Open AccessPredicting mucin-type O-glycosylation using enhancement value products from derived protein features
Author(s) -
Jonathon E. Mohl,
Thomas A. Gerken,
Ming-Ying Leung
Publication year - 2020
Publication title -
journal of theoretical and computational chemistry/journal of theoretical and computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.221
H-Index - 25
eISSN - 1793-6888
pISSN - 0219-6336
DOI - 10.1142/s0219633620400039
Subject(s) - glycosylation , gene isoform , mucin , chemistry , peptide , biochemistry , glycoprotein , glycoproteomics , computational biology , biology , glycan , gene
Mucin-type O-glycosylation is one of the most common post-translational modifications of proteins. This glycosylation is initiated in the Golgi by the addition of the sugar N-acetylgalactosamine (GalNAc) onto protein Ser and Thr residues by a family of polypeptide GalNAc transferases. In humans there are 20 isoforms that are differentially expressed across tissues that serve multiple important biological roles. Using random peptide substrates, isoform specific amino acid preferences have been obtained in the form of enhancement values (EV). These EVs alone have previously been used to predict O-glycosylation sites via the web based ISOGlyP (Isoform Specific O-Glycosylation Prediction) tool. Here we explore additional protein features to determine whether these can complement the random peptide derived enhancement values and increase the predictive power of ISOGlyP. The inclusion of additional protein substrate features (such as secondary structure and surface accessibility) was found to increase sensitivity with minimal loss of specificity, when tested with three different published in vivo O-glycoproteomics data sets, thus increasing the overall accuracy of the ISOGlyP predictions.