Figure 6.

The spectra and structures of the core pentasaccharide 4. (a) The lowest-energy structures of the core pentasaccharide calculated on the OPLS2005 and GLYCAM06/AMBER potential energy surfaces: (i) the isolated molecule; (ii) the triply hydrated complex (the water molecules were initially located at binding sites based upon the preferences of singly hydrated 1, 2, and the trimannosyl Man_E(Man_D)Man_C– head unit¹⁵); and (iii) in bulk water, (hydrogen bonds shown in red). (iv) An overlay of the “open” conformer of the trimannosyl Man_E(Man_D)Man_C– head unit and the core pentasaccharide in (v); (v) the preferred aqueous structure of the high mannose glycan, Man₉GlcNAc₂, determined through NMR measurements and molecular dynamics simulations.^12,13 Red dots represent transiently bound water molecules. (b) Distributions of the longest intramolecular distances (for conformers with energies <30 kJ mol^–1) in the core pentasaccharide, predicted by molecular mechanics (OPLS2005) simulations: isolated, unsolvated (red), explicitly hydrated (green), and in bulk water (black).