Carbohydrate-protein recognition: Molecular dynamics simulations and free energy analysis of oligosaccharide binding to Concanavalin A

Carbohydrate ligands are important mediators of biomolecular recognition. M icrocalorimetry has found the complex-type N-linked glycan core pentasaccha ride beta -GicNAc-(1 -->2)-alpha -Man-(1 -->3)-[beta -GlcNAc-(1 -->2)-alpha -Man-(1 -->6)]-Man to bind to the lectin, Concanavalin A, with almost the same affinity as the trimannoside, Man-alpha-(1 -->6)-[Man-alpha-(1 -->3)]- Man. Recent determination of the structure of the pentasaccharicle complex found a glycosidic linkage psi torsion angle to be distorted by 50 degrees from the NMR solution value and perturbation of some key mannose-protein in teractions observed in the structures of the mono- and trimannoside complex es. To unravel the free energy contributions to binding and to determine th e structural basis for this degeneracy, we present the results of a series of nanosecond molecular dynamics simulations, coupled to analysis via the r ecently developed MM-GB/SA approach (Srinivasan et al., J. Am. Chem. Soc. 1 998, 120:9401 9409). These calculations indicate that the strength of key m annose-protein interactions at the monosaccharide site is preserved in both the oligosaccharides. Although distortion of the pentasaccharicle is signi ficant, the principal factor in reduced binding is incomplete offset of lig and and protein desolvation due to poorly matched polar interactions. This analysis implies that, although Concanavalin A tolerates the additional 6 a rm GlcNAc present in the pentasaccharide, it does not serve as a key recogn ition determinant.