Team:NYMUTaipei/ymim1
From 2012.igem.org
Objective
Before designing our experiment, we would like to do a simple simulation to estimate the efficiency and productivity of nitrogen for our modified bacteria.
Description
In order to produce nitrogen from nitrate, we needed to use MichaelisMenten’s equation to help us simulate the substrate concentration in a single cell.
Where v=reaction rate, [P]=product concentration, Vmax=max reaction rate, [S]=substrate concentration, Km= equilibrium constant of enzyme, Kcat=turnover number.
Our pathway looked like this
Reaction 2, 3, 4 were already in the E.coli before we engineered the bacteria. Reaction 1, 5, 6, 7 are the new pathways that we engineered.
For reaction 2, 3, 4, we used the equation .
As for the rest, we used instead.
To determine the enzyme concentration for our new pathways, we needed another two equations.
Where nplasmid= plasmid copy number in E.coli, P=promoter strength, NA= Avogadaros' Number, VEcoli= cell volume of E.coli, deltamrna=degradation rate of mRNA, alpha= translation rate of mRNA, gammaEnzyme=degradation rate or Enzyme
Combined the two equations, we got the relationship between enzyme concentration and time.
Then we combined the equation above with MichaelisMenten’s equation.

Modeling