Carbohydrate-Protein Recognition: Molecular Dynamics Simulations and Free Energy Analysis of Oligosaccharide Binding to Concanavalin A

Abstract

Carbohydrate ligands are important mediators of biomolecular recognition. Microcalorimetry has found the complex-type N-linked glycan core pentasaccharide β-GlcNAc-(1→2)- α-Man-(1→3)-[ β-GlcNAc-(1→2)- α-Man-(1→6)]-Man to bind to the lectin, Concanavalin A, with almost the same affinity as the trimannoside, Man- α-(1→6)-[Man- α-(1→3)]-Man. Recent determination of the structure of the pentasaccharide complex found a glycosidic linkage ψ torsion angle to be distorted by 50° from the NMR solution value and perturbation of some key mannose–protein interactions observed in the structures of the mono- and trimannoside complexes. To unravel the free energy contributions to binding and to determine the structural basis for this degeneracy, we present the results of a series of nanosecond molecular dynamics simulations, coupled to analysis via the recently developed MM-GB/SA approach (Srinivasan et al., J. Am. Chem. Soc. 1998, 120:9401–9409). These calculations indicate that the strength of key mannose–protein interactions at the monosaccharide site is preserved in both the oligosaccharides. Although distortion of the pentasaccharide is significant, the principal factor in reduced binding is incomplete offset of ligand and protein desolvation due to poorly matched polar interactions. This analysis implies that, although Concanavalin A tolerates the additional 6 arm GlcNAc present in the pentasaccharide, it does not serve as a key recognition determinant.