I'm testing a novel small compound (300Da) for binding to a protein (22000Da) and it seems to bind, but I am not sure which model to use to determine the KD of that interaction.
If I use 1:1 binding it's KD in macromolar range, but if I apply steady-state model than its pM ???
I attached the graph.
Also, can KD depend on flow rate? and what does it mean?
For this kind of data I would use the steady state interaction.
The association and dissociation rates are to fast to be reliable determined with a 1:1 kinetics model (also the jump in front of the association will not help).
The kinetics should be independent of the flow rate (and ligand density) provided that there is no mass transport limitation.