Solution Conformations of a Trimannoside from Nuclear Magnetic Resonance and Molecular Dynamics Simulations

Abstract

N-linked oligosaccharides often act as ligands for receptor proteins in a variety of cell recognition processes. Knowledge of the solution conformations, as well as protein-bound conformations, of these oligosaccharides is required to understand these important interactions. In this paper we present a model for the solution conformations sampled by a simple trimannoside, methyl 3, 6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside, which contains two of the most commonly found glycosidic linkages in N-linked oligosaccharides. This model was derived from simulated annealing protocols incorporating distance restraints extracted from NOESY spectra along with torsional restraints computed from three-bond (1)H-(13)C coupling constants measured across the glycosidic bonds. The model was refined in light of unrestrained molecular dynamics simulations conducted in the presence of solvent water. The resulting model depicts a molecule undergoing conformational averaging in solution, adopting four major and two minor conformations. The four major conformations arise from a pair of two-state transitions, one each at the alpha(1-->3) and alpha(1-->6) linkages, whereas the minor conformations result from an additional transition of the alpha(1-->6) linkage. Our data also suggest that the alpha(1-->3) transition is fast and changes the molecular shape slightly, whereas the alpha(1-->6) is much slower and alters the molecular shape dramatically.

Shaping up for structural glycomics: a predictive protocol for oligosaccharide conformational analysis applied to N-linked glycans

“…6, panels C and D) 6 . The simulations predict a single and extremely broad free energy minimum centered on state XV and spanning ≈120° in both ϕ and ψ .…”

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

“…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). …”

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with13C CPMAS NMR as a Verification Method

“…[8] Molecular dynamic simulations of trimannoside revealed high flexibility of the (1→6) linkage. [9] Later, molecular dynamic simulation studies of eight disaccharides (including gentiobiose) were carried out [10] and showed in particular that (1→6)-linked disaccharides were characteristic with an increased flexibility. Conformational analysis of (1→6) disaccharides usually consists of making Ramachandran-like maps, which depict potential energy dependence on three dihedral angles defined around the glycosidic linkage.…”

“…The preparation of such maps is a difficult task due to the "local minima problem." [9,13] At each grid point, the arrangement of all exocyclic groups should be taken into account, which requires 3 9 × 18 3 relaxed optimizations assuming that conformational space would be searched with a resolution of φ, ψ, and ω torsion angles at 20 • .…”

“…An additional simplification concerning the free hydroxymethyl group can be made assuming that the gauche-gauche and gauche-trans positions are the most preferable. [11,14] In the random molecular mechanics (RAMM) method, [9,11] a preliminary random search for the best arrangement of exocyclic groups is carried out before relaxed optimization at a given point on the grid.…”