ArticleRNA (New York, N.Y.)2008
Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.
Article in RNA (New York, N.Y.), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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
27 citing papers in PubMed, 52 citations in OpenAlex.
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Free Energy Profile Decomposition Analysis for QM/MM Simulations of Enzymatic Reactions.Journal of chemical theory and computation · 2023Article
- Investigation of the pThe journal of physical chemistry. B · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides.RNA (New York, N.Y.) · 2017Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- Evidence for the role of active site residues in the hairpin ribozyme from molecular simulations along the reaction path.Journal of the American Chemical Society · 2014Article
- A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations.Journal of chemical theory and computation · 2013Article
- A combination of receptor-based pharmacophore modeling & QM techniques for identification of human chymase inhibitors.PloS one · 2013Article
- QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.The journal of physical chemistry. B · 2011Article
- The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine.The Journal of biological chemistry · 2011Article
- Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data.RNA (New York, N.Y.) · 2011Article
- 3D QSAR pharmacophore modeling, in silico screening, and density functional theory (DFT) approaches for identification of human chymase inhibitors.International journal of molecular sciences · 2011Article
- 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
- Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.The journal of physical chemistry. B · 2010Article
- Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.Journal of chemical theory and computation · 2010Article
- Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.Accounts of chemical research · 2010Article
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
- Exploring ribozyme conformational changes with X-ray crystallography.Methods (San Diego, Calif.) · 2009Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics simulations using a combined quantum mechanical/molecular mechanical potential are used to determine the two-dimensional free energy profiles for the mechanism of RNA transphosphorylation in solution and catalyzed by the hairpin ribozyme. A mechanism is explored whereby the reaction proceeds without explicit chemical participation by conserved nucleobases in the active site. The ribozyme lowers the overall free energy barrier by up to 16 kcal/mol, accounting for the majority of the observed rate enhancement. The barrier reduction in this mechanism is achieved mainly by the electrostatic environment provided by the ribozyme without recruitment of active site nucleobases as acid or base catalysts. The results establish a baseline mechanism that invokes only the solvation and specific hydrogen-bonding interactions present in the ribozyme active site and provide a departure point for the exploration of alternate mechanisms where nucleobases play an active chemical role.
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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.