ReviewJournal of molecular biology2016
Ribosome Mechanics Informs about Mechanism.
Review in Journal of molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 30 citations in OpenAlex.
- Interpreting human genetic variation at atomic resolution.Nature genetics · 2026Review
- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
- The influence of downstream structured elements within mRNA on the dynamics of intersubunit rotation in ribosomes.RNA (New York, N.Y.) · 2025Article
- Review
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Physiological cost of antibiotic resistance: Insights from a ribosome variant in bacteria.Science advances · 2024Article
- Tandem mass tag (TMT) labeling-based quantitative proteomic analysis reveals the cellular protein characteristics of 16HBE cells infected with coxsackievirus A10 and the potential effect of HMGB1 on viral replication.Archives of virology · 2023Article
- Predicting allosteric pockets in protein biological assemblages.Bioinformatics (Oxford, England) · 2023Article
- Modeling the ribosome as a bipartite graph.PloS one · 2022Article
- hdANM: a new comprehensive dynamics model for protein hinges.Biophysical journal · 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
- Network theory of the bacterial ribosome.PloS one · 2020Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- The Expansion Segments of 28S Ribosomal RNA Extensively Match Human Messenger RNAs.Frontiers in genetics · 2018Article
- The fluctuating ribosome: thermal molecular dynamics characterized by neutron scattering.Scientific reports · 2016Article
- Challenges in RNA Structural Modeling and Design.Journal of molecular biology · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The essential aspects of the ribosome's mechanism can be extracted from coarse-grained simulations, including the ratchet motion, the movement together of critical bases at the decoding center, and movements of the peptide tunnel lining that assist in the expulsion of the synthesized peptide. Because of its large size, coarse graining helps to simplify and to aid in the understanding of its mechanism. Results presented here utilize coarse-grained elastic network modeling to extract the dynamics, and both RNAs and proteins are coarse grained. We review our previous results, showing the well-known ratchet motions and the motions in the peptide tunnel and in the mRNA tunnel. The motions of the lining of the peptide tunnel appear to assist in the expulsion of the growing peptide chain, and clamps at the ends of the mRNA tunnel with three proteins ensure that the mRNA is held tightly during decoding and essential for the helicase activity at the entrance. The entry clamp may also assist in base recognition to ensure proper selection of the incoming tRNA. The overall precision of the ribosome machine-like motions is remarkable.
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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.