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Public Library of Science, PLoS Computational Biology, 1(8), p. e1002352, 2012

DOI: 10.1371/journal.pcbi.1002352

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Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism

Journal article published in 2012 by Fiona Achcar, Barbara M. Bakker, Eduard J. Kerkhoven, Michael P. Barrett, Rainer Breitling ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the parasitic protozoan Trypanosoma brucei is a particularly well analysed example of a quantitative metabolic model, but so far it has been studied with a fixed set of parameters only. Here we evaluate the effect of parameter uncertainty. In order to define probability distributions for each parameter, information about the experimental sources and confidence intervals for all parameters were collected. We created a wiki-based website dedicated to the detailed documentation of this information: the SilicoTryp wiki (http://silicotryp.ibls.gla.ac.uk/wiki/Glycolysis). Using information collected in the wiki, we then assigned probability distributions to all parameters of the model. This allowed us to sample sets of alternative models, accurately representing our degree of uncertainty. Some properties of the model, such as the repartition of the glycolytic flux between the glycerol and pyruvate producing branches, are robust to these uncertainties. However, our analysis also allowed us to identify fragilities of the model leading to the accumulation of 3-phosphoglycerate and/or pyruvate. The analysis of the control coefficients revealed the importance of taking into account the uncertainties about the parameters, as the ranking of the reactions can be greatly affected. This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies. ?? 2012 Achcar et al.