Prediction of O-glycosylation of mammalian proteins: specificity patterns of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase

Abstract

The specificity of the enzyme(s) catalysing the covalent link between the hydroxyl side chains of serine or threonine and the sugar moiety N-acetylgalactosamine (GalNAc) is unknown. Pattern recognition by artificial neural networks and weight matrix algorithms was performed to determine the exact position of in vivo O-linked GalNAc-glycosylated serine and threonine residues from the primary sequence exclusively. The acceptor sequence context for O-glycosylation of serine was found to differ from that of threonine and the two types were therefore treated separately. The context of the sites showed a high abundance of proline, serine and threonine extending far beyond the previously reported region covering positions -4 through +4 relative to the glycosylated residue. The O-glycosylation sites were found to cluster and to have a high abundance in the N-terminal part of the protein. The sites were also found to have an increased preference for three different classes of beta-turns. No simple consensus-like rule could be deduced for the complex glycosylation sequence acceptor patterns. The neural networks were trained on the hitherto largest data material consisting of 48 carefully examined mammalian glycoproteins comprising 264 O-glycosylation sites. For detection neural network algorithms were much more reliable than weight matrices. The networks correctly found 60-95% of the O-glycosylated serine/threonine residues and 88-97% of the non-glycosylated residues in two independent test sets of known glycoproteins. A computer server using E-mail for prediction of O-glycosylation sites has been implemented and made publicly available. The Internet address is NetOglyc@cbs.dtu.dk.

TLiSA1 (PTA1) Activation Antigen Implicated in T Cell Differentiation and Platelet Activation Is a Member of the Immunoglobulin Superfamily Exhibiting Distinctive Regulation of Expression

“…1. In addition, there are three potential O-glycosylation sites at Thr 7 , Thr 48 , and Ser 124 , as predicted by the method of Hansen et al (33). This extensive glycosylation probably accounts for the difference between the predicted (38.4 kDa) and observed (67 kDa) estimates of molecular mass and agrees well with previous experiments on the platelet protein using glycosidase enzymes (10).…”

The Fibrinogen-like Globe of Tenascin-C Mediates Its Interactions with Neurocan and Phosphacan/Protein-tyrosine Phosphatase-ζ/β

“…Areas of polystyrene dishes were either left uncoated (A and D), coated at a concentration of 8 g/ml with TN EFN Ϫ (B), or TN EFN 1-5Ϫ (E), or as in B and E with a second coating of 10 g/ml phosphacan (C and F). Bar, 100 m. type oligosaccharides in phosphacan (originally designated the 3F8 proteoglycan; 18), it can be calculated that the number of GalNAc residues in phosphacan from 7-day postnatal brain (64 mol/mol for a 173-kDa core protein) is in excellent agreement with the sum of 33 threonine and 30 serine GalNAc-Ser/Thr O-glycosylation sites indicated by a neural network analysis (31,32) of the phosphacan amino acid sequence. All of these sites (which account for only 17% of the total serine and threonine residues) are in the C-terminal portion of the protein outside of the carbonic anhydrase and fibronectin type III homology domains (3), and the high concentration of O-glycosidic oligosaccharides would tend to give this region an extended conformation.…”

Isolation of MYADM, a novel hematopoietic-associated marker gene expressed in multipotent progenitor cells and up-regulated during myeloid differentiation

“…All sequences were analyzed for openreading frame (ORF) by computer analysis using GeneWorks version 2.4 (IntelliGenetics, Mountain View, CA) and were compared at the NCBI server to known sequences with the BLAST and FASTA algorithms [18,19]. Protein motif analysis and prediction of protein features were performed via the EMBL-Heidelberg world-wide web service by different computer analysis programs [20][21][22][23][24][25][26].…”