Hi, I use photoactivatable compounds to study protein-ligand interactions. The compound (probe) is in excess and prior to a photoactivation stage, should noncovalently with the protein-ligand complex. I was wondering if anyone had any recommendations as to the best way to study the interaction of these compounds with the surface of a protein?
I have been thinking about solvating the protein with a mixture of water and this photoactivatable compound. However, I didn’t know
A) what metric I would use to gauge an ‘interaction’ of a probe with the protein (perhaps SASA?)
B) if the getting trapped in a free-energy minima would limit the usefulness of this approach
Any help/advice would be really appreciated.