Molecular dynamics simulations of two double-helical hexamer fragments of iota-carrageenan in aqueous solution

Abstract

The gelation of anionic carrageenans is known to occur through a coil-to-helix transition followed by further aggregation or association on which positive counterions play a significant role. In the present work, molecular dynamics (MD) simulations were performed on two double-helical iota-carrageenan hexamer fragments along with their sodium counterions using the Carbohydrate Solution Force Field (CSFF) in an aqueous (TIP4P) solution with the GROMACS molecular dynamics package. Results showed a counterion condensation between the two double helices and that the subsequent forces of interaction between them were predominantly attractive. By varying the distance separating the two double helices, the effect of distance on the counterion distribution and the forces of attraction was also investigated. In the presence of counterions, an increase in the forces of attraction was observed as the distance between the two double helices decreases which can be attributed to the greater counterion density between the two like-charged oligosaccharides.

Keywords: Counterion density; Forces of interaction; Iota-carrageenan; Molecular dynamics.