Computer modelling of sulfated carbohydrates: applications to carrageenans

In this study, X-ray crystallographic data of sulfated monosaccharides have been used to derive appropriate parameters for sulfate groups in the Tripos force field, previously parameterized for carbohydrates. A database of nine sulfated monosaccharides occurring as building blocks of sulfated polysaccharides such as carrageenans and sulfated glycosaminoglycans has been built. These tools have then been used to evaluate the conformational energies of the repeating units of the kappa-, iota- and lambda-carrageenan polymers, taking into account the rotation around the sulfate groups. In a third step, helical conformations of carrageenans have been explored and the results compared with the experimental data obtained by X-ray fibre diffraction. Stable, single, right-handed helices, with geometric and helical parameters in close correspondence with the best models derived from X-ray diffraction data, have been generated. Finally, the configurational statistics of random-coil carrageenan chains have been investigated and compared with experimental data currently available on these polymers. A highly flexible character is predicted for kappa- and iota-carrageenans, with lambda-carrageenan showing slightly more extension.