ArticleStructure (London, England : 1993)2010
Recognition of the regulatory nascent chain TnaC by the ribosome.
Article in Structure (London, England : 1993), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 44 citations in OpenAlex.
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.Nature chemistry · 2023Article
- Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria.Journal of molecular biology · 2022Review
- Exploring Allosteric Signaling in the Exit Tunnel of the Bacterial Ribosome by Molecular Dynamics Simulations and Residue Network Model.Frontiers in molecular biosciences · 2020Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel.Journal of molecular biology · 2017Article
- Regional discrimination and propagation of local rearrangements along the ribosomal exit tunnel.Journal of molecular biology · 2014Article
- Interactions of the TnaC nascent peptide with rRNA in the exit tunnel enable the ribosome to respond to free tryptophan.Nucleic acids research · 2014Article
- Single-molecule nanometry for biological physics.Reports on progress in physics. Physical Society (Great Britain) · 2013Review
- Cryo-electron microscopy modeling by the molecular dynamics flexible fitting method.Biopolymers · 2012Article
- Mechanisms of SecM-mediated stalling in the ribosome.Biophysical journal · 2012Article
- Computational studies of molecular machines: the ribosome.Current opinion in structural biology · 2012Review
- Arginine changes the conformation of the arginine attenuator peptide relative to the ribosome tunnel.Journal of molecular biology · 2012Article
- Crucial elements that maintain the interactions between the regulatory TnaC peptide and the ribosome exit tunnel responsible for Trp inhibition of ribosome function.Nucleic acids research · 2012Article
- A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.PLoS computational biology · 2012Article
- Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel.Journal of molecular biology · 2011Article
- Free energy of nascent-chain folding in the translocon.Journal of the American Chemical Society · 2011Article
- Applications of the molecular dynamics flexible fitting method.Journal of structural biology · 2011Article
- Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin.Biophysical journal · 2010Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Regulatory nascent chains interact with the ribosomal exit tunnel and modulate their own translation. To characterize nascent chain recognition by the ribosome at the atomic level, extensive molecular dynamics simulations of TnaC, the leader peptide of the tryptophanase operon, inside the exit tunnel were performed for an aggregate time of 2.1 mus. The simulations, complemented by quantum chemistry calculations, suggest that the critical TnaC residue W12 is recognized by the ribosome via a cation-pi interaction, whereas TnaC's D16 forms salt bridges with ribosomal proteins. The simulations also show that TnaC-mediated translational arrest does not involve a swinging of ribosomal protein L22, as previously proposed. Furthermore, bioinformatic analyses and simulations suggest nascent chain elements that may prevent translational arrest in various organisms. Altogether, the current study unveils atomic-detail interactions that explain the role of elements of TnaC and the ribosome essential for translational arrest.
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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.