Preferred conformational structures of disaccharides with β-1,4-linked N-acetylglucosamine and D-mannose in the gas phase: A tree-step computational approach study

Abstract

N-glycans are highly crucial to the potential application prospect of glycoprotein. However, its structural diversity and instability severely limit its further research. Here we apply the tree-step computational approach to investigate preferred structures of disaccharides with β-1,4-linked N-acetylglucosamine and D-mannose of core pentasaccharide in N-glycans. Due to the structural character of disaccharides, hydrogen bonds (H-bonds) are classified according to the upper and lower parts of GlcNAcβ(1,4)GlcNAc and Manβ(1,4)GlcNAc. Almost all building conformers (95 for GlcNAcβ(1,4)GlcNAc and 50 for Manβ(1,4)GlcNAc) are generated depending on the combination of H-bonds in the upper and lower parts, except for one conformer. After establishing initial configurations, theoretical simulations for optimization, preferred structures and frequency calculations are employed. Both energy and IR vibration signature are in good accord with the experimental and theoretical literature. Additionally, five new low-energy structures are found, which have not been reported by using the traditional conformational search.