MM3 Potential energy surfaces of β-4-linked mannobiose and mannotriose at different dielectric constants

Abstract

The adiabatic potential energy surface (PES) of β-4-linked mannobiose was obtained using the MM3 force field at ε=3 and ε=80, and plotted as contour maps and as 2D graphs representing the energy vs. the ψ angle. The surfaces of the corresponding trisaccharide were also obtained and represented by a single 3D contour map for which the energy is plotted against the two ψ glycosidic angles. The PES of the disaccharide contains a low-energy well comprising two different minima, and three more minima in different locations. No major change was observed by changing the dielectric constant. For the trisaccharide, four main minima were observed, located within one minimum-energy region. The minima have a geometry close to that experimentally obtained for mannobiose, mannotriose and mannan I in solid state, but differ from that expected in aqueous solutions. The flexibility of the glycosidic linkage increases at higher dielectric constant, whereas it decreases for the linkage closer to the reducing end when passing from the di-to the trisaccharide.

Guar Gum and Scleroglucan Interactions with Borax: Experimental and Theoretical Studies of an Unexpected Similarity

“…The starting conformations of the elongated structure were obtained by setting, for all the Man→Man nearest neighbor residues, torsional angles (ϕ and ψ, see Figure ) values close to those measured in the mannan fibers by electron, and X-ray diffraction. Such values are similar to those reported for the mannobiose and mannotriose crystal structures and also to the absolute minimum obtained for mannobiose, by using the MM3 force field. , Three dihedral angles define the orientation of the galactopyranose residue in the side chain (ϕ I , ψ I , and ω, see Figure ). The ϕ I and ψ I values of the starting structure were set in the absolute minimum found by Petkowicz and co-worker; the ω angles were initially set to 60°.…”

“…The minima above-reported roughly correspond to those identified in the adiabatic maps of mannobiose. , Other authors proposed a different set of minima, validating their results by comparison with NMR data . However, they did not identify the global minimum detected by X-ray diffraction of mannobiose and mannotriose and in the fibers of mannan by electron and X-ray diffraction.…”

“…During these simulations, three further relative minima in the ϕ−ψ map were populated (see Discussion). Such minima, already predicted for mannobiose, , were used to obtain the starting coiled structure for GG and GG/borax simulations. The same conformation was used to simulate both systems; about 18,500 water molecules were considered, and the trajectories lasted 10 ns.…”

“…As far as GG is concerned, adiabatic maps of the mannose and epimelibiose disaccharides (representing the GG repeating unit) were obtained by means of MM calculations, ,− semiempirical techniques, and also using short MD trajectories . Furthermore, QM methods were applied for the study of mannose analogues, where the hydroxyl groups were replaced by H atoms .…”

Establishing Rules for Self-Adhesion and Aggregation of N-Glycan Sugars Using Virus Glycan Shields

“…The endosperm of seeds (dates, coffee beans, ivory nuts, and so forth) is rich in polymers of mannose called mannans which serve as dense stores of energy for the seeds . X-ray crystallography reveals organized hydrogen-bonding across stacked mannose faces as responsible for the tight packing of these polymers. − Similar short-range hydrogen bonding interactions could be responsible for the Velcro-like adhesions between mannose residues in glycans. The tight packing among mannose polymers is loosened in mucilaginous materials (guar gum, locust bean gum, cassia gum) by interspersing the polymer with galactose. , The greater the galactose/mannose ratio is, the higher the swelling or loose-packing of the galactomannan polymers is .…”