The Use of NMR to Study Transient Carbohydrate—Protein Interactions

Abstract

Carbohydrates are biologically ubiquitous and are essential to the existence of all known living organisms. Although they are better known for their role as energy sources (glucose/glycogen or starch) or structural elements (chitin or cellulose), carbohydrates also participate in the recognition events of molecular recognition processes. Such interactions with other biomolecules (nucleic acids, proteins, and lipids) are fundamental to life and disease. This review focuses on the application of NMR methods to understand at the atomic level the mechanisms by which sugar molecules can be recognized by proteins to form complexes, creating new entities with different properties to those of the individual component molecules. These processes have recently gained attention as new techniques have been developed, while at the same time old techniques have been reinvented and adapted to address newer emerging problems.

The Interaction between Chondroitin Sulfate and Dermatan Sulfate Tetrasaccharides and Pleiotrophin

“…We prepared samples for transient NMR experiments with a small amount of PTN in the presence of a significant excess of tetrasaccharides (molar ratio 1:20). First, we recorded the transfer-NOESY experiments at several mixing times to calculate the initial growth rate and estimate the ligand’s interprotonic distances into the complex [ 12 ]. We observed the same NOE pattern as in the free compounds; the distances of the interglycosidic NOEs were the same as those of the free ligand.…”

“…We observed the same NOE pattern as in the free compounds; the distances of the interglycosidic NOEs were the same as those of the free ligand. In a previous work [ 12 ], we compared the NOE growing curves from the transfer NOESY sample with a similar model but without protein and showed the clear effect of the correlation time between both samples. As previously reported for MK [ 10 ], the ligands do not modify their 3D structures when they are complexed with PTN.…”

Conformationally Constrained Sialyl Analogues as New Potential Binders of h‐CD22

“…Overall, our structural and affinity data showed that the sialyl derivative 1 can strongly interact with h‐CD22; thus, a class of related compounds may be designed as promising candidate for glycoimmunotherapy targeting CD22. Furthermore, the functionalization and characterization of suitable nanomaterials coated with 1 ‐like ligands may lead to interesting therapeutic applications, for example to efficiently probe the cell surfaces [13–33] …”

“…The interpolation of the fluorescence data provided the corresponding dissociation constant K D = 2.0 � 0.1 μM (Figure 1b and Figure S13). Furthermore, STD NMR [24][25] and tr-NOESY [26] have been employed to dissect at molecular level the interaction between analogue 1 and h-CD22 and to map the ligand's interacting epitope and bioactive conformation (Figure 2). The STD NMR spectrum highlighted that the sialyl derivative was recognized by h-CD22 (Figure 2) as shown by the relative enhancements in the STD spectrum: a strong contribution from the neuraminic acid (Neu5Ac) moiety was detected, with the highest STD effect observed for its acetyl group.…”

Synthesis, structure and midkine binding of chondroitin sulfate oligosaccharide analogues

“…Finally, we performed an NMR analysis on the complexes between midkine and the synthesized CS mimetics. [45][46][47] Thus, we recorded NOESY and STD-NMR experiments at different saturation times for 1-4 in the presence of 20 µM midkine. The reference experiments (in the absence of protein) were recorded in the same buffer (10 mM phosphate, 150 mM NaCl pH = 7.5) used to measure the interactions in order to guarantee the same motional behaviour with or without midkine, avoiding the potential effects in the NMR spectrum of the salt concentration.…”