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The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification
Author(s) -
Houser Josef,
Kozmon Stanislav,
Mishra Deepti,
Hammerová Zuzana,
Wimmerová Michaela,
Koča Jaroslav
Publication year - 2020
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.202000593
Subject(s) - isothermal titration calorimetry , stacking , protein data bank (rcsb pdb) , protein data bank , chemistry , hydrogen bond , protein–protein interaction , crystallography , non covalent interactions , polar , molecular recognition , structural bioinformatics , protein structure , biochemistry , molecule , computational biology , biology , physics , organic chemistry , astronomy
The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell–cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal‐ion‐mediated interaction, and non‐polar dispersion interactions. The role of dispersion‐driven CH–π interactions (stacking) in protein–carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non‐polar interactions are equally important. In this study, we analyzed the CH–π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X‐ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH–π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol −1 . All the results show that the stacking CH–π interactions in protein–carbohydrate complexes can be considered to be a driving force of the binding in such complexes.