Involvement of water in carbohydrate-protein binding

Area of Science:

• Carbohydrate chemistry
• Biophysical chemistry
• Structural biology

Background:

• Protein-ligand interactions are crucial in biological systems.
• Ordered water molecules play a significant role in mediating these interactions.
• Understanding the thermodynamic basis of binding is key to drug design.

Purpose of the Study:

• To investigate the impact of displacing ordered water molecules on protein-ligand complexation thermodynamics.
• To compare the binding of trimannoside 1 and its derivative, trimannoside 2, to Con A.
• To elucidate the role of a hydroxyethyl moiety in protein binding site interactions.

Main Methods:

• Nuclear Magnetic Resonance (NMR) spectroscopy for structural analysis.
• Molecular Dynamics (MD) simulations to model complex formation.
• Isothermal Titration Microcalorimetry (ITC) for thermodynamic measurements.

Main Results:

• Trisaccharide 2, with a hydroxyethyl group, displaces a conserved water molecule in the Con A binding site.
• MD simulations revealed similar solution conformational properties for both ligands.
• ITC showed a more favorable entropy of binding for trimannoside 2, but a less favorable enthalpy.
• The hydroxyethyl side chain of 2 can form hydrogen bonds similar to those formed by the displaced water molecule.

Conclusions:

• Displacement of ordered water by a hydroxyethyl group in trimannoside 2 leads to altered binding thermodynamics.
• The favorable entropy gain from water displacement is offset by unfavorable enthalpy changes.
• Indirect interactions via water molecules may enhance protein-ligand complex stability through increased hydrogen bond occupancy.