Conformational properties of glucose-based disaccharides investigated using molecular dynamics simulations with local elevation umbrella sampling

Abstract

Explicit-solvent molecular dynamics (MD) simulations of the 11 glucose-based disaccharides in water at 300 K and 1 bar are reported. The simulations were carried out with the GROMOS 45A4 force-field and the sampling along the glycosidic dihedral angles ϕ and ψ was artificially enhanced using the local elevation umbrella sampling (LEUS) method. The trajectories are analyzed in terms of free-energy maps, stable and metastable conformational states (relative free energies and estimated transition timescales), intramolecular H-bonds, single molecule configurational entropies, and agreement with experimental data. All disaccharides considered are found to be characterized either by a single stable (overwhelmingly populated) state ((1→ n)-linked disaccharides with n = 1, 2, 3, or 4) or by two stable (comparably populated and differing in the third glycosidic dihedral angle ω ˜ ; gg or gt) states with a low interconversion barrier ((1→6)-linked disaccharides). Metastable ( anti- ϕ or anti- ψ) states are also identified with relative free energies in the range of 8–22 kJ mol −1. The 11 compounds can be classified into four families: (i) the α(1→1)α-linked disaccharide trehalose (axial–axial linkage) presents no metastable state, the lowest configurational entropy, and no intramolecular H-bonds; (ii) the four α(1→ n)-linked disaccharides ( n = 1, 2, 3, or 4; axial–equatorial linkage) present one metastable ( anti- ψ) state, an intermediate configurational entropy, and two alternative intramolecular H-bonds; (iii) the four β(1→ n)-linked disaccharides ( n = 1, 2, 3, or 4; equatorial–equatorial linkage) present two metastable ( anti- ϕ and anti- ψ) states, an intermediate configurational entropy, and one intramolecular H-bond; (iv) the two (1→6)-linked disaccharides (additional glycosidic dihedral angle) present no (isomaltose) or a pair of (gentiobiose) metastable ( anti- ϕ) states, the highest configurational entropy, and no intramolecular H-bonds. The observed conformational preferences appear to be dictated by four main driving forces (ring conformational preferences, exo-anomeric effect, steric constraints, and possible presence of a third glycosidic dihedral angle), leaving a secondary role to intramolecular H-bonding and specific solvation effects. In spite of the weak conformational driving force attributed to solvent-exposed H-bonds in water (highly polar protic solvent), intramolecular H-bonds may still have a significant influence on the physico-chemical properties of the disaccharide by decreasing its hydrophilicity. Along with previous work, the results also complete the suggestion of a spectrum of approximate transition timescales for carbohydrates up to the disaccharide level, namely: ∼30 ps (hydroxyl groups), ∼1 ns (free lactol group, free hydroxymethyl groups, glycosidic dihedral angle ω ˜ in (1→6)-linked disaccharides), ∼10 ns to 2 μs (ring conformation, glycosidic dihedral angles ϕ and ψ). The calculated average values of the glycosidic torsional angles agree well with the available experimental data, providing validation for the force-field and simulation methodology employed.