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A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression

Pandey, Ayush and Murray, Richard M. (2020) A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20201207-130405486

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Abstract

We derive phenomenological models of gene expression from a mechanistic description of chemical reactions using an automated model reduction method. Using this method, we get analytical descriptions and computational performance guarantees to compare the reduced dynamics with the full models. We develop a new two-state model with the dynamics of the available free ribosomes in the system and the protein concentration. We show that this new two-state model captures the detailed mass-action kinetics of the chemical reaction network under various biologically plausible conditions on model parameters. On comparing the performance of this model with the commonly used mRNA transcript-protein dynamical model for gene expression, we analytically show that the free ribosome and protein model has superior error and robustness performance.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.11.25.399287DOIDiscussion Paper
https://github.com/ayush9pandey/autoReduceRelated ItemData/Code
https://colab.research.google.com/drive/1JEqCgJAxy9jCYYcuicwLfy_Oa2RpbX11?usp=sharingRelated ItemData/Code
ORCID:
AuthorORCID
Pandey, Ayush0000-0003-3590-4459
Murray, Richard M.0000-0002-5785-7481
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. This version posted November 26, 2020. The authors thank Ankita Roychoudhury for improving and providing feedback on the AutoReduce Python package that is used to derive the different models shown in this document. This research is sponsored in part by the National Science Foundation under grant number: CBET-1903477 and the Defense Advanced Research Projects Agency (Agreement HR0011-17-2-0008). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred. The authors have declared no competing interest.
Funders:
Funding AgencyGrant Number
NSFCBET-1903477
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0008
Record Number:CaltechAUTHORS:20201207-130405486
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20201207-130405486
Official Citation:A two-state ribosome and protein model can robustly capture the chemical reaction dynamics of gene expression. Ayush Pandey, Richard M. Murray. bioRxiv 2020.11.25.399287; doi: https://doi.org/10.1101/2020.11.25.399287
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:106947
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:07 Dec 2020 21:11
Last Modified:07 Dec 2020 21:11

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