CH-pi Interactions Confer Orientational Flexibility in Protein-Carbohydrate Binding Sites

Protein-carbohydrate binding plays an essential role in biological processes including cellular recognition and immune signaling. However, glycans are hydrophilic with limited hydrophobic surfaces, a challenge for selective recognition by proteins. CH–pi stacking interactions are pervasive in protein-carbohydrate binding sites and have emerged as critical drivers of protein–carbohydrate recognition. They are highly favorable and have a broad orientational landscape. However, it is unknown how CH-pi stacking interaction orientational dynamics are influenced by the protein environment and what their functional interplay is with hydrogen bonds in protein–carbohydrate binding. Here, we employ well-tempered metadynamics simulations to obtain binding free energy landscapes for a set of protein-b-D-galactoside complexes with CH–pi stacking interactions. Our data show that the favored orientation of a CH-pi stacking interaction is controlled by the location of hydrogen bonds in the protein binding site. Complexes with extended carbohydrate ligands that form additional hydrogen bonds have more specific orientational dependences, while protein variant complexes with fewer hydrogen bonds have broader free energy landscapes with glycan ligands adopting multiple CH-pi stacking interaction orientations. We also show that forming multiple CH-pi stacking interactions facilitates the dynamics necessary for the translocation of oligosaccharide ligands within a processive enzyme. Our findings underscore the cooperative nature of hydrogen bonds and CH-pi stacking interactions, demonstrating that tuning the number and positions of these interactions through evolution or protein engineering can alter ligand recognition or support ligand movement in protein binding sites.