CH−π interactions confer orientational flexibility in protein–carbohydrate binding sites
Name
PIIS002192582502229X.pdf
Description
Published version
Size
2.35 MB
Format
Adobe PDF
Checksum (MD5)
25c6583143d2a91676f76fc33e9a06d0
Author(s)
Keys, Allison M
Kastner, David W
Kiessling, Laura L
Kulik, Heather J
Date Issued
August 2025
Journal
Journal of Biological Chemistry
Publisher
Elsevier BV
Citation
CH−π interactions confer orientational flexibility in protein–carbohydrate binding sites Keys, Allison M. et al. Journal of Biological Chemistry, Volume 301, Issue 8, 110379
Version
Final published version
Abstract
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-π stacking interactions are pervasive in protein-carbohydrate binding sites and have emerged as critical drivers of protein-carbohydrate recognition. These interactions are highly favorable and have a broad orientational landscape. However, it is unknown how the orientations of CH-π stacking interactions are influenced by the protein environment; their functional interplay with hydrogen bonds in protein-carbohydrate binding is also unclear. Here, we employ well-tempered metadynamics simulations to obtain binding free energy landscapes for a set of protein-β-D-galactoside complexes with CH-π stacking interactions. Our data show that the favored orientation of a CH-π 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 dependencies, while protein variant complexes with fewer hydrogen bonds have broader free energy landscapes with glycan ligands adopting multiple CH-π stacking interaction orientations. We also show that forming multiple CH-π 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-π 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.
MIT Department
Massachusetts Institute of Technology. Department of Chemical Engineering
Massachusetts Institute of Technology. Computational and Systems Biology Program
Massachusetts Institute of Technology. Department of Chemistry
Massachusetts Institute of Technology. Department of Biological Engineering
Broad Institute of MIT and Harvard
Koch Institute for Integrative Cancer Research at MIT
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1016/j.jbc.2025.110379
