Hi there,

What you could do starting with your protein preps is to find a mild condition to dissociate the homodimers (salt concentration, temperature, presence of chaotropic agent) and then mix the two and encourage the formation of dimer by eliminating the dissociating agent by dialysis and see what happens. What is important here is to be able to make the difference between homo and heterodimers...

Co expression might work too...

Hi Mervi, if you have purified monomers, you could try low concentrations (~10 mM) of zero-length crosslinkers like EDC. 

What type of protein are you working with? What are the concentrations you are using? Dimer exchange requires a rapid dissociation rate, and as Dominique rightly points out, the dissociation rate is dependent on a number of physiochemical parameters in your assay. For some protein-protein interactions, this is readily achieved, whereas others do not readily show exchange in vitro. In addition, thermodynamic considerations may favor homodimer over heterodimer formation, and so you need to consider whether differential affinities may strongly tilt the equilibrium in favor of one type of complex. This is probably not a concern if you are confident in the observation that heterodimer complexes are favored during co-translational expression.

If the homodimer dissociates when its concentration is low enough, you could dilute it sufficiently to let it dissociate essentially completely (well below the Kd), then add the other subunit at the same concentration, allowing time for equilbration. If the heterodimer interaction is substantially tighter than either homodimer interaction, when you reconcentrate the mixture you should get mostly heterodimer.

Do you know if this heterodimer is formed from an endoproteinase cleavage of one polypeptide chain and is this a covalent heterodimer?