Team:Botchan Lab Tokyo/Model
Modeling
Overview
Overview
Our purpose of modeling is to show correlation between the value of research and theoretical value by simulation the changing in accumulation amount of NH3 in time change.
Background
We incorporated it into MATLAB and visualized it by establishing a differential equation.
The flow of whole modeling project
The following model is a system affecting concentration change of NH3. Since nitrogenase is a catalyst, it influences the NH3 concentration increase. The rate of metabolism of ammonia is also considered in terms of increase.
The next ammonia produced will be reduced to glutamine via GS(glutamine synthetase) and the concentration will be reduced to make our final goal, glutamic acid. As for glutamine synthetase, occurrence is suppressed by using MSX. In the system that makes glutamic acid, α-ketoglutaric acid is used.
Therefore, the slight change in concentration of NH 3 can be described by the following differential equation. $$\frac{ d[NH3] }{ dt }=k_{Nit}[Nit]+v_{NH3}-k_{GluDH}[NH3][α-Keto]-k_GS[NH3][GSactive]$$ For nitrogenase, It was rewritten as $$k_{Nit}[Nit]=v_{Nit}= \frac{d[GFP]}{dt}$$ and the observed experimental value of GFP was used. It is rewritten as $$[GSactive] = 1-\frac{[GS-MSX]}{[MSX]}$$ and can be thought of as the MSX binding ability.
Result
At the result, we can know there is correlation because it is almost the same as the value of 0.02975 mM obtained by the experiment.