ArticleJournal of chemical theory and computation2007
Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.
Article in Journal of chemical theory and computation, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.Nucleic acids research · 2025Article
- Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024Article
- 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
- 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
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Progress in molecular biology and translational science · 2013Review
- Ground-state coordination of a catalytic metal to the scissile phosphate of a tertiary-stabilized Hammerhead ribozyme.RNA (New York, N.Y.) · 2012Article
- Characterization of the Structure and Dynamics of the HDV Ribozyme at Different Stages Along the Reaction Path.The journal of physical chemistry letters · 2011Article
- Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme.Journal of chemical theory and computation · 2011Article
- Computational mutagenesis studies of hammerhead ribozyme catalysis.Journal of the American Chemical Society · 2010Article
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
- Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation.Journal of molecular biology · 2009Article
- Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.Journal of computational chemistry · 2008Article
- Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.Journal of the American Chemical Society · 2008Article
- Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.Journal of the American Chemical Society · 2008Article
- Solvent structure and hammerhead ribozyme catalysis.Chemistry & biology · 2008Article
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5 authors.
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Abstract
Results of a series of 12 ns molecular dynamics (MD) simulations of the reactant state (with and without a Mg(2+) ion), early and late transition state mimics are presented based on a recently reported crystal structure of a full-length hammerhead RNA. The simulation results support a catalytically active conformation with a Mg(2+) ion bridging the A9 and scissile phosphates. In the reactant state, the Mg(2+) spends significant time closely associated with the 2'OH of G8, but remains fairly distant from the leaving group O(5') position. In the early TS mimic simulation, where the nucleophilic O(2') and leaving group O(5') are equidistant from the phosphorus, the Mg(2+) ion remains tightly coordinated to the 2'OH of G8, but is positioned closer to the O(5') leaving group, stabilizing the accumulating charge. In the late TS mimic simulation, the coordination around the bridging Mg(2+) ion undergoes a transition whereby the coordination with the 2'OH of G8 is replace by the leaving group O(5') that has developed significant charge. At the same time, the 2'OH of G8 forms a hydrogen bond with the leaving group O(5') and is positioned to act as a general acid catalyst. This work represents the first reported simulations of the full-length hammerhead structure and TS mimics, and provides direct evidence for the possible role of a bridging Mg(2+) ion in catalysis that is consistent with both crystallographic and biochemical data.
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