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Metabolic network modelling

Metabolic network showing interactions between enzymes and metabolites in the Arabidopsis thaliana citric acid cycle. Enzymes and metabolites are the red dots and interactions between them are the lines.
Metabolic network model for Escherichia coli

Metabolic network modelling, also known as metabolic network reconstruction or metabolic pathway analysis, allows for an in-depth insight into the molecular mechanisms of a particular organism. In particular, these models correlate the genome with molecular physiology.[1] A reconstruction breaks down metabolic pathways (such as glycolysis and the citric acid cycle) into their respective reactions and enzymes, and analyzes them within the perspective of the entire network. In simplified terms, a reconstruction collects all of the relevant metabolic information of an organism and compiles it in a mathematical model. Validation and analysis of reconstructions can allow identification of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. This knowledge can then be applied to create novel biotechnology.

In general, the process to build a reconstruction is as follows:

  1. Draft a reconstruction
  2. Refine the model
  3. Convert model into a mathematical/computational representation
  4. Evaluate and debug model through experimentation

The related method of flux balance analysis seeks to mathematically simulate metabolism in genome-scale reconstructions of metabolic networks.

  1. ^ Francke C, Siezen RJ, Teusink B (November 2005). "Reconstructing the metabolic network of a bacterium from its genome". Trends in Microbiology. 13 (11): 550–558. doi:10.1016/j.tim.2005.09.001. PMID 16169729.