query regarding N and O glycosylation prediction. - (Jul/19/2013 )
Hello
My plant proteins are predicted to be non-secretory proteins by TargetP (They are predicted to have no signal peptides, mTP or cTP). And I read that secretory proteins have exclusively N-glycosylation. Whereas secretory and nucleo/cytoplasmic proteins have O -glycosylation.
My proteins return both N and O-glycosylation by the program. So I was confused with how to interpret my results for the N-glycosyation.
I was wondering how to correlate the non-secretory status of the proteins with N-glycosylation. Any help in this regard
Thanks for your time.
Bioscientist
I think (but it would pay to check for yourself) that not all N-glycosylated proteins are secreted (perhaps only those that have solely N-glyc). If, as you say, O-glycosylated proteins are never secreted, then you have answered your question yourself
Bioscientist on Fri Jul 19 21:27:46 2013 said:
Hello
I used the program Ensemblgly for predicting the N and O glycosylation sites of my plant proteins.
My plant proteins are predicted to be non-secretory proteins by TargetP (They are predicted to have no signal peptides, mTP or cTP). And I read that secretory proteins have exclusively N-glycosylation. Whereas secretory and nucleo/cytoplasmic proteins have O -glycosylation.
My proteins return both N and O-glycosylation by the program. So I was confused with how to interpret my results for the N-glycosyation.
I was wondering how to correlate the non-secretory status of the proteins with N-glycosylation. Any help in this regard would be highly appreciated.
Thanks for your time.
Bioscientist
Hi,
If you are using MS/MS data..then there is a tool SimGlycan which upon data loading can identify N-Glycosylation sites (using NXT rule). If you are working with a particular Protein ID (for eg SWISS-Prot ID) then it will directly display N and O glycosylation sites. Here is the link to the tool: http://premierbiosoft.com/glycan/index.html.
Cheers!
Hank