Publication details
Carbohydrate-protein binding site interaction
| Authors | |
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| Year of publication | 2018 |
| Type | Conference abstract |
| MU Faculty or unit | |
| Citation | |
| Description | Interactions of saccharides with receptors belong to the most important ones in cell recognition, growth or differentiation, as well as in many pathological processes. These interactions are mediated by so-called glycocode – saccharide code which is read by many proteins. Saccharides interact with proteins in various ways. The most famous are hydrogen bridges but saccharides utilize also hydrophobic interactions or metal-ion mediated interaction. We concentrated mainly on CH-pi stacking interaction – the dispersion driven interaction between carbohydrate apolar faces and aromatic amino-acid residues. This interaction has been underestimated for a long time but we found out that it is a highly important interaction in carbohydrate-protein complexes. In our computational structure-based study we examined structures stored in Protein Data Bank (PDB) database. We examined complexes with a carbohydrate in a close proximity of an aromatic amino acid (tryptophan, tyrosine, phenylalanine, and histidine). We detected the presence of CH-pi stacking and examined the geometry parameters of these binding sites. Each aromatic amino acid showed a unique CH-pi stacking pattern, demonstrated by a characteristic orientation, bond distances, and bond angles between the carbohydrate and a particular amino acid. Besides CH-pi stacking interaction, we detected also hydrogen bridges and compare the frequencies of these two types of carbohydrate-protein interaction. These results provide insight into the importance of CH-pi stacking in carbohydrate-protein interactions and may help in drug development, receptor studies or protein engineering. |
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