A molecular builder for carbohydrates: application to polysaccharides and complex carbohydrates

A new procedure (POLYS) for producing three-dimensional structures of polysaccharides and complex carbohydrates is described. This employs a builder concept combining a database of monosaccharide structures with a database containing information on populations of independent neighboring glycosidic linkages in disaccharide fragments. The computer program is written in C, and it can cope with both the complexity and the diversity of carbohydrates and the unique topological features arising from multiple branching. A simple ASCII syntax was developed for describing the primary structures in accordance with IUPAC nomenclature. The translation of the primary structure is made through the combined use of a lexical analyzer and a command interpreter. In this way the program can be considered as a compiler of primary structures of carbohydrates. However, it also generates secondary and tertiary structures in the form of Cartesian coordinates in formats used by most molecular mechanics programs and packages. In our laboratory POLYS was exhaustively tested on standard homopolysaccharide systems such as cellulose and mannan and found to work very well. We now report the ease of use and the efficiency of the molecular builder in applications to more complex carbohydrate systems. These include the structural exploration of a pentaantennary oligosaccharide having 135 residues, the complex family of pectic polysaccharides including the organization and distribution of side chains (arabinan, arabinogalactan, and galactan) on the rhamnogalacturonan backbone.