Shared epitopes prediction?

Warren Gallin wgallin at
Mon Mar 7 11:40:22 EST 1994

In Article <mbxfd-070394141604 at>,
mbxfd at (Fergus Doherty) wrote:
>Perhaps someone can help me with a problem.  An antibody detects
>procarboxypeptidase B in rat pancreas, but the antibody is to an unrelated
>protein.  Comparing the sequence of the protein to which the ab was raised
>(165 aa) versus procarboxypeptidase B (>400 aa) with the GCG BESTFIT
>program shows 21% identity, 42% similarity.  21% identity is probably not
>significant as the identical aa are spread over the sequence of the smaller
>protein, there is no string of identical or non-identical aa that could be
>a common epitope.  Is there another program that might do this comparison
>better, ie look for a small (6-10) run of identical/near identical aa (that
>might be the common epitope)?  Could it be an epitope that depends on some
>secondary structure (retained or regained following SDS-PAGE and Western
>blotting) so that the epitope consists of residues close in space but
>non-adjacent?  What are the chances of this? If so is it possible to check
>for this with a suitable algorithm?  Any help appreciated.

   You might consider another possibility, that the antigen used to raise
the antibody was contaminated with procarboxypeptidase.  What was the
antigen and how was it prepared?  Were other people working with
procarboxypeptidase in the same lab (possible source of contamination)?
   Is it only the procarboxypeptidase that is reacting, and not the mature
carboxypeptidase?  That might relaly narrow it down.  Does the preimmune
serum not react with the procarboxypeptidase?  A lot of rabbits have
positive sera for different proteins even before they are immunized.
   This sounds like one of those problems that might be better explained by
a technical glitch than by abtruse epitope similarities.
   On the other hand, with antibodies many things are possible, especially
with polyclonal antibodies.  I'm afraid this isn't much help in your search
for algorithms, but I've seen the kinds of phenomena suggested above
actually happen, so you might want to follow them up.
Warren Gallin,
Department of Zoology, University of Alberta
wgallin at

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