Phage display systems

Dom Spinella dspinella at chugaibio.com
Wed Oct 22 09:21:03 EST 1997


> The solution also comes when you have a consensus sequence present in all
> (or most) of your binding peptides. You can have 10 different 12mer
> peptides with a strict 4 or 5 mer consensus sequence (not necessarily at
> the same place in the 12mer, so you need to "slide" the peptides between
> them.
> In some cases there are no consensus sequences, and some or all the
> binding peptides are not similar to the epitope but are called mimotopes.
> Mimotopes are structures (here, peptides) that bind the same Ab that your
> epitope because the important charasteristics for binding are present at
> the right places (you can have a peptide that is a mimotope of a
> non-peptidic epitope!).
> So remember that a binding peptide does not necessarily give you the
> sequence of your epitope (I mean the epitope on your Ag).
> 
> Pascal Mertens

Pascal and I seem to be in violent agreement here.  Clearly, one can
also establish a consensus binding sequence (be it epitope or mimotope)
by alligning several binding sequences and establishing the points of
homology.  This is one of the advantages of what I called the "sliding
window" available with long peptide phage display systems. It is not
always possible to do this however, either because there is no obvious
homology among independent binding peptide sequences, or because only a
single binding sequence was obtained.  This is perhaps less of a problem
with antibodies than with large protein receptors such as we use in my
lab for screening phage libraries, but still occasionally happens even
with antibody screens.  In the case of receptor binding peptides, we and
others have observed that there is virtually never direct primary
sequence homology between the mimetic peptides and the natural ligand of
the receptor target -- presumably because the actual binding motif of
the natural ligand is generated by the tertiary folding of the protein
which brings together amino acids that are not contiguous in the primary
sequence.  Although unusual, such "discontinuous epitopes" are also
found in some antigens, and of course it will be impossible to define
these by allignment of peptides to the primary sequence of the natural
antigen.
-- Dom Spinella



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