Extending the Martini 3 Coarse-Grained Force Field to Carbohydrates

Carbohydrates play an essential role in a large number
of chemical
and biochemical processes. High structural diversity and conformational
heterogeneity make it problematic to link their measurable properties
to molecular features. Molecular dynamics simulations carried out
at the level of classical force fields are routinely applied to study
the complex processes occurring in carbohydrate-containing systems,
while the usefulness of such simulations relies on the accuracy of
the underlying theoretical model. In this article, we present the
coarse-grained force field dedicated to glucopyranose-based carbohydrates
and compatible with the recent version of the Martini force field
(v. 3.0). The parameterization was based on optimizing bonded and
nonbonded parameters with a reference to the all-atom simulation results
and the experimental data. Application of the newly developed coarse-grained
carbohydrate model to oligosaccharides curdlan and cellulose displays
spontaneous formation of aggregates of experimentally identified features.
In contact with other biomolecules, the model is capable of recovering
the protective effect of glucose monosaccharides on a lipid bilayer
and correctly identifying the binding pockets in carbohydrate-binding
proteins. The features of the newly proposed model make it an excellent
candidate for further extensions, aimed at modeling more complex,
functionalized, and biologically relevant carbohydrates.