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Team:NYMU-Taipei/ymim1
From 2012.igem.org
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Latest revision as of 17:28, 26 October 2012
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 Michaelis-Menten’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 Michaelis-Menten’s equation.
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Modeling
