ArticleJournal of the American Chemical Society2008
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.
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 43 papers.
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Who cites it
43 citing papers in PubMed.
- Efficient QM/MM Modeling of Enzymatic Reactions Combining PathCV with OPES.Journal of chemical theory and computation · 2026Article
- A programmable ribozyme for RNA signal transduction.Nature communications · 2026Article
- Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.The journal of physical chemistry. B · 2025Article
- Investigation of the pThe journal of physical chemistry. B · 2021Article
- Comprehensive strategies of machine-learning-based quantitative structure-activity relationship models.iScience · 2021Review
- Two symmetric arginine residues play distinct roles inProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Mapping Free Energy Pathways for ATP Hydrolysis in theMolecules (Basel, Switzerland) · 2018Article
- Parametrization of Combined Quantum Mechanical and Molecular Mechanical Methods: Bond-Tuned Link Atoms.Molecules (Basel, Switzerland) · 2018Article
- 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
- Pressure modulates the self-cleavage step of the hairpin ribozyme.Nature communications · 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
- Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods.Journal of chemical theory and computation · 2014Article
- Computational approaches to predicting the impact of novel bases on RNA structure and stability.ACS chemical biology · 2013Review
- Molecular modeling of nucleic acid structure: energy and sampling.Current protocols in nucleic acid chemistry · 2013Review
- Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations.Journal of the American Chemical Society · 2013Article
- Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.The journal of physical chemistry letters · 2013Article
- A dynamic structural model of expanded RNA CAG repeats: a refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations.Journal of the American Chemical Society · 2013Article
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The molecular mechanism of hairpin ribozyme catalysis is studied with molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential with a recently developed semiempirical AM1/d-PhoT model for phosphoryl transfer reactions. Simulations are used to derive one- and two-dimensional potentials of mean force to examine specific reaction paths and assess the feasibility of proposed general acid and base mechanisms. Density-functional calculations of truncated active site models provide complementary insight to the simulation results. Key factors utilized by the hairpin ribozyme to enhance the rate of transphosphorylation are presented, and the roles of A38 and G8 as general acid and base catalysts are discussed. The computational results are consistent with available experimental data, provide support for a general acid/base mechanism played by functional groups on the nucleobases, and offer important insight into the ability of RNA to act as a catalyst without explicit participation by divalent metal ions.
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