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Dear Jacob, I offer you my opinion. Are you talking about electrophoresis? As far as I know it does not work for the mass. The velocity of a protein depends on the charge at a particular pH, the mass and shape of molecules etc. It's very difficult to take all these things into consideration. Otherwise this would be a very convenient method, much easier than the analytical centrifugation or gel-filtration that are usually used. However, electrophoresis does not work for mass determination. Besides, complex formation hugely depends on the protein concentration. If you dilute your mixture, your complexes might dissociate. There is equilibrium constant between different types of complexes. Maia Jacob Keller wrote: > Dear Crystallographers, > > I am trying to optimize a native gel experiment of a two-protein > complex, running the smallest-detectable amount of protein component A > with varying amounts of component B. > > MW Charge MW/Charge > A 22 -5 -4308 > B 17 -24 -702 > > This experiment is partly to determine stoichiometry, but also to > determine roughly the strength of the interaction. > > B definitely runs much faster than A alone, as predicted, but I am > wondering what to expect with various oligomers. Should ABB run faster > or slower than AB? What about AABB? Theoretically, AA should certainly > run slower than A, and BB slower than B, simply because the > mass/charge ratio is the same, but the overall mass is greater. But > what happens when you have AAB, for example? There must be an equation > relating the mass/charge and mass (and perhaps gel percentage) to the > speed traveled in the gel--but what is the equation? > > Thanks for your consideration, > > Jacob > > ******************************************* > Jacob Pearson Keller > Northwestern University > Medical Scientist Training Program > Dallos Laboratory > F. Searle 1-240 > 2240 Campus Drive > Evanston IL 60208 > lab: 847.491.2438 > cel: 773.608.9185 > email: [log in to unmask] > ******************************************* > >