ArticleBiophysical journal2006
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.
Article in Biophysical journal, 2006. 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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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
55 citing papers in PubMed, 127 citations in OpenAlex.
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- Similarities and Differences between NaJournal of chemical theory and computation · 2021Article
- Predicting Monovalent Ion Correlation Effects in Nucleic Acids.ACS omega · 2019Article
- Predicting RNA-Metal Ion Binding with Ion Dehydration Effects.Biophysical journal · 2019Article
- Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.PLoS computational biology · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Journal of chemical theory and computation · 2018Article
- Predicting Ion Effects in an RNA Conformational Equilibrium.The journal of physical chemistry. B · 2017Article
- Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Nucleic acids research · 2017Article
- Theory and Modeling of RNA Structure and Interactions with Metal Ions and Small Molecules.Annual review of biophysics · 2017Review
- Monte Carlo Tightly Bound Ion Model: Predicting Ion-Binding Properties of RNA with Ion Correlations and Fluctuations.Journal of chemical theory and computation · 2016Article
- Secondary structure confirmation and localization of Mg2+ ions in the mammalian CPEB3 ribozyme.RNA (New York, N.Y.) · 2016Article
- Computing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation Approach.PloS one · 2016Article
- Extended molecular dynamics of a c-kit promoter quadruplex.Nucleic acids research · 2015Article
- Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Physical chemistry chemical physics : PCCP · 2015Article
- The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.Physical chemistry chemical physics : PCCP · 2015Article
- Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.RNA (New York, N.Y.) · 2014Article
- pH-dependent dynamics of complex RNA macromolecules.Journal of chemical theory and computation · 2013Article
- The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation.Journal of chemical theory and computation · 2012Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
Abstract
The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.
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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.