Fitting kinetic parameters for a chemical reaction model without experimental data

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I need to use SimBiology to model monomeric enzyme systems without any experimental data. I am:
1) Writing the reaction scheme into the SimBiology workspace
2) Assigning random numbers as the kinetic parameters (This is where I think my largest problem is!!)
3) Creating the time-course data for multiple concentrations of substrate
4) Taking the first 10 percent and fitting it with a line (finding velocity)
5) Plotting Substrate concentration (x-axis) v.s. velocity (y-axis)
6) Fitting the plot to the Hill equation F(x)=(a.*x^(n))./(b.^n +x.^n) with the hopes of finding a Hill coefficient, n, greater than 2 to make the system cooperative.
I need to know:
1) how to chose kinetic parameters (rate constants) that will make the system cooperative ( n >= 2)
2) Will I need to use the optimization toolbox in conjunction with SimBiology?
Any help is greatly appreciated. -Rob

Answers (2)

Arthur Goldsipe
Arthur Goldsipe on 6 Mar 2014
I don't think it's possible for anyone to answer that question without knowing the details of your reaction scheme. It's quite possible that your model is simply not capable of yielding cooperative behavior for any numerical values. For example, the sort of cooperativity that you see in Hill kinetics often arises from having multiple binding sites.
If you want to definitely prove whether or not your model is capable of yielding cooperative behavior, you may need to take a different approach. For example, I have seen perturbation analysis used to understand the different modes of behavior of biochemical models.
Good luck!
-Arthur

Aakriti Jain
Aakriti Jain on 29 Apr 2015
Hi, I have a similar question as Robert, but maybe I can explain my model a little better:
I have a protein which only gets activated when three different binding sites on DNA are all bound; however, the three sites are independent and interacting (so binding on one site affects binding in the next one differently).. I've attached a picture that might help to see the three layers of reactions (or it might be just confusing, in which case, you can just ignore it!)
I'm trying to do a parameter scan to find cooperativity in this system, but I'm kind of stuck... I don't know how to figure out the values for the binding constants in such as way as to achieve cooperativity? Is it mostly guess and check or am I missing something in simbiology that I can use the help me find the cooperativity factor?

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