This is a more theoretical or definition question that is related to the terms "hydrophobic effect", "hydrophilic interaction", and "van der Waals' forces" (and others I may have missed).
In case I would like to describe a hydrophobic ligand that is binding to a protein binding pocket that has also hydrophobic residues (such as Leucine, valine) that stabilize (or favor) the binding of the ligand. What would be the best description to use to describe the binding?
Although it seems the definition for these terms is also confusing, generally these terms have the meaning of:
- hydrophobic effect (the low solubility of hydrophobic solutes in water)
- hydrophobic interaction or force (the unusually strong attraction of hydrophobic surfaces and groups in water, it is specifically describing the repulsion of water)
- van der Waal's force (attractions/repulsions between molecules or atoms, other than attractions like ionic attractions, and covalent attractions)
I also know that hydrophobic interaction is stronger than van der Waal's force (vdW). Given the "definition" of the hydrophobic interaction, I assume using this term to describe the interaction between the ligand and protein is not very appropriate because there is no necessary repulsion of the water molecules (that is usually used for forming the protein core). Please correct me if I am wrong.
Therefore vdW seems to be the answer. However, the problem is why the interaction between hydrophobic ligand and the hydrophobic protein surface is favorable? To be more specific, or in other words, whether there will be the same/ similar stability for a hydrophilic ligand to bind?
As also mentioned in this question, there is Deybe force or induced dipole if the ligand is polar or even charged. Should I assume the "stacking" of the London dispersal effect is much greater than Deybe force, although the London dispersal effect is weak if they are alone?