Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.RNA (New York, N.Y.) · 2018Article
- Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Predicting Molecular Crowding Effects in Ion-RNA Interactions.The journal of physical chemistry. B · 2016Article
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Engineering and characterization of fluorogenic glycine riboswitches.Nucleic acids research · 2016Article
- Review
- Probing the kinetic and thermodynamic consequences of the tetraloop/tetraloop receptor monovalent ion-binding site in P4-P6 RNA by smFRET.Biochemical Society transactions · 2015Review
- DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch.Journal of biochemistry · 2014Article
- Global analysis of riboswitches by small-angle X-ray scattering and calorimetry.Biochimica et biophysica acta · 2014Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
Riboswitches are gene-regulating RNAs that are usually found in the 5'-untranslated regions of messenger RNA. As the sugar-phosphate backbone of RNA is highly negatively charged, the folding and ligand-binding interactions of riboswitches are strongly dependent on the presence of cations. Using small angle X-ray scattering (SAXS) and hydroxyl radical footprinting, we examined the cation dependence of the different folding stages of the glycine-binding riboswitch from Vibrio cholerae. We found that the partial folding of the tandem aptamer of this riboswitch in the absence of glycine is supported by all tested mono- and divalent ions, suggesting that this transition is mediated by nonspecific electrostatic screening. Poisson-Boltzmann calculations using SAXS-derived low-resolution structural models allowed us to perform an energetic dissection of this process. The results showed that a model with a constant favorable contribution to folding that is opposed by an unfavorable electrostatic term that varies with ion concentration and valency provides a reasonable quantitative description of the observed folding behavior. Glycine binding, on the other hand, requires specific divalent ions binding based on the observation that Mg(2+), Ca(2+), and Mn(2+) facilitated glycine binding, whereas other divalent cations did not. The results provide a case study of how ion-dependent electrostatic relaxation, specific ion binding, and ligand binding can be coupled to shape the energetic landscape of a riboswitch and can begin to be quantitatively dissected.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.