Modeling
Flux balance analysis is a way to visualize the flow of metabolites through a metabolic network. First this system takes into account the stoichiometry of the biophysical kinetics equations within the natural metabolic network. Then the system looks at the rate at which metabolites are converted into various cellular products such as nucleotides and amino acids to be utilized by the cell. Due to different concentrations of amino acids in different organisms, creating an organism that produces a protein from a different organism may require certain metabolites to be upregulated. This modeling system allows us to predict which metabolites might need to be increased in order to produce enough amino acids the transgenic protein would require to get made accurately.
This graph compares and contrasts the different amino acid concentrations in our chassis, Glycine Max, compared to the concentrations of amino acids encoded by our milk proteins. By observing which amino acids are at lower concentrations in our chassis that are required for protein production, we can analyze which metabolites in the metabolic network of our chassis that might be beneficial to upregulate.
By pin-pointing where the deficits in amino acid concentrations are, we are able to use this map of amino acid biosynthesis to determine which metabolites will need to be upregulated. For example, cysteine levels are very low in Glycine max but required for protein synthesis of both Alpha-Lactobulin and Beta-Lactoglobulin. We can target specific metabolites to upregulate via the addition of the gene that creates that metabolite to our final plasmid
In the case of cystine, adding another gene that codes for Phosphoserine and Cystathionine into our Glycine Max chassis could lead to the production of more Cysteine within the plant.