The high degree of internal flexibility observed for an oligomannose oligosaccharide does not alter the overall topology of the molecule

Abstract

The conformational properties of oligosaccharides are important in determining their biological properties, such as recognition by proteins. The structural and dynamic properties of many oligosaccharides are poorly understood both because of a lack of experimental data (usually obtained from solution NMR parameters) and because of gross approximations frequently invoked in theoretical models. To characterise the oligomannose oligosaccharide Man,GlcNAc2 we have acquired a more extensive NMR data set and performed the first unrestrained molecular dynamics (MD) simulation in water of this large oligosaccharide (employing the GLYCAM_93 parameter set with the AMBER force field). Good agreement is seen between the computed dynamics data and the results of both an isolated spin pair (ISPA) analysis of short mixing time NOE data and NOE build-up curves for mixing times from 100 to 2000 ms. The number of experimental conformational constraints obtained in this study are in principle sufficient to fully define a rigid structure. The fact that this could not be done indicates a high degree of internal flexibility and/or the presence of multiple conformations about the glycosidic linkages. Independently, the same conclusions are reached from an analysis of the MD results. In addition, the theoretical results allow the overall topology of the molecule and its intra-molecular and solvent-mediated hydrogen bonding pattern to be defined. Extensive re-organisation of solvent and inter-residue hydrogen bonds is shown to be required for significant conformational changes to occur, resulting in relatively long life-times for distinct glycosidic linkage conformations, despite the high local flexibility of the glycosidic linkages. This factor is also seen in the overall topology of the molecule, where the considerable internal flexibility is not translated into gross changes in structure. The control exerted by the solvent over both the flexibility and overall topology of an oligosaccharide has important implications for recognition processes and for the conformational properties of glycans attached to glycoproteins.

Conformational flexibility of N-glycans in solution studied by REMD simulations

“…The number of pairs of dihedral glycosidic angles rapidly increases; 22 parameters for typical bianntenary complex-type N-glycan (André et al 2009). Actually, the number of different conformers of glycans is less than that predicted from the flexibilities of all the individual linkages (Woods et al 1998).…”

“…Extensive conformational sampling is required to access the multiple conformers of N-glycans. For this reason, past conventional MD simulations in explicit solvent have been limited to small fragments like mono-, di-, or trisaccharides (Sayers and Prestegaud 2000;Kim et al 2009;Kirschner and Woods 2001;Almond 2005;Perić-Hassler et al 2010;Corzana et al 2004;Landström and Widmalm 2010), or larger fragments with short sampling (Naidoo et al 1997;Woods et al 1998;André et al 2009). …”

Restrained electrostatic potential atomic partial charges for condensed-phase simulations of carbohydrates

“…In addition to the case of these relatively rigid structural elements, electrostatic forces may also influence dynamic motions. For example, the frequently observed dynamic behavior of carbohydrates in a solution depends on a subtle balance of forces between intramolecular hydrogen bonds and those between the solute and the solvent [1]. The structures and energies of carbohydrate-protein complexes are similarly sensitive to subtle differences in electrostatics between the free and bound states [2].…”

Relative Energies of Binding for Antibody−Carbohydrate-Antigen Complexes Computed from Free-Energy Simulations

“…Standard deviations of less than 15° are typical of glycosidic angles confined to a single conformation. 34 In these simulations the φ-angles adopt conformations close to those seen in the bound state (see Table 2). The ψ-angles show more variability, and the average values are slightly further from those of the bound state.…”

“…From the thermodynamic cycle it can be seen that the relative free energies for the theoretical mutation (ΔΔG 34 ) are identical to the experimental relative free energies (ΔΔG 12 ). The theoretical free energies can be readily calculated in a FEP simulation, although they are not experimentally measurable.…”