ArticleJournal of the American Chemical Society2008
Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.
Article in Journal of the American Chemical Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- 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
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 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
- Computational mutagenesis studies of hammerhead ribozyme catalysis.Journal of the American Chemical Society · 2010Article
- Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?Molecules (Basel, Switzerland) · 2010Article
- Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.The journal of physical chemistry. B · 2010Article
- Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme.Biophysical journal · 2009Article
- Exploring ribozyme conformational changes with X-ray crystallography.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
- Does water relay play an important role in phosphoryl transfer reactions? Insights from theoretical study of a model reaction in water and tert-butanol.The journal of physical chemistry. B · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
A series of ten 60 ns molecular dynamics (MD) simulations of the native and mutated full length hammerhead ribozymes in the reactant state and in an activated precursor state (G8:2'OH deprotonated) are reported. Mutant simulations include the C3U, G8A, and G8I single mutants and a C3U/G8A double mutant that exhibits an experimental rescue effect. The results provide critical details into the origin of the observed mutation effects and support a mechanism where the 2'OH of G8 acts as a general acid catalyst that is held in position through Watson-Crick hydrogen bonding between G8 and C3.
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Registered trials
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