ArticleThe journal of physical chemistry. B2011
QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.
Article in The journal of physical chemistry. B, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 36 citations in OpenAlex.
- Efficient QM/MM Modeling of Enzymatic Reactions Combining PathCV with OPES.Journal of chemical theory and computation · 2026Article
- Investigation of the pThe journal of physical chemistry. B · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Thermodynamics and kinetics of RNA tertiary structure formation in the junctionless hairpin ribozyme.Biophysical chemistry · 2017Article
- 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
- Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.Biopolymers · 2015Article
- Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations.Journal of the American Chemical Society · 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
- 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
- Intermolecular domain docking in the hairpin ribozyme: metal dependence, binding kinetics and catalysis.RNA biology · 2013Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
- General acid-base catalysis mediated by nucleobases in the hairpin ribozyme.Journal of the American Chemical Society · 2012Article
- Molecular modeling of nucleic acid structure: energy and sampling.Current protocols in nucleic acid chemistry · 2001Review
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
The hairpin ribozyme is a prominent member of small ribozymes since it does not require metal ions to achieve catalysis. Guanine 8 (G8) and adenine 38 (A38) have been identified as key participants in self-cleavage and -ligation. We have carried out hybrid quantum-mechanical/molecular mechanical (QM/MM) calculations to evaluate the energy along several putative reaction pathways. The error of our DFT description of the QM region was tested and shown to be ~1 kcal/mol. We find that self-cleavage of the hairpin ribozyme may follow several competing microscopic reaction mechanisms, all with calculated activation barriers in good agreement with those from experiment (20-21 kcal/mol). The initial nucleophilic attack of the A-1(2'-OH) group on the scissile phosphate is predicted to be rate-limiting in all these mechanisms. An unprotonated G8(-) (together with A38H(+)) yields a feasible activation barrier (20.4 kcal/mol). Proton transfer to a nonbridging phosphate oxygen also leads to feasible reaction pathways. Finally, our calculations consider thio-substitutions of one or both nonbridging oxygens of the scissile phosphate and predict that they have only a negligible effect on the reaction barrier, as observed experimentally.
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