An Investigation of the Conformation of β-Carrageenan by Molecular Mechanics and Molecular Dynamics Simulations

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Abstract
Carrageenan is known to change its conformation from coil to helix and to form a gel. However, the accurate conformation and the transition mechanism have not yet been detailed. In this work, the conformational behavior of β-carrageenan (a copolymer with a carrabiose repeating unit, 1,4-linked 3,6-anhydro-α-d-galactose (A) and 1,3-linked β-d-galactose (B)), was studied by using molecular mechanics and molecular dynamics simulation methods with the program CHARMM22. The energy maps of the carrabiose as a function of the dihedral angles of the glycosidic linkages between the A–B (1–3 linkage) and B–A (1–4 linkage) carrabiose units were calculated. Both carrabiose units were found to have five deep potential energy minima. Based on these carrabiose conformations, 25 conformers of the single helical chain carradodecaose were constructed and their minimum energy conformations were investigated by molecular mechanics and molecular dynamics simulations. From the results of these analyses, a possible single helical structure of β-carrageenan was elucidated. The stability of this helical conformation is discussed by comparing it with a double helical conformation, which was found from X-ray diffraction analyses of oriented fiber samples of κ-and ι-carrageenans, which are well-studied members of the carrageenan family.