Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations

Journal article

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

Authors: Shearer, J; Khalid, S

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Nature Research
• Journal: Scientific Reports
• Volume: 8
• Issue: 1
• Pages: 1805-1805
• Publication date: 2018-01-23
• DOI: 10.1038/s41598-018-20227-1
• EISSN: 2045-2322
• ISSN: 2045-2322
• Language: English
• Keywords: Biology; Biophysics; Computational chemistry; Membrane protein; Biochemistry; Barrel (horology); Leaflet (botany); Chemistry; Physics; Receptor; Materials science; Chemical physics; Membrane; Molecular dynamics; Botany; Transmembrane protein; Dynamics (music)