Martini Coarse-Grained Force Field: Extension to Carbohydrates

Abstract

We present an extension of the Martini coarse-grained force field to carbohydrates. The parametrization follows the same philosophy as was used previously for lipids and proteins, focusing on the reproduction of partitioning free energies of small compounds between polar and nonpolar phases. The carbohydrate building blocks considered are the monosaccharides glucose and fructose and the disaccharides sucrose, trehalose, maltose, cellobiose, nigerose, laminarabiose, kojibiose, and sophorose. Bonded parameters for these saccharides are optimized by comparison to conformations sampled with an atomistic force field, in particular with respect to the representation of the most populated rotameric state for the glycosidic bond. Application of the new coarse-grained carbohydrate model to the oligosaccharides amylose and Curdlan shows a preservation of the main structural properties with 3 orders of magnitude more efficient sampling than the atomistic counterpart. Finally, we investigate the cryo- and anhydro-protective effect of glucose and trehalose on a lipid bilayer and find a strong decrease of the melting temperature, in good agreement with both experimental findings and atomistic simulation studies.

Folding and insertion thermodynamics of the transmembrane WALP peptide

“…29,[40][41][42][43] The key idea is to represent characteristic chemical moieties with a limited set of CG bead types, determined from the overall charge, hydrogenbond capability, and water/oil partitioning coefficient. 29 Martini reproduces a number of lipid-membrane characteristics: self-assembly, area per lipid, elastic properties, as well as a reasonable bilayer stress profile.…”

Amylose folding under the influence of lipids

“…8,9 Molecular dynamics (MD) simulations have proven to be a useful tool for providing a link between dynamics and structure. Many force fields have been extensively parameterized for carbohydrates, [10][11][12][13][14][15][16][17] and have been used to provide details of the structure and dynamics at an all atom (AA) level; for example to explore the ring puckering of glucose, 18,19 conformational changes in disaccharides and trisaccharides. 11,[20][21][22] However, previous MD studies of amylose have mainly dealt with small amylose fragments in water or studies of V-amylose in low polarity solvents.…”

Computer Simulations of Soft Matter: Linking the Scales

“…In thermodynamic coarse graining approaches, individual elements of the CG interaction function are separately parameterized based on thermodynamic reference data such as solvation free energies and partitioning data, liquid densities, surface tension, etc. [65][66][67][68][69][70][71][72][73][74][75][76]. (These are usually experimental reference data, but in a multiscale simulation approach the reference data can of course also be obtained from an atomistic simulation, to keep the CG and atomistic level thermodynamically consistent).…”