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Concept
Metabolic network modelling
Summary
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. 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:
Draft a reconstruction
Refine the model
Convert model into a mathematical/computational representation
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.
A metabolic reconstruction provides a highly mathematical, structured platform on which to understand the systems biology of metabolic pathways within an organism. The integration of biochemical metabolic pathways with rapidly available, annotated genome sequences has developed what are called genome-scale metabolic models. Simply put, these models correlate metabolic genes with metabolic pathways. In general, the more information about physiology, biochemistry and genetics is available for the target organism, the better the predictive capacity of the reconstructed models. Mechanically speaking, the process of reconstructing prokaryotic and eukaryotic metabolic networks is essentially the same. Having said this, eukaryote reconstructions are typically more challenging because of the size of genomes, coverage of knowledge, and the multitude of cellular compartments.
Official source
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