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DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression

View ORCID ProfileLaurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
doi: https://doi.org/10.1101/319962
Laurence Yang
aDepartment of Bioengineering, University of California at San Diego, La Jolla, CA 92093
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  • ORCID record for Laurence Yang
Ali Ebrahim
aDepartment of Bioengineering, University of California at San Diego, La Jolla, CA 92093
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Colton J. Lloyd
aDepartment of Bioengineering, University of California at San Diego, La Jolla, CA 92093
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Michael A. Saunders
cDepartment of Management Science and Engineering, Stanford University, Stanford, CA 94305
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Bernhard O. Palsson
aDepartment of Bioengineering, University of California at San Diego, La Jolla, CA 92093
bNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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  • For correspondence: palsson@ucsd.edu
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Abstract

Genome-scale models of metabolism and macromolecular expression (ME models) enable systems-level computation of proteome allocation coupled to metabolic phenotype. We develop dynamicME, an algorithm enabling time-course simulation of cell metabolism and protein expression. Our dynamicME correctly predicted the substrate utilization hierarchy on mixed carbon substrate medium. We also found good agreement between predicted and measured time-course expression profiles. ME models involve considerably more parameters than metabolic models (M models). We thus present two methods to calibrate ME models, specifically using time-course measurements such as from a (fed-) batch culture. Overall, dynamicME and the methods presented provide novel methods for understanding proteome allocation and metabolism under complex and transient environments, and to utilize time-course cell culture data for model-based interpretation or model refinement.

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Posted May 15, 2018.
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DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression
Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
bioRxiv 319962; doi: https://doi.org/10.1101/319962
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DynamicME: Dynamic simulation and refinement of integrated models of metabolism and protein expression
Laurence Yang, Ali Ebrahim, Colton J. Lloyd, Michael A. Saunders, Bernhard O. Palsson
bioRxiv 319962; doi: https://doi.org/10.1101/319962

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