Well, seeing as how there are no obvious answers, I guess some pure
speculation isn't out of order . . .
Have you tried running an acid gel? e.g., acid/urea? Maybe your protein
doesn't like going toward red electrodes. My old labmate was studying a
small very basic DNA binding protein (you can look up Volkman and
Oppenheimer . . . baculovirus p6.9) and had to use those gels instead of
the usual SDS/native systems.
Do you have any idea how big your monomer is? Maybe it's running with the
dye front or something wacky like that.
Although the pronase/proteinase K experiment is highly suggestive, it may
be that amides are important in the structure but that it's not all
You have a very interesting problem. Please keep us updated!
Lou Hom >K'93
lhom at ocf.berkeley.eduhttp://www.ocf.berkeley.edu/~lhom/