A vector projection method for predicting the specificity of GalNAc‐transferase
- 1 February 1995
- journal article
- research article
- Published by Wiley in Proteins-Structure Function and Bioinformatics
- Vol. 21 (2) , 118-126
- https://doi.org/10.1002/prot.340210205
Abstract
The specificity of UDP-Gal-NAc:polypeptide N-acetylgalactosaminytransferase (GalNAc-transferase) is consistent with the existence of an extended site composed of nine subsites, denoted by P4, P3, P2, P1, P0, P1′, P2′, P3′, and P4′, where the acceptor at P0 is being either Ser or Thr. To predict whether a peptide will react with the enzyme to form a Ser- or Thr-conjugated glycopeptide, a vector projection method is proposed which uses a training set of amino acid sequences surrounding 90 Ser and 106 Thr O-glycosylation sites extracted from the National Biomedical Research Foundation Protein Database. The model postulates independent interactions of the 9 amino acid moieties with their respective binding sites. The high ratio of correct predictions vs. total predictions for the data in both the training and the testing sets indicates that the method is self-consistent and efficient. It provides a rapid means for predicting O-glycosylation and designing effective inhibitors of GalNAc-transferase.Keywords
This publication has 16 references indexed in Scilit:
- On the size of the active site in proteases. I. PapainPublished by Elsevier ,2005
- Glycosylation sites identified by solid-phase Edman degradation: O-linked glycosylation motifs on human glycophorin AGlycobiology, 1993
- A vector projection approach to predicting HIV protease cleavage sites in proteinsProteins-Structure Function and Bioinformatics, 1993
- A new approach to predicting protein folding typesProtein Journal, 1993
- Structure of the N- and O-glycans of the A-chain of human plasma .alpha.2HS-glycoprotein as deduced from the chemical compositions of the derivatives prepared by stepwise degradation with exoglycosidasesBiochemistry, 1992
- Amino acid sequence of human plasma galactoglycoprotein: identity with the extracellular region of CD43 (sialophorin).Proceedings of the National Academy of Sciences, 1992
- Nuclear and cytoplasmic glycosylation: novel saccharide linkages in unexpected placesTrends in Biochemical Sciences, 1988
- How good are predictions of protein secondary structure?FEBS Letters, 1983
- Enzymic O-glycosylation of synthetic peptides from sequences in basic myelin proteinBiochemistry, 1979
- Carbohydrate-peptide linkage in glycoproteinsArchives of Biochemistry and Biophysics, 1976