Martini extension to carbohydrates

Sweet Martini now available!

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C.A. López, A.J. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Hünenberger, S.J. Marrink, 5:3195-3210, 2009, JCTC.



We present an extension of the Martini coarse grained force field to carbohydrates. The parameterization 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 non polar 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 an accurate representation of the rotameric states. Application of the new coarse grained carbohydrate model to the oligosaccharides amylose and curdlan shows a preservation of the main structural properties, with three orders of magnitude more efficient sampling than the atomistic counterpart. Finally we investigate the cryo- and anhydro-protective e¤ect 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.

Martini carbohydrate parameters can be downloaded here.