ArticleNature chemistry2020
Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme.
Article in Nature chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 54 citations in OpenAlex.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- MgJournal of the American Chemical Society · 2026Article
- Hammerhead Ribozymes: Structural Insights, Catalytic Mechanisms, and Cutting-Edge Applications in Synthetic Biology.International journal of molecular sciences · 2025Review
- Transferability of MACE Graph Neural Network for Range Corrected Δ-Machine Learning Potential QM/MM Applications.The journal of physical chemistry. B · 2025Article
- Article
- Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.The Journal of chemical physics · 2024Article
- Simulations predict preferred MgBiophysical journal · 2024Article
- RNA targeting and cleavage by the type III-Dv CRISPR effector complex.Nature communications · 2024Article
- Catalytic Metal Ion-Substrate Coordination during Nonenzymatic RNA Primer Extension.Journal of the American Chemical Society · 2024Article
- Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development.ACS omega · 2024Review
- Modern Alchemical Free Energy Methods for Drug Discovery Explained.ACS physical chemistry Au · 2023Review
- AmberTools.Journal of chemical information and modeling · 2023Article
- Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis.Biochemistry · 2023Article
- Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology.Nucleic acids research · 2023Article
- Estimation of frequency factors for the calculation of kinetic isotope effects from classical and path integral free energy simulations.The Journal of chemical physics · 2023Article
- Dissociative Transition State in Hepatitis Delta Virus Ribozyme Catalysis.Journal of the American Chemical Society · 2023Article
- RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis.The journal of physical chemistry. B · 2022Article
- Article
- Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign.ACS chemical biology · 2022Article
- Structural Basis for Fluorescence Activation by Pepper RNA.ACS chemical biology · 2022Article
Corrections and comments
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
Abstract
The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligation, and serves as an important model system to understand RNA catalysis. Here, we combine stereospecific phosphorothioate substitution, precision nucleobase mutation and linear free-energy relationship measurements with molecular dynamics, molecular solvation theory and ab initio quantum mechanical/molecular mechanical free-energy simulations to gain insight into the catalysis. Through this confluence of theory and experiment, we unify the existing body of structural and functional data to unveil the catalytic mechanism in unprecedented detail, including the degree of proton transfer in the transition state. Further, we provide evidence for a critical Mg
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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.