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NetCGlyc 1.0: prediction of mammalian C-mannosylation sites
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics.
2007 (English)In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 17, no 8, 868-876 p.Article in journal (Refereed) Published
Abstract [en]

C-mannosylation is the attachment of an alpha-mannopyranose to a tryptophan via a C-C linkage. The sequence WXXW, in which the first Trp becomes mannosylated, has been suggested as a consensus motif for the modification, but only two-thirds of known sites follow this rule. We have gathered a data set of 69 experimentally verified C-mannosylation sites from the 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, and Thr) is preferred and a Phe or a Len residue 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 a 21-residue sequence input window and information on the presence/ absence of the 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.

Place, publisher, year, edition, pages
2007. Vol. 17, no 8, 868-876 p.
Keyword [en]
c-mannosylation, machine learning, neural networks, prediction
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:su:diva-56175DOI: 10.1093/glycob/cwm050ISI: 000248792200011OAI: oai:DiVA.org:su-56175DiVA: diva2:410002
Note
authorCount :1Available from: 2011-04-12 Created: 2011-04-12 Last updated: 2017-12-11Bibliographically approved

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