The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

Abstract

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.

Visualization of hydrogen atoms in a perdeuterated lectin-fucose complex reveals key details of protein-carbohydrate interactions

“…The fucose methine and methyl groups at C3-C5 and C6, respectively, are involved in the CD/p interactions with the tryptophan side chains. The average distances between the deuterium atom and the ring centroid of the relevant tryptophan residue are in the range 2.62-3.49 Å , which is in agreement with the recently published analysis of CH-p interactions based on the 3D structures of protein-carbohydrate complexes deposited in the PDB (Houser et al, 2017(Houser et al, , 2020. Experimentally determined structures of CH-p dispersion interactions are necessary for a better understanding of the nature and physics behind the dispersion forces involved in the protein-carbohydrate interactions.…”

“…Protein-carbohydrate interactions are involved in many important physiological and pathological processes, including cell (Asensio et al, 2013;Houser et al, 2020). The molecular mechanisms behind these interactions are predominantly studied at the atomic level by X-ray crystallography, which can locate individual hydrogens only at subatomic resolution (Takaba et al, 2019).…”

Transcriptomic and Drug Discovery Analyses Reveal Natural Compounds Targeting the KDM4 Subfamily as Promising Adjuvant Treatments in Cancer

“…In addition to the contribution of coordination bonds that favor specificity, there are other non-covalent binding forces that can also have an impact on specificity and binding affinity such as salt bridges, hydrophobic interactions, hydrogen bonds, and pi-stacking interactions. In particular, pi-stacking interactions among aromatic rings are an important factor in the protein-ligand complex formation; in such interactions, the geometric orientation of the rings change the dipole attraction forces among them as well as the hydrophobic and van der Waals forces rearrange ( Churchill and Wetmore, 2009 ; Wilson et al, 2014 ; Houser et al, 2020 ). The presence of five aromatic residues and one histidine in KDM4 active sites promotes a favorable environment to design specific inhibitors ( Churchill and Wetmore, 2009 ; Brylinski, 2018 ).…”

Prebiotic Peptides Based on the Glycocodon Theory Analyzed with FRET

“…In monosaccharide binding sites, tryptophan (W) >> tyrosine (Y) > histidine (H) are greatly preferred, asparagine (N) > aspartic acid (D) >> glutamine (Q) are slightly preferred, and aliphatic residues are disfavored [ 17 ]. The CH–π stacking contribution to the overall binding energy ranges from −4 kcal/mol to −8 kcal/mol; currently, stacking CH–π interactions are considered driving forces of protein–carbohydrate complexation [ 18 ]. However, the calculated energies in the systems without CH–π interactions are in the range from −0.2 to −3.2 kcal/mol; hence, they can also be important for aromatic amino acid and carbohydrate binding processes [ 19 ].…”