Experimental design for kinetic analysis of protein-protein interactions with surface plasmon resonance biosensors

The reaction between antibody immobilized to surfaces, with and without a dextran matrix, and antigen in solution was studied using surface plasmon resonance detection. The use of a reference surface made it possible to identify conditions where a response related to changes in matrix conformation could be ignored. It was possible therefore to improve data quality by separating signals related to binding events from signals due to differences in refractive index between sample and running buffer. When antigen was injected over antibody immobilized to surfaces with and without dextran matrix the binding curves were virtually superimposable. Consequently, no binding artifacts associated with the dextran matrix were observed. Sets of binding curves obtained with different antigen concentrations were analyzed using numerical integration of differential rate equations and global fitting. When data was inconsistent with a one to one reaction it was possible to obtain good fits to an entire data set assuming several other reaction schemes including parallel, competitive and two-state reactions. Thus data analysis alone was not sufficient to discriminate between different reaction schemes. In contrast several reaction schemes could be ruled out with simple experiments; the duration of antigen injection, and reanalysis of antigen recovered in fractions from the antibody surface. In view of these findings experimental design appears to be the key to successful interaction analysis.