FRET data analysis with simulation

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Parul Tewatia
Parul Tewatia on 23 May 2020
Commented: Parul Tewatia on 27 May 2020
I am having FRET data where the FRET ratio of AKAR the reporter for active PKA is calculated from the graph going from ratio 1.08 (dephosphorylated AKAR) to 1.9 (fully phos AKAR i.e AKARp)
the reaction is PKAc+AKAR4<-> PKAcAKAR4-> AKARp
i have developed a model in simbiology and want to fit the experimetal data to the output ratio of model and then calculate maximum Active PKA (PKAc) based on the ratio.
is there any example to do the same or anyone has done something similar.

Answers (1)

Arthur Goldsipe
Arthur Goldsipe on 26 May 2020
Hi Parul,
This sounds like a fitting problem that can be solved using sbiofit from the command line or using a fit program within the SimBiology graphical app. You can find an example of fitting from the command line on this reference page.
But maybe the detail you are struggling with is how to fit to ratio? If that's the case, I can think of a couple of ways to accomplish that. Perhaps the most straightforward would be to add the relevant ratio to your SimBiology model using a repeated assignment rule. If I understand correctly, your measurements correspond to the ratio of AKAR to AKARp. In that case, you could add a parameter (let's call it FRET) to the model, make sure it is non-constant, and then add a repeated assignment rule FRET = AKAR/AKARp. Then, you can fit your simulated values of FRET to your actual measurements.
If you need more details, please let me know whether you want a command-line example or an example in the SimBiology graphical app, and what version of MATLAB you are using.
Parul Tewatia
Parul Tewatia on 27 May 2020
aha thank you arthur, now i have a reference to look at.
Thanks again for all your help.

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