ArticleThe journal of physical chemistry. B2013
Molecular simulations of RNA 2'-O-transesterification reaction models in solution.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- A Multidimensional B-Spline Correction for Accurate Modeling Sugar Puckering in QM/MM Simulations.Journal of chemical theory and computation · 2017Article
- Charge-dependent many-body exchange and dispersion interactions in combined QM/MM simulations.The Journal of chemical physics · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- Characterization of the three-dimensional free energy manifold for the uracil ribonucleoside from asynchronous replica exchange simulations.Journal of chemical theory and computation · 2015Article
- Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations.Physical chemistry chemical physics : PCCP · 2014Article
- Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2'-O-transphosphorylation.Current opinion in chemical biology · 2014Review
- Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models.Journal of computational chemistry · 2014Article
- Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.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
- Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
We employ quantum mechanical/molecular mechanical umbrella sampling simulations to probe the free energy surfaces of a series of increasingly complex reaction models of RNA 2'-O-transesterification in aqueous solution under alkaline conditions. Such models are valuable for understanding the uncatalyzed processes underlying catalytic cleavage of the phosphodiester backbone of RNA, a reaction of fundamental importance in biology. The chemically reactive atoms are modeled by the AM1/d-PhoT quantum model for phosphoryl transfer, whereas the aqueous solvation environment is modeled with a molecular mechanics force field. Several simulation protocols were compared that used different ionic conditions and force field models. The results provide insight into how variation of the structural environment of the nucleophile and leaving group affects the free energy profile for the transesterification reaction. Results for a simple RNA backbone model are compared with recent experiments by Harris et al. on the specific base-catalyzed cleavage of a UpG dinucleotide. The calculated and measured free energies of activation match extremely well (ΔF(‡) = 19.9-20.8 vs 19.9 kcal/mol). Solvation is seen to play a crucial role and is characterized by a network of hydrogen bonds that envelopes the pentacoordinate dianionic phosphorane transition state and provides preferential stabilization relative to the reactant state.
Indexed as
Identifiers
What OpenQuestion holds
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.