New Insights into α-GalNAc−Ser Motif:  Influence of Hydrogen Bonding versus Solvent Interactions on the Preferred Conformation

Abstract

The structural features of the mucin-type simplest model, namely, the glycopeptide alpha-O-GalNAc-l-Ser diamide, have been investigated by combining NMR spectroscopy, molecular dynamics simulations, and DFT calculations. In contrast to previous reports, the study reveals that intramolecular hydrogen bonds between sugar and peptide residues are very weak and, as a consequence, not strong enough to maintain the well-defined conformation of this type of molecule. In fact, the observed conformation of this model glycopeptide can be satisfactorily explained by the presence of water pockets/bridges between the sugar and the peptide moieties. Additionally, DFT calculations reveal that not only the bridging water molecules but also the surrounding water molecules in the first hydration shell are essential to keep the existing conformation.

1H‐MRS can detect aberrant glycosylation in tumour cells: a study of the HeLa cell line

“…2) points to the presence of GalNAc unprocessed residues. Chemical shifts of the 1D (8.02 ppm) and 2D COSY cross peak (7.99-4.16 ppm) of this signal are in fact compatible with NH signals of free GalNAc in solution (Table 1) and with those of GalNAc bound to Ser in mucin-derived O-linked glycopeptides (30,31). The assignment of the Gal CH3 signal to the CH 3 of the same GalNAc molecule could be confirmed by the observation that both NH and CH 3 signals increase as cells approach confluency (Figs.…”

Deciphering the Non‐Equivalence of Serine and Threonine O‐Glycosylation Points: Implications for Molecular Recognition of the Tn Antigen by an anti‐MUC1 Antibody

“…In fact, the conformational analysis performed on glycopeptides 1* and 2* in the free state in water by means of NMR experiments and Molecular Dynamics (MD) simulations with time-averaged restraints [9] indicates that compound 2* displays this conformation with ap opulation approximately 20 %(see the Supporting Information). As previously observed by us, [8,9] while in compound 1*,t he glycosidic linkage adopts mainly the typical eclipsed conformation, in variant 2* it prefers to adopt the alternate conformation. According to the X-ray structure,t he unusual conformation of the glycosidic linkage in compound 2* bound to the antibody is stabilized by two intramolecular hydrogen bonds with the peptide chain ( Figure 5).…”

“…Then, the glycosidic linkage exhibits the typical parallel orientation found for this compound in the free state. [8] To reinforce the significance of the b-methyl group of the threonine residue for the conformation of the glycosidic linkage,and to corroborate the exceptional 3D conformation of glycopeptide 2* in the complex with the antibody,w es olved the structure of the cysteine analogue in complex with scFv-SM3 (compound 3* in Figure 2, PDB ID:5 a2L). Notably,t he GalNAc unit and the peptide backbone adopt an almost identical spatial conformation in glycopeptides 2* and 3*, with the main difference being the conformation of the side chain of Arg5 ( Figure 5).…”

Dynamics and Hydration Properties of Small Antifreeze‐Like Glycopeptides Containing Non‐Natural Amino Acids

“…On the other hand, as also reported in the literature, the existence of this hydrogen bond is negligible in solution for Ser-derived glycopeptides. [23] Once the structure features were elucidated, the next step should be to try to deduce a possible structure-activity relationship. It is noteworthy to mention that the structure of the first hydration shell should play a pivotal role in defin-ing the antifreeze activity of these molecules.…”