ArticleNature communications2020
A steric gate controls P/E hybrid-state formation of tRNA on the ribosome.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- Ribosomal protein bL27 protects translating ribosomes from tmRNA-SmpB.Science advances · 2026Article
- Observing intersubunit dynamics in single yeast ribosomes.Nucleic acids research · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Ribosomal Protein bL27 Protects Translating Ribosomes from tmRNA-SmpB.bioRxiv : the preprint server for biology · 2026Article
- Tracking the protein conformational motions driving HIV-1 membrane fusion.Scientific reports · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Sequence-dependent conformational preferences of disordered single-stranded RNA.Cell reports. Physical science · 2024Article
- Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.Nature communications · 2024Article
- Structural insights into the mechanism of GTP initiation of microtubule assembly.Nature communications · 2023Article
- Study of fusion peptide release for the spike protein of SARS-CoV-2.RSC advances · 2023Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- Article
- The dynamics of subunit rotation in a eukaryotic ribosome.Biophysica · 2021Article
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ribosome is a biomolecular machine that undergoes multiple large-scale structural rearrangements during protein elongation. Here, we focus on a conformational rearrangement during translocation, known as P/E hybrid-state formation. Using a model that explicitly represents all non-hydrogen atoms, we simulated more than 120 spontaneous transitions, where the tRNA molecule is displaced between the P and E sites of the large subunit. In addition to predicting a free-energy landscape that is consistent with previous experimental observations, the simulations reveal how a six-residue gate-like region can limit P/E formation, where sub-angstrom structural perturbations lead to an order-of-magnitude change in kinetics. Thus, this precisely defined set of residues represents a novel target that may be used to control functional dynamics in bacterial ribosomes. This theoretical analysis establishes a direct relationship between ribosome structure and large-scale dynamics, and it suggests how next-generation experiments may precisely dissect the energetics of hybrid formation on the ribosome.
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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.