The κ-carrageenan is an ionic polysaccharide extracted from marine red algae constituted by the copolymeric repetitive units of α-(1-3)D-galactose 4 - sulfate and β-(1-4) 3,6-anhydro-D-galactose. The knowledge of the molecular bases that determine the three-dimensional conformation of this polysaccharide is fundamental to understand the interactions leading to gel formation, as well as the regulation of its industrial properties. As with other biopolymers, even though its primary structure is well-known, the secondary structure is still a matter of debate. This work present and discuss the results of Molecular Dynamics (MD) simulations of a decamer of the repeating disaccharide unit constituting the κ-carrageenan. The simulations were run using the GROMACS MD package, with the solute immersed in molecular solvent, either DMSO or water, and using Na+ atoms as counterions. The dynamics of the central glycosidic angles are presented, as well as the pattern of possible intramolecular and solvent mediated H-bonds and some characteristics interatomic distances. These results are in good agreement with the available experimental data, as well as those of previous molecular mechanics and dynamics.

Estudio mediante dinámica molecular de la estructura tridimensional del κ-carragenano en diferentes solventes (Study of molecular dynamics in a tridimensional structure of kappa-carragenan in different solvents)

PAOLETTI, SERGIO;
2010

Abstract

The κ-carrageenan is an ionic polysaccharide extracted from marine red algae constituted by the copolymeric repetitive units of α-(1-3)D-galactose 4 - sulfate and β-(1-4) 3,6-anhydro-D-galactose. The knowledge of the molecular bases that determine the three-dimensional conformation of this polysaccharide is fundamental to understand the interactions leading to gel formation, as well as the regulation of its industrial properties. As with other biopolymers, even though its primary structure is well-known, the secondary structure is still a matter of debate. This work present and discuss the results of Molecular Dynamics (MD) simulations of a decamer of the repeating disaccharide unit constituting the κ-carrageenan. The simulations were run using the GROMACS MD package, with the solute immersed in molecular solvent, either DMSO or water, and using Na+ atoms as counterions. The dynamics of the central glycosidic angles are presented, as well as the pattern of possible intramolecular and solvent mediated H-bonds and some characteristics interatomic distances. These results are in good agreement with the available experimental data, as well as those of previous molecular mechanics and dynamics.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11368/2832941
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