Structure and dynamics in oligomannose-type oligosaccharides

Using a combination of 1H NMR nuclear Overhauser effect measurements, molecular orbital calculation, and molecular dynamics simulations, the authors have determined the tertiary structure and dynamic properties of the oligomannose oligosaccharide Manα6(Manα3)Manβ6(Manα3)Manβ4GlcNAcβ4GlcNAc. While the calculated potential surfaces for the majority of the glycosidic linkages could be described by a single deep potential well, similar calculations for the Manα1-6Manα and Manα1-6Manβ linkages described a diffuse, shallow well, suggesting that a larger degree of flexibility exists about the latter. These conclusions are supported by the results of molecular dynamics simulations, which suggest that the NMR data should be interpreted in terms of a degree of flexibility about the Manα1-6Manβ and Manα1-6Manα linkages. In contrast, a similar series of investigations suggests that the conformation of the Manα1-6Manβ linkage in Manα2Man6(Manα2Manα3)Manα6(Manα2Manα2Manα3)Manβ4GlcNAcβ4GlcNAc is more restricted, resulting in an overall structure that is restrained