Conformational properties of acidic oligo- and disaccharides and their ability to bind calcium: a molecular modeling study

The conformational analysis of disaccharides composed of two constituents of alginic acid (β-D-mannuronic and α-L-guluronic acids) was performed. Several additional aspects, such as pH and the type of ionic environment were taken into account. The calculations were performed on the two levels of theory: semi-empirical (PM3) conformational search in vacuo and molecular dynamics with explicit solvent based on the biomolecular (GROMOS) force field. The results indicate that the values of glycosidic dihedral angles can vary in a very similar range, independently of the disaccharide composition. The presence of interresidual hydrogen bonds involving carboxyl groups reduces the ability for calcium ion binding. The type and the concentration of cations in the solution do not practically affect the conformation of disaccharides. Both disaccharides and the oligosaccharides composed of corresponding units exhibit a similar degree of conformational flexibility; only in the case of oligosaccharides containing the α-l-guluronate units, the glycosidic bonds are much more rigid when compared to those of disaccharides.