Exploiting Uniformly ¹³C-Labeled Carbohydrates for Probing Carbohydrate–Protein Interactions by NMR Spectroscopy

Abstract

NMR of a uniformly 13C-labeled carbohydrate was used to elucidate the atomic details of a sugar-protein complex. The structure of the 13C-labeled Manα(1–2)Manα(1–2)ManαOMe trisaccharide ligand when bound to cyanovirin-N was characterized and revealed that in the complex the glycosidic linkage torsion angles between the two reducing-end mannoses are different from the free trisaccharide. Distances within the carbohydrate were employed for conformational analysis, and NOE-based distance mapping between sugar and protein revealed that Manα(1–2)Manα(1–2)ManαOMe is bound more intimately with its two reducing-end mannoses into the domain A binding site of CV-N than with the non-reducing end unit. Taking advantage of the 13C spectral dispersion of 13C-labeled carbohydrates in isotope-filtered experiments is a versatile means for a simultaneous mapping of the binding interactions on both, the carbohydrate and the protein.

Harnessing13C-labeledmyo-inositol to interrogate inositol phosphate messengers by NMR

“…Instead of isotopically labeling these proteins to investigate their ligand-binding via NMR, applying a labeled ligand can have advantages. For example, using a 13 C-labeled mannose trisaccharide has recently informed the binding mode between the sugar and its protein binding domain 50. By analogy, the 13 C-labeled compounds reported here could help to obtain structural information on the conformation and the biochemical environment of the InsP ligands.…”

Structural Characterization of N‐Linked Glycans in the Receptor Binding Domain of the SARS‐CoV‐2 Spike Protein and their Interactions with Human Lectins

“…A NMR‐based approach [17, 27–31] was employed to perform the glycoprofile analysis of the N‐linked glycans at N331 and N343 at the S B domain of RBD (residues 328‐533). Key regions of the spectra are shown in Figure 2 and Figure S1.…”

Solid-State NMR of highly 13C-enriched cholesterol in lipid bilayers

“…In similar manner, we anticipate that studies with 13 C-Chol will yield insight into the structural basis of the sterol-specificity of AmB analogs with reduced toxicity [50–52]. A related approach has been demonstrated recently by Gronenborn [53] and colleagues, who used a 13 C labeled carbohydrate probe with a 13 C labeled protein to investigate intermolecular distances in a sugar-protein complex in order to elucidate not only the binding site of the sugar to the protein, but also the conformation of the bound sugar. These studies underscore the potential of using 13 C-labeled small molecules to elucidate their key role in biology.…”