I am measuring protein-protein interaction using fluorescence polarization. Is there a tool to calculate theoretic fluorescence polarization vs. M.W. using dyes with different fluorescence lifetimes. The example figure is attached (from Fisher).
The difficulty with measuring a protein-protein interaction by fluorescence polarization is that the initial mass change is often not that large compared to the mass of the labeled protein, resulting in a small change in polarization.
FRET is more likely to give a good signal, but takes more effort to set up, since both proteins have to be labeled specifically, and the labels have to be close enough together to get a decent FRET efficiency. Usually this means doing some site-directed mutagenesis.
Chemical crosslinking, co-immunoprecipitation, and surface plasmon resonance are some other approaches.
Here is a paper that may help you with your calculations. Polarization is very powerful for determination of protein-protein interactions in part since polarization measurements are so accurate. Even if the MWs involved seem to large for the lifetime of the probe as long as there is even a small change on the polarization before and after the interaction the Kd can be determined. The second paper shows a dissociation curve based on only a small change in observed polarization.
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