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  Bringing metabolic networks to life: convenience rate law and thermodynamic constraints

Liebermeister, W., & Klipp, E. (2006). Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theoretical Biology & Medical Modelling, 3, 41-41. doi:10.1186/1742-4682-3-41.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8307-5 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-8308-3
Genre: Journal Article
Alternative Title : Theor Biol Med Model

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 Creators:
Liebermeister, Wolfram1, Author
Klipp, Edda2, Author              
Affiliations:
1Max Planck Society, escidoc:persistent13              
2Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, escidoc:1433554              

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 Abstract: Background Translating a known metabolic network into a dynamic model requires reasonable guesses of all enzyme parameters. In Bayesian parameter estimation, model parameters are described by a posterior probability distribution, which scores the potential parameter sets, showing how well each of them agrees with the data and with the prior assumptions made. Results We compute posterior distributions of kinetic parameters within a Bayesian framework, based on integration of kinetic, thermodynamic, metabolic, and proteomic data. The structure of the metabolic system (i.e., stoichiometries and enzyme regulation) needs to be known, and the reactions are modelled by convenience kinetics with thermodynamically independent parameters. The parameter posterior is computed in two separate steps: a first posterior summarises the available data on enzyme kinetic parameters; an improved second posterior is obtained by integrating metabolic fluxes, concentrations, and enzyme concentrations for one or more steady states. The data can be heterogenous, incomplete, and uncertain, and the posterior is approximated by a multivariate log-normal distribution. We apply the method to a model of the threonine synthesis pathway: the integration of metabolic data has little effect on the marginal posterior distributions of individual model parameters. Nevertheless, it leads to strong correlations between the parameters in the joint posterior distribution, which greatly improve the model predictions by the following Monte-Carlo simulations. Conclusion We present a standardised method to translate metabolic networks into dynamic models. To determine the model parameters, evidence from various experimental data is combined and weighted using Bayesian parameter estimation. The resulting posterior parameter distribution describes a statistical ensemble of parameter sets; the parameter variances and correlations can account for missing knowledge, measurement uncertainties, or biological variability. The posterior distribution can be used to sample model instances and to obtain probabilistic statements about the model's dynamic behaviour.

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Language(s): eng - English
 Dates: 2006-12-15
 Publication Status: Published in print
 Pages: -
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 Identifiers: eDoc: 309257
DOI: 10.1186/1742-4682-3-41
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Title: Theoretical Biology & Medical Modelling
  Alternative Title : Theor Biol Med Model
Source Genre: Journal
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Pages: - Volume / Issue: 3 Sequence Number: - Start / End Page: 41 - 41 Identifier: ISSN: 1742-4682