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
> [log in to unmask] <mailto:[log in to unmask]>
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