CH-π interactions confer orientational flexibility in protein-carbohydrate binding sites

Area of Science:

• Biochemistry
• Structural Biology
• Computational Biology

Background:

• Protein-carbohydrate binding is crucial for cellular functions like recognition and immune signaling.
• Hydrophilic glycans present challenges for selective protein recognition due to limited hydrophobic surfaces.
• CH-π stacking interactions are prevalent in protein-carbohydrate binding sites and are key drivers of recognition.

Purpose of the Study:

• To investigate how the protein environment influences the orientations of CH-π stacking interactions.
• To clarify the functional interplay between CH-π stacking interactions and hydrogen bonds in protein-carbohydrate binding.
• To understand how these interactions affect glycan ligand recognition and dynamics.

Main Methods:

• Utilized well-tempered metadynamics simulations.
• Obtained binding free energy landscapes for protein-β-D-galactoside complexes.
• Analyzed the influence of hydrogen bond networks on CH-π stacking orientations.

Main Results:

• Favored CH-π stacking orientation is dictated by hydrogen bond locations within the protein binding site.
• Extended carbohydrate ligands with more hydrogen bonds exhibit specific orientational dependencies.
• Proteins with fewer hydrogen bonds show broader free energy landscapes, allowing multiple CH-π stacking orientations.
• Multiple CH-π stacking interactions facilitate oligosaccharide ligand translocation in processive enzymes.

Conclusions:

• Hydrogen bonds and CH-π stacking interactions work cooperatively in protein-carbohydrate binding.
• Modulating these interactions via evolution or protein engineering can alter ligand recognition.
• Tuning these interactions can also influence ligand movement within enzymes.