- Last Updated: Friday, 12 February 2021 12:00
Carbohydrates (saccharides), the most abundant product of photosynthesis, play an important role in the energetic metabolism of living species and the signaling and immunological responses and are a fundamental component of the external cell wall of many organisms. In addition, saccharides are present in a variety of emerging classes of biomimetic materials. Furthermore, due to their cryo- and anhydro-protective properties, many sugars have been shown to be effective stabilizers of biological components, such as proteins and membranes, in the low-temperature or dehydrated states. This class of compounds encompasses a huge variety of possible monomeric units (differing in stereochemistry and functionalization) that can be connected in chains presenting a virtually infinite number of possible residue sequences, linkage types, and degrees of branching.
The large size of most oligosaccharides warrants the use of a coarse-grained model, yet the complexity of carbohydrate physico-chemical properties makes this a very challenging undertaking. In 2009, Martini has been parameterized for common mono- and disaccharides [1,5] that can serve as a basis for further carbohydrate modeling. Based on this model, oligosaccharides such as amylose , cellulose [2,6], and cyclodextrins  have been parameterized as well.
Other extensions include the important class of glyco-lipids, with parameters for MGDG, DGDG, SQDG, PI, PIPn, GCER, and GM1 , as well as lipopolysaccharides , and the ability to simulate glycans .
-  C.A. Lopez, A. Rzepiela, A.H. de Vries, L. Dijkhuizen, P.H. Huenenberger, S.J. Marrink. The Martini coarse grained force field: extension to carbohydrates. J. Chem. Th. Comp., 5:3195-3210, 2009.
-  J. Wohlert, L.A. Berglund. A coarse-grained model for molecular dynamics simulations of native cellulose. J. Chem. Theo. Comp. 7:753-760, 2011.
-  C.A. Lopez, Z. Sovova, F.J. van Eerden, A.H. de Vries, S.J. Marrink. Martini force field parameters for glycolipids. JCTC, 9:1694–1708, 2013. abstract
-  C.A. Lopez, A.H. de Vries, S.J. Marrink. Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes. Sci. Rep., 3:2071, 2013. open access
-  G. Moiset, C.A. López, R. Bartelds, L. Syga, E. Rijpkema, A. Cukkemane, M. Baldus, B. Poolman, S.J. Marrink. Disaccharides impact the lateral organization of lipid membranes. JACS, 136:16167-16175, 2014. open access
-  C.A. López, G. Bellesia, A. Redondo, P. Langan, S.P.S. Chundawat, B.E. Dale, S.J. Marrink, S. Gnanakaran. MARTINI coarse-grained model for crystalline cellulose microfibers. JPCB, 119:465–473, 2015. abstract
-  A.T. Shivgan, J.K. Marzinek, R.G. Huber, A. Krah, R.H. Henchman, P. Matsudaira, C.S. Verma, P.J. Bond. Extending the Martini Coarse-Grained Force Field to N-Glycans. J. Chem. Inf. Mod. 60:3864-3883, 2020. open access