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

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-carrageen...

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Published in:Journal of molecular graphics & modelling 2020-07, Vol.98, p.107588-107588, Article 107588
Main Authors: Perez, Ser John Lynon P., Claudio, Gil C.
Format: Article
Language:English
Subjects:
Counterion density
Forces of interaction
Iota-carrageenan
Molecular dynamics
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Summary: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. [Display omitted] •Attractive forces due to Na+ counterions of two parallel iota-carrageenan double-helical (DH) hexamers were elucidated.•Na+counterions provide strong attractive forces when the two double-helix separation distance (rDH1-DH2) is less than 4 nm.•Attractive electrostatic forces due to Na+ counterions surpass the repulsion of the OSO3- groups between the DHs .•The Lennard-Jones forces became relevant at rDH1-DH2 < 2 nm.•Cations provide attractive forces that facilitate the aggregation process of carrageenan gelation.
ISSN:1093-3263
1873-4243
DOI:10.1016/j.jmgm.2020.107588