ArticlePhysical biology2008
The ribosome structure controls and directs mRNA entry, translocation and exit dynamics.
Article in Physical biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 69 citations in OpenAlex.
- Interplay of the ribosome A and CAR sites.NAR genomics and bioinformatics · 2026Article
- Mutations in ribosomal protein uS5 alter translation fidelity and mutagenesis inJournal of bacteriology · 2025Article
- Antiviral responses versus virus-induced cellular shutoff: a game of thrones between influenza A virus NS1 and SARS-CoV-2 Nsp1.Frontiers in cellular and infection microbiology · 2024Review
- Ribosomal Protein uS5 and Friends: Protein-Protein Interactions Involved in Ribosome Assembly and Beyond.Biomolecules · 2023Review
- Sarecycline inhibits protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism.Nucleic acids research · 2023Article
- Unravelling How Single-Stranded DNA Binding Protein Coordinates DNA Metabolism Using Single-Molecule Approaches.International journal of molecular sciences · 2023Review
- Modeling the ribosome as a bipartite graph.PloS one · 2022Article
- The energetics of subunit rotation in the ribosome.Biophysical reviews · 2021Review
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
- Programmed -1 ribosomal frameshifting from the perspective of the conformational dynamics of mRNA and ribosomes.Computational and structural biotechnology journal · 2021Review
- Selective translation by alternative bacterial ribosomes.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Network theory of the bacterial ribosome.PloS one · 2020Article
- Dual DNA Rulers to Study the Mechanism of Ribosome Translocation with Single-Nucleotide Resolution.Journal of visualized experiments : JoVE · 2019Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Structures of Mycobacterium smegmatis 70S ribosomes in complex with HPF, tmRNA, and P-tRNA.Scientific reports · 2018Article
- Dual DNA rulers reveal an 'mRNA looping' intermediate state during ribosome translocation.RNA biology · 2018Article
- Unique localization of the plastid-specific ribosomal proteins in the chloroplast ribosome small subunit provides mechanistic insights into the chloroplastic translation.Nucleic acids research · 2017Article
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- Distributions of experimental protein structures on coarse-grained free energy landscapes.The Journal of chemical physics · 2015Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine-Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit.
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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.