ArticleJournal of chemical theory and computation2024
Refined Protein-Sugar Interactions in the Martini Force Field.
Article in Journal of chemical theory and computation, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Sugar molecules play important roles as mediators of biomolecular interactions in cellular functions, disease, and infections. Molecular dynamics simulations are an indispensable tool to explore these interactions at the molecular level. The large time and length scales involved frequently necessitate the use of coarse-grained representations, which heavily depend on the parametrization of sugar-protein interactions. Here, we adjust the sugar-protein interactions in the widely used Martini 2.2 force field to reproduce the experimental osmotic second virial coefficients between sugars and proteins. In simulations of two model proteins in glucose solutions with adjusted force field parameters, we observe weak protein-sugar interactions. The sugar molecules are thus acting mainly as crowding agents, in agreement with experimental measurements. The procedure to fine-tune sugar-protein interactions is generally applicable and could also prove useful for atomistic force fields.
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