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Dear Jacob, somewhat adding to list of 'not really answering your question', here is the reference for native page that still uses a dye thereby trying to limit the influence of the charge on the speed. Might be helpful as they discuss some applications. Otherwise AUC really sounds like the way to go. Nat Protoc. 2006;1(1):418-28. Blue native PAGE. Wittig I, Braun HP, Schägger H. best, hannes uchtenhagen Hannes Uchtenhagen Karolinska Institutet Center for Infectious Medicine (CIM) Karolinska University Hospital Huddinge, F59 SE-141 86 Stockholm, Sweden Office: +46-(0)8-524 86981 Mobile: +46-(0)7-36901461 On 2010-05-18 22:04, 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] > *******************************************