Sugar Type Discrimination in O-glycosylation Based on Protein Primary Sequences

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.

Keywords

• bioinformatics
• o-glycosylation
• oligosaccharide
• position-specific scoring matrix
• post-translational modification
• discrimination