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.