I am working with SimBiology to fit the parameters of a three-step kinetic model (rate constants: k1, ki1, k2, ki2, k3, ki3) to a series of experimental time courses of an enzyme reaction. Additionally, I have independently obtained experimental values of kcat and Km for the reaction. The expressions for kca and Km terms of the rate constants for the three-step model are:
kcat = (k2.*k3)./(k2 + ki2+ k3)
Km = ((k2.*k3 + ki1.*(ki2 + k3))/(k1.*(k2 + ki2 + k3))).
To constrain the estimation of the rate constants, I included two 'Algebraic Rules' in SimBiology:
1) 20 < (k2.*k3)./(k2 + ki2+ k3)
2) 20 < ((k2.*k3 + ki1.*(ki2 + k3))/(k1.*(k2 + ki2 + k3)))
In this way, I aim to ensure that the estimated rate constants satisfy the known values of kcatk_{cat}kcat and KmK_mKm. However, when I run the SimBiology interface to perform the fitting, I receive the following error messages:
- "Model is overdetermined by the following algebraic rules: '20 < (k2·k3)/(k2 + ki2 + k3)' and '20 < ((k2·k3 + ki1·(ki2 + k3))/(k1·(k2 + ki2 + k3)))'. At least one species, parameter, or compartment in this rule must be non-constant and not defined by a reaction rate, rate rule, or repeated assignment rule."
- "An error occurred while trying to compile the model."
How should I proceed to constrain the fitting of the rate constants for the three-step kinetic model using these two expressions for kcat and Km?"
Best regards
Luis B
