Publication details
CH-pi stacking interaction in carbohydrate-protein complexes
| Authors | |
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| Year of publication | 2017 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | Interactions of saccharides with receptors belong to the most important ones as in cell recognition, growth or differentiation and in many diseases. These interactions are mediated by so-called glycocode – saccharide code which is read by many proteins. There are several ways how saccharides interact with proteins: hydrogen bridges, metal-ion-mediated interaction etc. The role of dispersion-driven CH-pi interactions in protein-carbohydrate interactions has been underestimated for a long time. This type of interaction occurs between carbohydrate apolar faces and aromatic amino-acid residues. The CH-pi stacking is a non-covalent interaction where a CH group interacts with an aromatic ring and can be recognized as a special type of the hydrogen bond. We investigated CH-pi stacking interactions in protein/carbohydrate complexes by the bioinformatic structure-based study. The Protein Data Bank (PDB) database has been used as a source of structural data of the carbohydrate/protein complexes. The database contains more than 10 000 entries of protein complexes with carbohydrates. We have searched the PDB database to examine complexes with carbohydrates in a close proximity of the aromatic amino acid (tryptophan, tyrosine, phenylalanine, and histidine). In these complexes, we have found that CH-pi stacking is highly important interaction, being detected in 61 % of these complexes. The analysis has shown that the most frequent residue involved in the CH-pi stacking complexes is tryptophan. We have also identified the differences in the interaction preferences between individual aromatic amino acid residues and carbohydrates. Our findings may help in a better description of carbohydrate-protein interaction and thus help in drug development, receptor studies or protein engineering. |