Molecular modelling of helix stability in carrageenans

Molecular models of disaccharides, and single and double helices up to eigh t monomers in length have been constructed of the two types of glycosidic l inkage in the carrageenan chain. These links are a galactose to anhydrogala ctose link (GA link), and an anhydrogalactose to galactose link (AG link). These models are also based on kappa-carrageenan, which contains a 4-sulpha te galactose ring. The effects of the sulphate groups on the conformation o f the helices may be seen by the angles of phi and psi explored during the simulations by the AG and GA linkages. It has been observed that the molecu le can explore a greater area of conformational space about the GA link tha n the AG link. This could be due to steric hindrance caused by the bulky su lphate group near the AG link. The sulphate group is further away from the GA link than from the AG link, and this may provide a possible explanation for the relatively unhindered movement about the GA link compared to the AG link. The results have also shown that the conformational space for the AG linkages, as well as the GA linkages vary between different lengths of the polysaccharide chain. Single helix models show little stability in molecul ar dynamics simulation, whereas the eight monomer double helix model is mor e stable than a six monomer double helix model.