Sorry to burst your bubble, but making large, soluble, and biologically active proteins is not an easy task.  The only way to determine binding kinetics is using purified constituents.  Throwing in phosphorylation as another variable, at multiple sites no less, makes this even more difficult. 

Sigh. Crap.  Why is this hard?  They are not membrane bound proteins in the specific complexes I'm interested in, so shouldn't they be readily soluble?  Thank you very much for your input!

Many proteins will not be soluble in a nuclear lysate when bound to chromatin, but even if they are, you still need to purify them out.  That is no easy task either and requires mg amounts of nuclear lysates to get ng amounts of your specific protein.  For most protein interaction studies you cannot use complex mixtures so individual proteins are tested in pairs.   People make recombinant proteins in bacteria or in insect cells and these can be difficult to refold properly and remain soluble.  Furthermore, they are unlikely to be phosphorylated at the appropriate serines, tyrosines, etc.  Last but not least, your purified protein needs to be tagged, such as with biotin, for most of the automated systems now in use (such as the Octet-Red).  All of this is feasible but would take an experienced biochemists anywhere form 3-9 months depending on how quickly things work. 

Thank you Dr. Dressler.  I guess model validation of this type must wait for the data to appear in the literature then.