Rapid and Reliable Conformational Analysis of Glycans by Small Angle X-Ray Scattering Guided Molecular Dynamics Simulations

Abstract

Glycan conformations play essential roles in biological recognition, immune response, and cellular communication, as well as the properties of carbohydrate-based materials. Despite their importance, analyzing their secondary structures poses significant challenges due to their inherent molecular flexibility and extensive hydration. Traditional techniques like nuclear magnetic resonance (NMR) and X-ray crystallography often struggle to capture their dynamic nature accurately. Computational approaches, particularly molecular dynamics (MD) simulations, have emerged as a powerful tool to study glycan conformations, but their accuracy relies heavily on validation against experimental data. In this study, the conformation of glycans in the solution state is investigated by integrating small-angle X-ray scattering (SAXS) and MD simulations. By explicitly accounting for the conformational dynamics and hydration effects, the MD simulations accurately predicted the SAXS intensities of two glycan hairpins with similar primary sequences. This approach enables the resolving of their intricate conformational properties, including distinct secondary structures, radii of gyration, and conformational rigidity and dynamics. These findings offer a robust, label-free analytical strategy for glycan conformational studies, with potential applications in the molecular design of glycan-based materials and therapeutics.