A1 Refereed original research article in a scientific journal

Martini 3 Coarse-Grained Force Field for Carbohydrates




AuthorsGrünewald Fabian, Punt Mats H., Jefferys Elizabeth E., Vainikka Petteri A., König Melanie, Virtanen Valtteri, Meyer Travis A., Pezeshkian Weria, Gormley Adam J., Karonen Maarit, Sansom Mark S.P., Souza Paulo C.T., Marrink Siewert J.

PublisherAmerican Chemical Society

Publication year2022

JournalJournal of Chemical Theory and Computation

Journal name in sourceJournal of Chemical Theory and Computation

eISSN1549-9626

DOIhttps://doi.org/10.1021/acs.jctc.2c00757

Web address https://pubs.acs.org/doi/10.1021/acs.jctc.2c00757

Self-archived copy’s web addresshttps://research.utu.fi/converis/portal/detail/Publication/177210890


Abstract

The Martini 3 force field is a full re-parametrization of the Martini coarse-grained model for biomolecular simulations. Due to the improved interaction balance it allows for more accurate description of condensed phase systems. In the present work we develop a consistent strategy to parametrize carbohydrate molecules accurately within the framework of Martini 3. In particular, we develop a canonical mapping scheme that decomposes arbitrarily large carbohydrates into a limited number of fragments. Bead types for these fragments have been assigned by matching physicochemical properties of mono- and disaccharides. In addition, guidelines for assigning bonds, angles, and dihedrals are developed. These guidelines enable a more accurate description of carbohydrate conformations than in the Martini 2 force field. We show that models obtained with this approach are able to accurately reproduce osmotic pressures of carbohydrate water solutions. Furthermore, we provide evidence that the model differentiates correctly the solubility of the poly-glucoses dextran (water soluble) and cellulose (water insoluble, but soluble in ionic-liquids). Finally, we demonstrate that the new building blocks can be applied to glycolipids, being able to reproduce membrane properties and to induce binding of peripheral membrane proteins. These test cases demonstrate the validity and transferability of our approach.


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