Hello,
Say you have a protein that is giving variable KD values for its natural ligand (for reasons not completely understood) from assay to assay, but very consistent results within a given assay. Say you have the following data for control (C) and inhibitor treated (T) samples, where T is an inhibitor:
Assay 1: C: 1 nM, T: 10 nM
Assay 2: C: 8 nM, T: 80 nM
Assay 3: C: 5 nM, T: 50 nM
It's clear that the inhibitor treatment interferes with substrate binding, but it wouldn't show this if you averaged and plotted the binding curves. However, if you normalize the ligand concentrations (x axis) in each binding curve to the control KD of that assay, the data are very tight, because the normalized KD values are 1 KD for the uninhibited control in every assay, and 10 KDs for the inhibited samples. As example, in assay 2, 8 nM would be normalized to 1 KD, 1 nM would be normalized to 0.125 KDs, whereas in assay 1, 8 nM would be 8 KDs and 1 nM 1 KD.
Is it acceptable to do this? I have seen it done in Michaelis-menten kinetics (normalizing concentrations to KM), but I'm not sure how well accepted it is.
Thanks,
Nathan
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