Conformational dynamics of oligosaccharides characterized by paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics simulation.

Abstract

Oligosaccharides play pivotal roles in physiological and pathological contexts primarily through their interactions with proteins on cell surfaces and in intracellular environments. Although crystallographic approaches provide cumulative information about the atomic details of oligosaccharides complexed with proteins, quantitative characterization of the dynamic conformation of uncomplexed oligosaccharides is essential for better understanding of the energetics of carbohydrate–protein interactions. Nuclear magnetic resonance (NMR) spectroscopy is a potentially powerful tool for describing the conformational dynamics of oligosaccharides in solutions at an atomic resolution. However, methodological improvements are needed in applying NMR techniques to the analyses of the dynamic conformations of oligosaccharides during sample preparation, spectral observation, and data interpretation. This presentation outlines our recently developed method of dealing with dynamic conformational ensembles of oligosaccharides using paramagnetism-assisted NMR spectroscopy in conjunction with molecular dynamics (MD) simulation. A key to this approach is the introduction of a paramagnetic lanthanide ion to the reducing end of oligosaccharides as the source of the atomic long-distance information. We successfully applied this method to the validation of MD-derived conformational spaces occupied by a series of sialyl oligosaccharide moieties of GM1, GM2, and GM3 gangliosides. The applicability of NMR is also revealed for characterizing the dynamic interactions of ganglioside clusters with intrinsically disordered proteins associated with neurodegenerative disorders using ganglioside-embedding small bicelles as nanoscale standardized membrane mimics.