ArticleNature2010
Principles of stop-codon reading on the ribosome.
Article in Nature, 2010. 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, 68 citations in OpenAlex.
- Article
- Collateral Toxicity Limits the Evolution of Bacterial Release Factor 2 toward Total Omnipotence.Molecular biology and evolution · 2020Article
- Molecular determinants of release factor 2 for ArfA-mediated ribosome rescue.The Journal of biological chemistry · 2020Article
- The structural basis for release-factor activation during translation termination revealed by time-resolved cryogenic electron microscopy.Nature communications · 2019Article
- Ribosome Structure, Function, and Early Evolution.International journal of molecular sciences · 2018Review
- Mechanism of premature translation termination on a sense codon.The Journal of biological chemistry · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Atomic mutagenesis of stop codon nucleotides reveals the chemical prerequisites for release factor-mediated peptide release.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Origin of the omnipotence of eukaryotic release factor 1.Nature communications · 2017Article
- R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteriaThe Journal of biological chemistry · 2017Article
- A close-up view of codon selection in eukaryotic initiation.RNA biology · 2017Article
- Dynamic basis of fidelity and speed in translation: Coordinated multistep mechanisms of elongation and termination.Protein science : a publication of the Protein Society · 2017Review
- Induced fit of the peptidyl-transferase center of the ribosome and conformational freedom of the esterified amino acids.RNA (New York, N.Y.) · 2017Article
- Structural Insights into tRNA Dynamics on the Ribosome.International journal of molecular sciences · 2015Review
- Why base tautomerization does not cause errors in mRNA decoding on the ribosome.Nucleic acids research · 2014Article
- Computational prediction of alanine scanning and ligand binding energetics in G-protein coupled receptors.PLoS computational biology · 2014Article
- Recoding the genetic code with selenocysteine.Angewandte Chemie (International ed. in English) · 2014Article
- Article
- Efficiency of puromycin-based technologies mediated by release factors and a ribosome recycling factor.Protein engineering, design & selection : PEDS · 2013Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In termination of protein synthesis, the bacterial release factors RF1 and RF2 bind to the ribosome through specific recognition of messenger RNA stop codons and trigger hydrolysis of the bond between the nascent polypeptide and the transfer RNA at the peptidyl-tRNA site, thereby releasing the newly synthesized protein. The release factors are highly specific for a U in the first stop-codon position and recognize different combinations of purines in the second and third positions, with RF1 reading UAA and UAG and RF2 reading UAA and UGA. With recently determined crystal structures of termination complexes, it has become possible to decipher the energetics of stop-codon reading by computational analysis and to clarify the origin of the high release-factor binding accuracy. Here we report molecular dynamics free-energy calculations on different cognate and non-cognate termination complexes. The simulations quantitatively explain the basic principles of decoding in all three codon positions and reveal the key elements responsible for specificity of the release factors. The overall reading mechanism involves hitherto unidentified interactions and recognition switches that cannot be described in terms of a tripeptide anticodon model. Further simulations of complexes with tRNA(Trp), the tRNA recognizing the triplet codon for Trp, explain the observation of a 'leaky' stop codon and highlight the fundamentally different third position reading by RF2, which leads to a high stop-codon specificity with strong discrimination against the Trp codon. The simulations clearly illustrate the versatility of codon reading by protein, which goes far beyond tRNA mimicry.
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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.