I am looking for a software/online tool that will help to identify possible sites prone to post-translational modifications (including deamidation, isomerization, protease cleavage, oxidation sites, succinimide formation, C-terminal lysine cleavage, glycosylation etc.) in a protein especially antibody sequence. Thank you for help.
Hi,
I guess such tools are available.
Generally speaking, a few rules of thumb exist:
Deamidation tends to predominantly occur on asparagine residues that are followed by glycine (G), or asparagine (N), like in the infamous PENNY peptide in IgGs. Succinimide is an intermediate in that reaction, which can be converted either to Asp, or isoAsp.
Protease cleavage sites are of course dependent on the protease used; a lot of in silico digest algorithms exist that can predict what peptides are formed.
N-terminal pyroglutamate formation and C-terminal lysine cleavage tends to occur at the N- and C-terminus, respectively ;). In IgGs, the latter can be succeeded by glycine cleavage and proline amidation.
N-glycosylation (on IgGs) usually occurs on ..NX(S/T).. motifs, primarily on that motif present in the constant domain of the heavy chain around asparagine-300.
Lastly, oxidation can occur on methionine (and tryptophan) residues; in IgGs, two methionines in the constant domain tend to be most prone to oxidation: that in the sequence ..DTLMISR.. and in the sequence ..FSCSVMHEAL..
Hope this helps!
Hi Eef,
Thank you very much for answer and help:)
The information are very useful for my work, but still I am looking for tool to analyze many sequences at one time taking into consideration above information.
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