Molecular Dynamics Study of Supramolecular Complexes to the Carbohydrate-Cation System.

Authors

Dhaidan Khalaf Kafi, Ali Taher Mohi

Published in

F1000Research. Volume 15. Pages 503. Epub Aug 21, 2026.

Abstract

It is known that calcium ions lead to aggregation of disaccharides, while magnesium ions do not. In this study, simulation results indicated that the cations primarily bind to the sulfate groups of the disaccharides.
From molecular dynamics simulations, the differences between the calcium and magnesium cation systems can be explained. Additionally, when a modified water model is used in the case of the magnesium system, in which the charges of the water atoms are reduced, the magnesium ions bind the hydration shell less strongly than in the 'normal' water model, which facilitates complex formation with the disaccharides. To verify whether the stability differences between the two saccharides are also observed in the simulations, the simulations of the calcium system were repeated with the monosaccharide.
Moreover, result in the formation of carbohydrate-cation-carbohydrate complexes, with the disaccharides primarily binding to the glucose unit, which is attached to the sulfate group. If the cation is not present, the sulfate groups repel each other and complex formation is not possible. The differences between the two cation systems can be explained as follows: Magnesium ions bind much weaker to the disaccharide than calcium ions. The reason is that magnesium ions bind more strongly to the hydration shell due to their smaller ion radius compared to calcium ions. This is energetically more expensive in the case of magnesium ions, which leads to a kinetic hindrance of complex formation compared to the calcium system. The other significant difference between the two cation complexes is that in the case of calcium ions, both disaccharides bind directly to the cation through the sulfate groups.
As expected, the binding energy of the monosaccharide complex was found to be lower than that of the disaccharide complex (6 kJ/mol). The difference in binding energies between the two complexes was relatively small. A significantly lower rupture force was found in the simulations for an individual complex.

PMID:
42740815
Bibliographic data and abstract were imported from PubMed on 15 Sep 2026.

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