Martini 3 Coarse-Grained Force Field for Carbohydrates

Area of Science:

• Computational chemistry
• Biomolecular simulations
• Coarse-grained modeling

Background:

• The Martini 3 force field offers improved accuracy for condensed phase systems.
• Accurate parametrization of diverse molecules is crucial for biomolecular simulations.

Purpose of the Study:

• To develop a consistent and accurate strategy for parametrizing carbohydrate molecules within the Martini 3 force field.
• To enable more precise simulation of carbohydrate behavior in various environments.

Main Methods:

• Developed a canonical mapping scheme to decompose carbohydrates into limited fragments.
• Assigned bead types by matching physicochemical properties of mono- and disaccharides.
• Established guidelines for bonds, angles, and dihedrals to improve conformational accuracy.

Main Results:

• Accurately reproduced osmotic pressures of carbohydrate-water solutions.
• Correctly differentiated the solubility of dextran and cellulose.
• Successfully applied new building blocks to glycolipids, reproducing membrane properties and protein binding.

Conclusions:

• The developed Martini 3 parametrization strategy provides accurate and transferable models for carbohydrates.
• This approach enhances the simulation of carbohydrate-related systems, including glycolipids and their interactions.
• The findings validate the utility of the new building blocks for biomolecular modeling.