References
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.