Unified picture for the conformation and stabilization of the O-glycosidic linkage in glycopeptide model structures

• Published in: Structural chemistry Vol. 26; no. 5-6; pp. 1367 - 1376
• Main Authors: Mezei, Pál D., Csonka, Gábor I.
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.12.2015
• Subjects: Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Original Research; Physical Chemistry; Theoretical and Computational Chemistry; Glycoproteins; Density functional calculations; Glycosidic linkage; Glycopeptides
• ISSN: 1040-0400; 1572-9001
• DOI: 10.1007/s11224-015-0666-9

Glycoproteins play a central role in the immune response. In this study, we focus on the core of the common O -linked mucin-type glycopeptides. It has been observed that glycosylation stabilizes the protein in a stiffened, extended structure. We provide a unified picture for the conformation and stabilization of the O -glycosidic linkage using O -(2-acetylamino-2-deoxy-α- or -β- d -galacto- or -mannopyranosyl)- N -acetyl- l -serinamide model structures. We have calculated equilibrium geometries of the model structures with the B3LYP/6-31G(2 df , p ) method suggested in the Gaussian-4 theory. According to the relative energies, we confirm that the GalNAc-Ser linkage is more stable than its mannose analogues. The natural preference for the α-GalNAc-Ser over the β-GalNAc-Ser anomers can be explained by entropic effects. We explored the hydrogen bonding patterns on the carbohydrate unit calculating highly accurate dRPA@PBE0.25 and dRPA75 energies and found that in some cases, the acetamido group can be fixed by hydrogen bonding from the (O3 Carb )H atom, but in most of the cases, it can rotate more freely. The torsion angles in the glycosidic linkage show that the linkage is stiffened more in the α-anomers and the most in the α-GalNAc-Ser structure because of the steric strains in the axial position and by two or three intramolecular hydrogen bonds. We also found that although, in our gas-phase model geometries, the peptide backbone prefers to be in a γ L -turn, a structural water molecule can stabilize a polyproline II helix of a proline-rich sequence, a β-sheet, or more likely random coils.