FRET data analysis with simulation

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.

Answer 1

[Arthur Goldsipe]

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.

-Arthur

[Parul Tewatia]

Thanks a lot Arthur for your answer.

You got it right, I am struggling with fitting the ratio. A command line example would be a great help. My matlab version is R2019b

I already added the reaction to the model and made repeated assignemnt, as its activity ratio i put in as AKARp/totalAKAR

where total AKAR has all forms of AKAR4 i.e. AKAR4+PKAc_AKAR4+AKAR4p

the main aim is to obtain parameter set that fits the model.

and then test it with some mutaion data that i have.

thanks again for your help.

best

Parul

[Arthur Goldsipe]

If you want a command-line example, I suggest the one from the sbiofit reference page or one of these examples. The main difference is that when you map the model response to a column in the data, you will use the name of the repeated assignment variable on the left-hand side of the expression and the name of the relevant variable in your experimental data as the right-hand side of the expression.

[Parul Tewatia]

aha thank you arthur, now i have a reference to look at.

Thanks again for all your help.

best

Parul