Hello
A while ago, I reported the structure determination of a protein in two
different space groups. In both structures, the electron density maps
revealed a well defined supplementary electron density. We built an
oligopeptide and a putative sequence has been assigned. To confirm the
sequence, we have set up several MS experiments and Edman sequencing
from purified protein batches and dissolved crystals. For some reasons,
the peptide could not be easily characterized using these approaches. As
a last resort, we are planning to separate the peptide from the protein
on gel and in solution before mass spectrometry.
I would be much grateful for any advice on peptide separation methods?
For instance, what kind of gel or extraction protocols would you suggest?
Thank you
Fabien
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Hello
We’re resolving a structure of a soluble protein and in the electronic
density map (maximum resolution at 2.2Å), we observe a supplementary
density that does not belong to the protein. This density is present
in two different crystalline forms obtained in different
crystallization conditions.
This density could be represented by an oligopeptide ~10 residues long
for which there is no ambiguity about its polarity. Furthermore, side
chains are quite easily visible and a sequence can therefore be assigned.
The deduced sequence doesn’t belong to the sequence of the protein of
interest, meaning that the oligopeptide has been co-purified and
co-crystallized.
Has somebody met a similar situation? Could you please give us some
advices in terms of refinement, validation, etc.?
Thanks in advance
Best regards
Fabien
PhD student
fabien.berge...@ipbs.fr <mailto:fabien.berge...@ipbs.fr>
