Say you have an enzyme with 3 ligands: a substrate, a cofactor, and an inhibitor. They all interact and effect one another. If one was to conduct a 3-dimensional titration of these ligands, are there any ways to analyze that data to learn about the interaction between all the ligands?
I would like to say a screening of ligands. A microarray, but for enzymes. (HTS). Maybe an enzymatic assay of the kind.
It would be helpful to know a bit more about the system in question. What is the nature of the cofactor? Does the reaction happen without the cofactor, or is the cofactor essential? What type of inhibition is happening? What do you know about the binding sites of the substrate, inhibitor, and cofactor?
You could start with the simpler 2-D approach. You could do separate kinetic analyses of the substrate-inhibitor system at various cofactor concentrations to see what effect the cofactor concentration has on the kinetic parameters. That would allow you to use the rate equation for the substrate-inhibitor system, without having to include the cofactor. Similarly, you could do 2-D kinetic analyses of the substrate-cofactor system at various inhibitor concentrations.
If the cofactor is a nonessential activator and the inhibitor is competitive with the activator, then you can refer to system A2, page 231 and following in I. Segel, Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, Wiley Interscience, 1993, Inhibitor Competitive with Nonessential Activator, where you can find the rate equation for the system, including interaction factors. If you have a really good set of 3-D rate data, you could use nonlinear regression to fit the 7 parameters of this rate equation. This is a very ambitious approach.
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