Carbohydrate CH/p interactions – Theoretical investigation of the favourable regions in the carbohydrate surroundings


Stanislav Kozmon1, Radek Matuška1, Vojtěch Spiwok2, Jaroslav Koča1


1National Centre for Biomolecular Research, Masaryk University, Brno 611 37, Czech Republic

2Institute of Chemical Technology, Department of Biochemistry & Microbiology, Technická 5 Prague 166 28, Czech Republic


Molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, cell-cell adhesion and so forth [1-5]. The list of proteins that recognise carbohydrates via aromatic residues include lectins, carbohydrate-binding modules, glycosidases, glycosyl transferases, “greasy slides” of carbohydrate transporters and complimentary sugar-binding sites (“sugar tongs”). Carbohydrates typically interact with aromatic systems in a parallel orientation.

In this study we present the first systematic computational three-dimensional scan of carbohydrate hydrophobic patches for the ability to interact via CH/p dispersion interactions. The carbohydrates b-d-glucopyranose, b-d-mannopyranose and a-l-fucopyranose were studied in a complex with a benzene molecule, which served as a model of the CH/p interaction in carbohydrate/protein complexes.


[1]           H. Lis, N. Sharon, Chemical Reviews 1998, 98, 637-674.

[2]           M. Ambrosi, N. R. Cameron, B. G. Davis, Organic & Biomolecular Chemistry 2005, 3, 1593-1608.

[3]           H. J. Gabius, H. C. Siebert, S. Andre, J. Jimenez-Barbero, H. Rudiger, Chembiochem 2004, 5, 741-764.

[4]           J. Holgersson, A. Gustafsson, M. E. Breimer, Immunology and Cell Biology 2005, 83, 694-708.

[5]           N. Sharon, H. Lis, Glycobiology 2004, 14, 53r-62r.



This work was funded by the European Community's Seventh Framework Programme under grant agreement n° 205872, the Ministry of Education of the Czech Republic (MSM0021622413, LC06030, MSM6046137305), Czech Science Foundation (GD301/09/H004). The authors would like thank the Czech National Supercomputer Centre, METACENTRUM, for the support of computational power. Access to the MetaCentrum computing facilities provided under the research intent MSM6383917201 is acknowledged.