ArticleNucleic acids research2020
Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Exploring Secondary Structure Predictions for RNA-Targeted Drug Discovery: Power and Challenges.Journal of chemical information and modeling · 2026Article
- Article
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.Nature communications · 2025Article
- Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations.Nucleic acids research · 2024Article
- Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression.Nature communications · 2024Article
- Scaffold-enabled high-resolution cryo-EM structure determination of RNA.bioRxiv : the preprint server for biology · 2024Article
- RNA target highlights in CASP15: Evaluation of predicted models by structure providers.Proteins · 2023Article
- Single-molecule FRET observes opposing effects of urea and TMAO on structurally similar meso- and thermophilic riboswitch RNAs.Nucleic acids research · 2023Article
- Structure and function analysis of a type III preQThe Journal of biological chemistry · 2023Article
- Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state.Structure (London, England : 1993) · 2023Article
- A riboswitch separated from its ribosome-binding site still regulates translation.Nucleic acids research · 2023Article
- Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches.Journal of molecular biology · 2022Review
- Interrogating RNA-Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations.ACS central science · 2022Article
- A small RNA that cooperatively senses two stacked metabolites in one pocket for gene control.Nature communications · 2022Article
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- A chemical probe based on the PreQNature communications · 2021Article
- A natural riboswitch scaffold with self-methylation activity.Nature communications · 2021Article
- Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing.Crystals · 2021Article
- Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors.The Journal of biological chemistry · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1-exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1-sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.
Indexed as
Identifiers
What OpenQuestion holds
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.