ArticleNature2017
Structures of riboswitch RNA reaction states by mix-and-inject XFEL serial crystallography.
Article in Nature, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 175 papers.
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Who cites it
175 citing papers in PubMed, 308 citations in OpenAlex.
- Recovering Small Molecule Ligand-RNA Binding Pocket Binding Modes and Exploring Potential Binding Pathways Using Metadynamics.Molecules (Basel, Switzerland) · 2026Article
- From Static Structures to Molecular Dynamics: Emerging Directions in X-Ray and Electron Materials Characterization.Materials (Basel, Switzerland) · 2026Review
- Design and discovery of 'tug-of-war' riboswitches.bioRxiv : the preprint server for biology · 2026Article
- Modular Scaffold Crystals for Programmable Installation and Structural Observation of DNA-Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Minimized sample consumption for time-resolved serial crystallography applied to the redox cycle of human NQO1.Communications chemistry · 2026Article
- DNP-Enhanced Magic Angle Spinning Solid-State NMR Spectroscopy to Determine RNA-Ligand Interactions.Journal of the American Chemical Society · 2026Article
- Glyoxalase activities of Parkinson's disease relevant protein DJ-1/PARK7: Past discoveries and future perspectives.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- Real-time capture of domain movements during copper amine oxidase catalysis by mix-and-inject serial crystallography.Nature communications · 2025Article
- Sensitive detection of structural dynamics using a statistical framework for comparative crystallography.Science advances · 2025Article
- Sample delivery methods for protein X-ray crystallography with a special focus on sample consumption.Nature communications · 2025Review
- Article
- RLDOCKScore: A Scoring Function for RNA-Ligand Docking and Small Molecule Virtual Screening.Journal of chemical theory and computation · 2025Article
- Direct Modeling of DNA and RNA Aptamers with AlphaFold 3: A Promising Tool for Predicting Aptamer Structures and Aptamer-Target Interactions.ACS synthetic biology · 2025Article
- Advancing time-resolved structural biology: latest strategies in cryo-EM and X-ray crystallography.Nature methods · 2025Review
- Advances in microfluidic mixers for time-resolved structural biology with X-rays.Biophysical reviews · 2025Review
- Article
- Macromolecular crystallography and biology at the Linac Coherent Light Source.Journal of synchrotron radiation · 2025Article
- Ligand-binding pockets in RNA and where to find them.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
115 more citing papers are in PubMed but not listed here.
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Authors and funding
38 authors at 12 institutions in 2 countries.
Funding
Abstract
Riboswitches are structural RNA elements that are generally located in the 5' untranslated region of messenger RNA. During regulation of gene expression, ligand binding to the aptamer domain of a riboswitch triggers a signal to the downstream expression platform. A complete understanding of the structural basis of this mechanism requires the ability to study structural changes over time. Here we use femtosecond X-ray free electron laser (XFEL) pulses to obtain structural measurements from crystals so small that diffusion of a ligand can be timed to initiate a reaction before diffraction. We demonstrate this approach by determining four structures of the adenine riboswitch aptamer domain during the course of a reaction, involving two unbound apo structures, one ligand-bound intermediate, and the final ligand-bound conformation. These structures support a reaction mechanism model with at least four states and illustrate the structural basis of signal transmission. The three-way junction and the P1 switch helix of the two apo conformers are notably different from those in the ligand-bound conformation. Our time-resolved crystallographic measurements with a 10-second delay captured the structure of an intermediate with changes in the binding pocket that accommodate the ligand. With at least a 10-minute delay, the RNA molecules were fully converted to the ligand-bound state, in which the substantial conformational changes resulted in conversion of the space group. Such notable changes in crystallo highlight the important opportunities that micro- and nanocrystals may offer in these and similar time-resolved diffraction studies. Together, these results demonstrate the potential of 'mix-and-inject' time-resolved serial crystallography to study biochemically important interactions between biomacromolecules and ligands, including those that involve large conformational changes.
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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.