ArticlePLoS biology2013
Positively charged residues are the major determinants of ribosomal velocity.
Article in PLoS biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 188 papers.
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Who cites it
188 citing papers in PubMed, 314 citations in OpenAlex.
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- Transfer RNA acetylation regulates in vivo mammalian stress signaling.Science advances · 2025Article
- Increasing recombinant protein production in E. coli via FACS-based selection of N-terminal coding DNA libraries.The FEBS journal · 2025Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- AntigenBoost: enhanced mRNA-based antigen expression through rational amino acid substitution.Briefings in bioinformatics · 2024Article
- Transfer RNA acetylation regulates in vivo mammalian stress signaling.bioRxiv : the preprint server for biology · 2024Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
128 more citing papers are in PubMed but not listed here.
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Both for understanding mechanisms of disease and for the design of transgenes, it is important to understand the determinants of ribosome velocity, as changes in the rate of translation are important for protein folding, error attenuation, and localization. While there is great variation in ribosomal occupancy along even a single transcript, what determines a ribosome's occupancy is unclear. We examine this issue using data from a ribosomal footprinting assay in yeast. While codon usage is classically considered a major determinant, we find no evidence for this. By contrast, we find that positively charged amino acids greatly retard ribosomes downstream from where they are encoded, consistent with the suggestion that positively charged residues interact with the negatively charged ribosomal exit tunnel. Such slowing is independent of and greater than the average effect owing to mRNA folding. The effect of charged amino acids is additive, with ribosomal occupancy well-predicted by a linear fit to the density of positively charged residues. We thus expect that a translated poly-A tail, encoding for positively charged lysines regardless of the reading frame, would act as a sandtrap for the ribosome, consistent with experimental data.
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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.