ArticleJournal of molecular biology2013
Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch.
Article in Journal of molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- R3DCID: circular interaction diagrams for RNA and DNA 3D structures of all sizes.RNA (New York, N.Y.) · 2026Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Article
- Mechanism of Ligand Discrimination by theJournal of chemical information and modeling · 2023Article
- Disentangling contact and ensemble epistasis in a riboswitch.Biophysical journal · 2023Article
- Inactivation of the riboswitch-controlled GMP synthase GuaA inRNA biology · 2021Article
- Riboswitches for Controlled Expression of Therapeutic Transgenes Delivered by Adeno-Associated Viral Vectors.Pharmaceuticals (Basel, Switzerland) · 2021Review
- Base-intercalated and base-wedged stacking elements in 3D-structure of RNA and RNA-protein complexes.Nucleic acids research · 2020Article
- Transcriptional and translational S-box riboswitches differ in ligand-binding properties.The Journal of biological chemistry · 2020Article
- High Affinity Binding of N2-Modified Guanine Derivatives Significantly Disrupts the Ligand Binding Pocket of the Guanine Riboswitch.Molecules (Basel, Switzerland) · 2020Article
- Article
- Structural basis for 2'-deoxyguanosine recognition by the 2'-dG-II class of riboswitches.Nucleic acids research · 2019Article
- Effect of mutations on binding of ligands to guanine riboswitch probed by free energy perturbation and molecular dynamics simulations.Nucleic acids research · 2019Article
- Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Allosteric mechanism of theeLife · 2018Article
- Cobalamin riboswitches exhibit a broad range of ability to discriminate between methylcobalamin and adenosylcobalamin.The Journal of biological chemistry · 2017Article
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning.Journal of molecular biology · 2015Article
- Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context.The Journal of biological chemistry · 2015Article
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6 authors.
Funding
Abstract
Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs.
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