I have immobilized a membrane protein (approx 65 kDa) as ligand via biotin on an avidin chip (target level approx 800 pg/mm2) and measured the binding of an antibody to it. The Kd is around 500 pM. When inverting the setup (i.e. ligand: antibody immobilized via amine-coupling; analyte: membrane protein), the Kd increases to approx 120 nM. Has anyone observed such an effect and has an explanation for it?
Thank you very much for advice.