Simplified mechanistic models of gene regulation for analysis and design
File(s)
Published version
Supporting information
Author(s)
Hancock, E
Stan, G-B
Arpino, J
Papachristodoulou, A
Type
Journal Article
Abstract
Simplified mechanistic models of gene regulation are fundamental to systems biology and essential for synthetic biology. However, conventional simplified models typically have outputs that are not directly measurable and are based on assumptions that do not often hold under experimental conditions. To resolve these issues, we propose a ‘model reduction’ methodology and simplified kinetic models of total mRNA and total protein concentration, which link measurements, models and biochemical mechanisms. The proposed approach is based on assumptions that hold generally and include typical cases in systems and synthetic biology where conventional models do not hold. We use novel assumptions regarding the ‘speed of reactions’, which are required for the methodology to be consistent with experimental data. We also apply the methodology to propose simplified models of gene regulation in the presence of multiple protein binding sites, providing both biological insights and an illustration of the generality of the methodology. Lastly, we show that modelling total protein concentration allows us to address key questions on gene regulation, such as efficiency, burden, competition and modularity.
Date Issued
2015-06-10
Date Acceptance
2015-05-06
Citation
Journal of the Royal Society Interface, 2015, 12 (108)
ISSN
1742-5689
Publisher
The Royal Society
Journal / Book Title
Journal of the Royal Society Interface
Volume
12
Issue
108
Copyright Statement
© 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.
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Publication Status
Published