Carbohydrates

 

sugars2Carbohydrates (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 [1], cellulose [2,6], and cyclodextrins [4] 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 [3], as well as lipopolysaccharides [7], and the ability to simulate glycans  [8].

  • [1] 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.
  • [2] J. Wohlert, L.A. Berglund. A coarse-grained model for molecular dynamics simulations of native cellulose. J. Chem. Theo. Comp. 7:753-760, 2011.
  • [3] 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
  • [4] 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
  • [5] 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
  • [6] 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
  • [7] P.C. Hsu, B.M.H. Bruininks, D. Jefferies, P.C. Telles de Souza, J. Lee, D.S. Patel, S.J .Marrink, Y. Qi, S. Khalid, W. Im. CHARMM‐GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides. J. Comput. Chem., 38:2354–2363, 2017. abstract
  • [8] 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