CH-pi stacking interaction in carbohydrate-protein complexes

ŽUFANOVÁ, Zuzana, Josef HOUSER, Stanislav KOZMON, Deepti MISHRA, Jaroslav KOČA and Michaela WIMMEROVÁ. CH-pi stacking interaction in carbohydrate-protein complexes. In XVIII. setkání biochemiků a molekulárních biologů. 2017. ISBN 978-80-210-8765-1.

Basic information

• Original name: CH-pi stacking interaction in carbohydrate-protein complexes
• Authors: ŽUFANOVÁ, Zuzana, Josef HOUSER, Stanislav KOZMON, Deepti MISHRA, Jaroslav KOČA and Michaela WIMMEROVÁ.
• Edition: XVIII. setkání biochemiků a molekulárních biologů, 2017.

Other information

• Original language: English
• Type of outcome: Conference abstract
• Field of Study: 10600 1.6 Biological sciences
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• Organization unit: Faculty of Science
• ISBN: 978-80-210-8765-1
• Keywords in English: CH-pi stacking; carbohydrate-protein interactions; aromatic amino-acid residues; PDB database

Abstract

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.