Add Enzyme concentration

[Kiana Hadd]

Hi,

I am new to kinetic modelling. I like to model a network of eight reactions that have the following kinetics:

In this model, Enzyme and substrate concentrations are unknown, but I have the value for fluxes and kinetic parameters. When defining a function for kinetics, we can only include substrates, products, modifiers and parameters. I am wondering how can I add the enzyme concentration to the kinetics and how can I run some simulations to obtain changes of enzyme concentration per event.

Alternatively, I used MATLAB ODE15 to solve this system but the results were not satisfactory (concentrations became negative).

I appreciate any reply to this threat.

Thank you.

[Frank Bergmann]

Hello Kianah, 

whether you use the enzyme as product, substrate or modifier, depends entirely on the abstractions you use for your reaction. Modifiers are in generally used for species (including enzymes) that are not consumed or produced by a reaction, but still take part in it. That fits enzymes for most reactions, where you don't explicitly model the complex formation. 

If you show us your matlab code you used, it would be easier to give you a definite answer. 

cheers

Frank