ArticleScientific reports2015
Sensitivity of mRNA Translation.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Negative feedback and oscillations in a model for mRNA translation.Journal of the Royal Society, Interface · 2025Article
- On the gain of entrainment in theJournal of the Royal Society, Interface · 2023Article
- Translation in the cell under fierce competition for shared resources: a mathematical model.Journal of the Royal Society, Interface · 2022Article
- Determinants of efficient modulation of ribosomal traffic jams.Computational and structural biotechnology journal · 2021Article
- Networks of ribosome flow models for modeling and analyzing intracellular traffic.Scientific reports · 2019Article
- Genome-Scale Analysis of Perturbations in Translation Elongation Based on a Computational Model.Scientific reports · 2018Article
- Entrainment in the master equation.Royal Society open science · 2018Article
- Dynamics of translation can determine the spatial organization of membrane-bound proteins and their mRNA.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Ribosome flow model with extended objects.Journal of the Royal Society, Interface · 2017Article
- Optimal Translation Along a Circular mRNA.Scientific reports · 2017Article
- Optimal Down Regulation of mRNA Translation.Scientific reports · 2017Article
- Article
- A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics.PloS one · 2017Article
- Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution.Nucleic acids research · 2016Article
- A model for competition for ribosomes in the cell.Journal of the Royal Society, Interface · 2016Article
- Article
- Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.RNA biology · 2015Article
- Controllability Analysis and Control Synthesis for the Ribosome Flow Model.IEEE/ACM transactions on computational biology and bioinformaticsArticle
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3 authors.
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Abstract
Using the dynamic mean-field approximation of the totally asymmetric simple exclusion process (TASEP), we investigate the effect of small changes in the initiation, elongation, and termination rates along the mRNA strand on the steady-state protein translation rate. We show that the sensitivity of mRNA translation is equal to the sensitivity of the maximal eigenvalue of a symmetric, nonnegative, tridiagonal, and irreducible matrix. This leads to new analytical results as well as efficient numerical schemes that are applicable for large-scale models. Our results show that in the usual endogenous case, when initiation is more rate-limiting than elongation, the sensitivity of the translation rate to small mutations rapidly increases towards the 5' end of the ORF. When the initiation rate is high, as may be the case for highly expressed and/or heterologous optimized genes, the maximal sensitivity is with respect to the elongation rates at the middle of the mRNA strand. We also show that the maximal possible effect of a small increase/decrease in any of the rates along the mRNA is an increase/decrease of the same magnitude in the translation rate. These results are in agreement with previous molecular evolutionary and synthetic biology experimental studies.
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