ArticleNature communications2016
Steric interactions lead to collective tilting motion in the ribosome during mRNA-tRNA translocation.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 66 citations in OpenAlex.
- Ribosomal protein bL27 protects translating ribosomes from tmRNA-SmpB.Science advances · 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
- Mettl15-Mettl17 modulates the transition from early to late pre-mitoribosome.Structure (London, England : 1993) · 2025Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Simulating biomolecules for physiological timescales.Current opinion in structural biology · 2025Review
- Alternate conformational trajectories in ribosome translocation.PLoS computational biology · 2024Article
- Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk.Nature communications · 2024Article
- High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.International journal of molecular sciences · 2023Article
- Structural insights into the mechanism of GTP initiation of microtubule assembly.Nature communications · 2023Article
- Cryo-electron microscopy structure and translocation mechanism of the crenarchaeal ribosome.Nucleic acids research · 2023Article
- Study of fusion peptide release for the spike protein of SARS-CoV-2.RSC advances · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Ratchet, swivel, tilt and roll: a complete description of subunit rotation in the ribosome.Nucleic acids research · 2023Article
- Hyper-swivel head domain motions are required for complete mRNA-tRNA translocation and ribosome resetting.Nucleic acids research · 2022Article
- Druggable differences: Targeting mechanistic differences between trans-translation and translation for selective antibiotic action.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Article
- Selection of start codon during mRNA scanning in eukaryotic translation initiation.Communications biology · 2022Article
- SMOG 2 and OpenSMOG: Extending the limits of structure-based models.Protein science : a publication of the Protein Society · 2022Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translocation of mRNA and tRNA through the ribosome is associated with large-scale rearrangements of the head domain in the 30S ribosomal subunit. To elucidate the relationship between 30S head dynamics and mRNA-tRNA displacement, we apply molecular dynamics simulations using an all-atom structure-based model. Here we provide a statistical analysis of 250 spontaneous transitions between the A/P-P/E and P/P-E/E ensembles. Consistent with structural studies, the ribosome samples a chimeric ap/P-pe/E intermediate, where the 30S head is rotated ∼18°. It then transiently populates a previously unreported intermediate ensemble, which is characterized by a ∼10° tilt of the head. To identify the origins of head tilting, we analyse 781 additional simulations in which specific steric features are perturbed. These calculations show that head tilting may be attributed to specific steric interactions between tRNA and the 30S subunit (PE loop and protein S13). Taken together, this study demonstrates how molecular structure can give rise to large-scale collective rearrangements.
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