ArticleNucleic acids research2015
Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation.
Article in Nucleic acids research, 2015. 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.
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- A model for ribosome translocation based on the alternated displacement of its subunits.European biophysics journal : EBJ · 2023Article
- Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.Nucleic acids research · 2023Article
- Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation.The EMBO journal · 2021Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- The dynamics of subunit rotation in a eukaryotic ribosome.Biophysica · 2021Article
- A steric gate controls P/E hybrid-state formation of tRNA on the ribosome.Nature communications · 2020Article
- tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition.Biophysical journal · 2020Article
- Aminoglycoside interactions and impacts on the eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- The ribosome moves: RNA mechanics and translocation.Nature structural & molecular biology · 2017Article
- The translation elongation cycle-capturing multiple states by cryo-electron microscopy.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Whither Ribosome Structure and Dynamics Research? (A Perspective).Journal of molecular biology · 2016Review
- A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest.Nature communications · 2016Article
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4 authors.
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Abstract
During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation.
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