Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

Abstract

<p>Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 ms trajectories; these simulations find a predominance of closed conformer and a range of low occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the <sup>4</sup>C<sub>1</sub> form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution, corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.</p>

Analysis of protein-glycan recognition using absolute binding free energies

“…20 Carbohydrate ligands are not particularly druglike, though, being considerably higher in complexity than small organic molecules: typically, they are larger and more polar, especially in their oligomeric linear or branched forms, with numerous stereogenic centres and rotatable bonds. 21 Nevertheless, application of ABFEs to computing the protein binding free energies of monosaccharides, 22,23 disaccharides 22 and, in one case, a trisaccharide 24 has proved encouraging, yielding deviations of 1 -3 kcal/mol from experiment for these systems.…”