Computer modeling of carbohydrate molecules

Abstract

Although computer modeling of carbohydrates has had a long history, almost comparable to that of protein modeling, there are still some technical problems to be solved at present due to their complexity and versatility. Carbohydrates which comprise many polar functional groups, as represented by the hydroxyl group, exhibit significant flexibility in their three-dimensional structures. They change the electronic configurations depending on the three-dimensional configurations and conformations resulting in the specific stereochemical features, such as anomeric effect, exoanomeric effect, and gauche effect. In computer modeling, these stereochemical features of carbohydrates have required developments of the force fields and/or the parameter sets designed to reproduce them. The hydroxyl groups on a sugar residue form a hydrogen bond with water molecules and the solvation environment affects conformational behavior of the carbohydrate molecule. In fact, a stable water-mediated interresidue hydrogen bond has been detected in the molecular dynamics simulations for solvated carbohydrate molecules. Since carbohydrate molecules readily exhibit various conformations arising from the intrinsic flexibility of glycosidic linkages, conformational analysis was required to systematically explore possible conformations and evaluate their steric energies. On the other hand, carbohydrate molecules often generate a large and complex conformational space derived from diversities of sugar residues and substitutents, and formation of branching structures. Several algorithms intended for an effective search for such a conformational space have been examined. ©2005 FCCA (Forum: Carbohydrates Coming of Age).