Article abstract


REFERENCE

NetCGlyc 1.0: Prediction of mammalian C-mannosylation sites.
Karin Julenius
Glycobiology, 17:868-876, 2007.

Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden

Stockholm Bioinformatics Center, Albanova, Stockholm University, SE-106 91 Stockholm, Sweden


ABSTRACT

C-mannosylation is the attachment of an alpha-mannopyranose to a tryptophan via a C-C link. The sequence WXXW, in which the first Trp becomes mannosylated has been suggested as a consensus rule for the modification, but only 2/3 of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from literature. We analyzed these for sequence context and found that apart from Trp in position +3, Cys is accepted in the same position. We also find a clear preference in position +1, where a small and/or polar residue (Ser, Ala, Gly, Thr) is preferred and a Phe or Leu discriminated against. The Protein Data Bank was searched for structural information and five structures of C-mannosylated proteins were obtained. We showed that modified tryptophan residues are at least partly solvent-exposed. A method predicting the location of C-mannosylation sites in proteins was developed using a neural network approach. The best overall network used as input sequence information in a 21-residue window plus information on presence/absence of WXXW motif. NetCGlyc 1.0 correctly predicts 93% of both positive and negative C-mannosylation sites. This is a significant improvement over the WXXW consensus motif itself, which only identifies 67% of positive sites. NetCGlyc 1.0 is available at http://www.cbs.dtu.dk/services/NetCGlyc/. Using NetCGlyc 1.0, we scanned the human genome and found 2573 exported or transmembrane transcripts with at least one predicted C-mannosylation site.



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