Weak Carbohydrate–Protein Interactions by NMR

Abstract

Nuclear magnetic resonance (NMR) provides several complementary tools to characterise and study biomolecular interactions between molecules. In particular, the fast and weak interactions between a small ligand and a large receptor can be analysed in the equilibrium state. In adequate conditions, it can characterise if a small molecule is interacting with a protein, if the conformation of the ligand changes upon binding, the regions of the ligand that are involved in the binding, and even the bound conformation within the complex. The process of association‐dissociation should be fast, and consequently, a single set of averaged signals carrying the information of both states detected. Typically, the protein is in lower proportion than the ligand and practically the signals from the ligand dominate the spectra. Besides, as the magnitudes used depend on the tumbling of the molecule (NOE, transfer of magnetisation or relaxation times) the average becomes very displaced towards the complex due to its larger correlation times. Key Concepts Fast equilibrium in the NMR time scale between the free and the bound ligand is needed. Magnitudes depending on the molecular correlation time (dipolar coupling, saturation transference, relaxation times) are monitored. Small amounts of complex thank the favourable molecular correlation time dominate the average of the corresponding magnitude. The behaviour of the ligand complexed can be deduced from the observation of the free ligand signals. In Transfer NOESY, dipolar transference within the bound ligand is observed. In STD‐NMR transference between the ligand and the receptor, which is proportional to the closeness between ligand and receptor, is monitored. In relaxation times analysis, differences between bound and free ligand are compared. The WaterLOGSY experiment traces the magnetisation transfer between water – ligand and receptor.