ArticleJournal of molecular biology2009
Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.
Article in Journal of molecular biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 40 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Systematic discovery of novel ribozymes with gene silencing properties from global deep-sea RNA viromes.Frontiers in microbiology · 2026Article
- Hammerhead Ribozymes: Structural Insights, Catalytic Mechanisms, and Cutting-Edge Applications in Synthetic Biology.International journal of molecular sciences · 2025Review
- Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design.RNA (New York, N.Y.) · 2020Article
- Dynamical ensemble of the active state and transition state mimic for the RNA-cleaving 8-17 DNAzyme in solution.Nucleic acids research · 2019Article
- Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme.RNA (New York, N.Y.) · 2019Article
- Bulky cations greatly increase the turnover of a native hammerhead ribozyme.RSC advances · 2019Article
- Coupling between conformational dynamics and catalytic function at the active site of the lead-dependent ribozyme.RNA (New York, N.Y.) · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Divalent Metal Ion Activation of a Guanine General Base in the Hammerhead Ribozyme: Insights from Molecular Simulations.Biochemistry · 2017Article
- Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation.Journal of the American Chemical Society · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Two Divalent Metal Ions and Conformational Changes Play Roles in the Hammerhead Ribozyme Cleavage Reaction.Biochemistry · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Hammerhead ribozyme activity and oligonucleotide duplex stability in mixed solutions of water and organic compounds.FEBS open bio · 2014Article
- Active-site monovalent cations revealed in a 1.55-Å-resolution hammerhead ribozyme structure.Journal of molecular biology · 2013Article
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
The relationship between formation of active in-line attack conformations and monovalent (Na(+)) and divalent (Mg(2+)) metal ion binding in hammerhead ribozyme (HHR) has been explored with molecular dynamics simulations. To stabilize repulsions between negatively charged groups, different requirements of the threshold occupancy of metal ions were observed in the reactant and activated precursor states both in the presence and in the absence of a Mg(2+) in the active site. Specific bridging coordination patterns of the ions are correlated with the formation of active in-line attack conformations and can be accommodated in both cases. Furthermore, simulation results suggest that the HHR folds to form an electronegative recruiting pocket that attracts high local concentrations of positive charge. The present simulations help to reconcile experiments that probe the metal ion sensitivity of HHR catalysis and support the supposition that Mg(2+), in addition to stabilizing active conformations, plays a specific chemical role in catalysis.
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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.