6t9b

Publication Abstract from PubMed

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 (ITC, X-ray crystallography) and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. 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 kcal/mol up to 8 kcal/mol. 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.

The CH-pi interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification.,Houser J, Kozmon S, Mishra D, Hammerova Z, Wimmerova M, Koca J Chemistry. 2020 Mar 24. doi: 10.1002/chem.202000593. PMID:32208534^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.