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Carbohydrate-protein binding site interaction

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HAMMEROVÁ Zuzana HOUSER Josef KOZMON Stanislav MISHRA Deepti KOČA Jaroslav WIMMEROVÁ Michaela

Rok publikování 2018
Druh Konferenční abstrakty
Fakulta / Pracoviště MU

Přírodovědecká fakulta

Citace
Popis 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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