ArticleJournal of the American Chemical Society2015
Peptide Bond Formation Mechanism Catalyzed by Ribosome.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed.
- Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation.Journal of the American Chemical Society · 2026Article
- The pivotal role of β-lactone stereochemistry in the development of SARS-CoV-2 MProtein science : a publication of the Protein Society · 2026Article
- Asymmetric isopeptide bond steers directional genomic RNA egress from icosahedral virus.Science advances · 2025Article
- Comparing Force Field Treatments in QM/MM Studies of the SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Mechanism.Journal of chemical theory and computation · 2025Article
- Electrostatics as a Guiding Principle in Understanding and Designing Enzymes.Journal of chemical theory and computation · 2024Review
- Perspectives on Multiscale Colloid-Based Materials for Biomedical Applications.Langmuir : the ACS journal of surfaces and colloids · 2023Review
- Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.ACS central science · 2023Article
- The Peptidyl Transferase Center: a Window to the Past.Microbiology and molecular biology reviews : MMBR · 2021Article
- Inhibition of the Eukaryotic 80S Ribosome as a Potential Anticancer Therapy: A Structural Perspective.Cancers · 2021Review
- Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Mechanistic alternatives for peptide bond formation on the ribosome.Nucleic acids research · 2018Article
- Origins of the Mechanochemical Coupling of Peptide Bond Formation to Protein Synthesis.Journal of the American Chemical Society · 2018Article
- Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4'-O-Nucleotidyltransferase.Frontiers in chemistry · 2018Article
- A close-up view of codon selection in eukaryotic initiation.RNA biology · 2017Article
- Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation-A Theoretical Study.Molecules (Basel, Switzerland) · 2017Article
- Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease.Journal of the American Chemical Society · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
In this paper we present a study of the peptide bond formation reaction catalyzed by ribosome. Different mechanistic proposals have been explored by means of Free Energy Perturbation methods within hybrid QM/MM potentials, where the chemical system has been described by the M06-2X functional and the environment by means of the AMBER force field. According to our results, the most favorable mechanism in the ribosome would proceed through an eight-membered ring transition state, involving a proton shuttle mechanism through the hydroxyl group of the sugar and a water molecule. This transition state is similar to that described for the reaction in solution (J. Am. Chem. Soc. 2013, 135, 8708-8719), but the reaction mechanisms are noticeably different. Our simulations reproduce the experimentally determined catalytic effect of ribosome that can be explained by the different behavior of the two environments. While the solvent reorganizes during the chemical process involving an entropic penalty, the ribosome is preorganized in the formation of the Michaelis complex and does not suffer important changes along the reaction, dampening the charge redistribution of the chemical system.
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.