Exploration of Conformational Spaces of Oligosaccharides byCombining Molecular Dynamics Simulation and NMR Spectroscopy

Abstract

Oligosaccharides are highly flexible molecules having branched structures and significant degrees of freedom in internal motion. To gain insights into the molecular basis of their biological functions, it is essential to describe the conformational dynamics of oligosaccharides. By combining NMR spectroscopy and molecular simulation, we developed a method giving the quantitative interpretation of dynamic behaviors of oligosaccharides. Paramagnetism-assisted NMR approaches with replica-exchange molecular dynamics simulations revealed the conformations of a series of oligosaccharides involved in the glycoprotein quality control system in cells. Exploration of the conformational spaces of the oligosaccharides also provided dynamical views of the interaction mechanisms of carbohydrate recognition proteins, complementing the static crystallographic analyses.