title: Defining the structural origin of the substrate sequence independence of O-GlcNAcase using a combination of molecular docking and dynamics simulation.
abstract: Protein glycosylation with O-linked N-acetylglucosamine (O-GlcNAc) is a post-translational modification of serine/threonine residues in nucleocytoplasmic proteins. O-GlcNAc has been shown to play a role in many different cellular processes and O-GlcNAcylation is often found at sites that are also known to be phosphorylated. Unlike phosphorylation, O-GlcNAc levels are regulated by only two enzymes, O-GlcNAc transferase (OGT) and O-GlcNAc hydrolase (O-GlcNAcase or OGA). So far, no obvious consensus sequence has been found for sites of O-GlcNAcylation. Additionally, O-GlcNAcase recognizes and cleaves all O-GlcNAcylated proteins, independent of their sequence. In this work, we generate and analyze five models of O-GlcNAcylated peptides in complex with a bacterial OGA. Each of the five glycopeptides bind to OGA in a similar fashion, with OGA-peptide interactions primarily, but not exclusively, involving the peptide backbone atoms, thus explaining the lack of sensitivity to peptide sequence. Nonetheless, differences in peptide sequences, particularly at the -1 to -4 positions, lead to variations in predicted affinity, consistent with observed experimental variations in enzyme kinetics. The potential exists, therefore, to employ the present analysis to guide the development glycopeptide-specific inhibitors, or conversely, the conversion of OGA into a reagent that could target specific O-GlcNAcylated peptide sequences.
authors.affiliation: School of Chemistry, National University of Ireland, University Road, Galway, Ireland.
authors.forename: Joanne C
authors.initials: JC
authors.lastname: Martin
authors.forename: Elisa
authors.initials: E
authors.lastname: Fadda
authors.forename: Keigo
authors.initials: K
authors.lastname: Ito
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Woods
mesh_terms: D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics; D001439:Bacteroides / Q000201:enzymology* / Q000235:genetics; D004791:Enzyme Inhibitors / Q000737:chemistry; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D020539:Sequence Analysis, Protein; D001619:beta-N-Acetylhexosaminidases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; C110628:hexosaminidase C; D001619:beta-N-Acetylhexosaminidases
keywords: GLYCAM; Molecular dynamics; O-Linked N-acetyl-glucosamine (O-GlcNAc); Protein glycosylation; β-N-Acetylglucosaminidase (O-GlcNAcase)