Sugar type discrimination in O-glycosylation based on protein primary sequences

Kenji Etchuya, Yuri Ikeda

Research output: Contribution to journalArticle

Abstract

Glycosylation is one of the most important protein post-translational modifications. O-glycosylation plays important roles in biological functions. There are several variations of O-glycosylation, with each having a different function. In this work, in order to discriminate sugar types in O-glycosylation from protein primary sequences, the characteristics of the sequences around the glycosylated sites were extracted. Fucose (Fuc) and xylose (Xyl) were discriminated with high accuracy by the position-specific scoring matrix (PSSM) based on the amino acid propensities around the glycosylated sites. It was suggested that the characteristics of the sequences modified by Fuc and Xyl could be extracted. However, the discrimination of N-acetylgalactosamine (GalNAc) and N-acetylglucosamine (GlcNAc) was inaccurate, and it was considered that the characteristics could not be extracted because information from the primary sequences was insufficient. The results indicate that PSSM based on protein primary sequences can effectively discriminate some sugar types in O-glycosylation.

Original languageEnglish
Pages (from-to)225-232
Number of pages8
JournalJournal of Biomechanical Science and Engineering
Volume7
Issue numberSPECIALISSUE.3
Publication statusPublished - 1 Dec 2012

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Keywords

  • Bioinformatics
  • Discrimination
  • O-glycosylation
  • Oligosaccharide
  • Position-specific scoring matrix
  • Post-translational modification

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