ArticleNature chemistry2015
How do metal ions direct ribozyme folding?
Article in Nature chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed, 132 citations in OpenAlex.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Poly(ADP-ribose) (PAR) exhibits ion-dependent structural properties distinct from RNA.Nucleic acids research · 2026Article
- Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.The Journal of chemical physics · 2024Article
- Article
- RNA G-quadruplex folding is a multi-pathway process driven by conformational entropy.Nucleic acids research · 2024Article
- Direct Observation ofJACS Au · 2023Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time.Nucleic acids research · 2023Article
- Impact of hierarchical water dipole orderings on the dynamics of aqueous salt solutions.Nature communications · 2023Article
- Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes.bioRxiv : the preprint server for biology · 2023Article
- Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Influence of MgACS omega · 2023Article
- Review
- FebRNA: An automated fragment-ensemble-based model for building RNA 3D structures.Biophysical journal · 2022Article
- Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics.Nature chemistry · 2022Article
- Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology.ACS central science · 2022Article
- Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly.Nature methods · 2022Article
- Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding.Journal of chemical theory and computation · 2022Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribozymes, which carry out phosphoryl-transfer reactions, often require Mg(2+) ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner that is not fully understood. Here we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg(2+) concentrations, and are transiently stabilized by the coordination of Mg(2+) ions to specific nucleotides. However, competition for scarce Mg(2+) and topological constraints that arise from chain connectivity prevent the complete folding of the ribozyme. A much higher Mg(2+) concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg(2+) is replaced by Ca(2+) the ribozyme folds, but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.
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