Carbohydrate-protein binding site interaction

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F18%3A00105744" target="_blank" >RIV/00216224:14310/18:00105744 - isvavai.cz</a>

Výsledek na webu

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DOI - Digital Object Identifier

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Jazyk výsledku

angličtina

Název v původním jazyce

Carbohydrate-protein binding site interaction

Popis výsledku v původním jazyce

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.

Název v anglickém jazyce

Carbohydrate-protein binding site interaction

Popis výsledku anglicky

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.

Druh

O - Ostatní výsledky

CEP obor

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OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/LQ1601" target="_blank" >LQ1601: CEITEC 2020</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů