期刊
CHEMISTRY-A EUROPEAN JOURNAL
卷 26, 期 47, 页码 10769-10780出版社
WILEY-V C H VERLAG GMBH
DOI: 10.1002/chem.202000593
关键词
carbohydrates; density functional calculations; glycosylation; ligand binding; stacking interaction
资金
- project CALIPSOplus from the EU Framework Programme for Research and Innovation HORIZON 2020 [730872]
- Czech Science Foundation [18-18964S]
- project CEITEC 2020 from the Czech Ministry of Education, Youth and Sports [LQ1601]
- project INTER-COST from the Czech Ministry of Education, Youth and Sports [LTC17076]
- CIISB research infrastructure - MEYS CR [LM2018127]
- People Programme (Marie Curie Actions 7FP) [0005/01/02, 609427]
- Scientific Grant Agency of the Ministry of Education of the Slovak Republic
- Slovak Academy of Sciences [0005/01/02, VEGA-02/0024/16, 02/0058/16]
- CESNET under the programme Projects of Large Research, Development, and Innovations Infrastructures [LM2015042]
- CERIT Scientific Cloud under the programme Projects of Large Research, Development, and Innovations Infrastructures [LM2015085]
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-pi 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-pi 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-pi stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol(-1). All the results show that the stacking CH-pi interactions in protein-carbohydrate complexes can be considered to be a driving force of the binding in such complexes.
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