ArticleProceedings of the National Academy of Sciences of the United States of America2006
Trapped water molecules are essential to structural dynamics and function of a ribozyme.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
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Who cites it
50 citing papers in PubMed, 104 citations in OpenAlex.
- Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition.Current research in structural biology · 2026Article
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- Complex Water Networks Visualized through 2.2-2.3 Å Cryogenic Electron Microscopy of RNA.bioRxiv : the preprint server for biology · 2025Article
- Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes.Nucleic acids research · 2024Article
- Water as an Intrinsic Structural Element in Cellulose Fibril Aggregates.The journal of physical chemistry letters · 2022Article
- Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs.Nucleic acids research · 2020Article
- Hofmeister Series for Metal-Cation-RNA Interactions: The Interplay of Binding Affinity and Exchange Kinetics.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Nucleic acids research · 2017Article
- Pressure modulates the self-cleavage step of the hairpin ribozyme.Nature communications · 2017Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.RNA (New York, N.Y.) · 2014Article
- Single molecule fluorescence approaches shed light on intracellular RNAs.Chemical reviews · 2014Review
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.Journal of chemical theory and computation · 2012Article
- Direct structural analysis of modified RNA by fluorescent in-line probing.Nucleic acids research · 2012Article
- The role of conserved waters in conformational transitions of Q61H K-ras.PLoS computational biology · 2012Article
- QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.The journal of physical chemistry. B · 2011Article
- Allosteric activation via kinetic control: potassium accelerates a conformational change in IMP dehydrogenase.Biochemistry · 2011Article
- Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.Journal of molecular biology · 2011Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular dynamics simulation and single molecule fluorescence spectroscopy approaches, we find that a ribozyme from a subviral plant pathogen exhibits a coupled hydrogen bonding network that communicates dynamic structural rearrangements throughout the catalytic core in response to site-specific chemical modification. Trapped long-residency water molecules are critical for this network and only occasionally exchange with bulk solvent as they pass through a breathing interdomain base stack. These highly structured water molecules line up in a string that may potentially also be involved in specific base catalysis. Our observations suggest important, still underappreciated roles for specifically bound water molecules in the structural dynamics and function of noncoding RNAs.
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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.