Interactions of carbohydrate and aromatic amino acid in protein binding sites
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| Year of publication | 2019 |
| Type | Conference abstract |
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| 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. There are several ways how saccharides interact with proteins; hydrogen bridges, metal-ion mediated interaction, hydrophobic interaction etc. CH-pi stacking, dispersion driven interaction has been underestimated for a long time. However, 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 with focuse on the complexes with carbohydrates in close proximity of aromatic amino acid (tryptophan, tyrosine, phenylalanine, and histidine). We detected CH-pi stacking interaction being involved in sugar binding in 61 % of these complexes. 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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