Question

A. You are performing experiments with your protein of interest and its ligand. You are attempting to mutate the binding site of your protein to disrupt binding to ligand to see what happens inside the cell. You make a series of mutations and one in particular gives you surprising results: you observe that the mutation that you made in an amino acid that sticks out into the binding pocket actually increases the protein’s affinity for the ligand. Give a molecular explanation for these results.

Answer 1

The binding between a receptor (protein) and a ligand is an intricate process and it essentially relies on the extent of molecular interactions between a receptor and its ligand. In the given case, mutation causes an increase in the affinity of ligand towards receptor. A possible reason for this could be that mutation altered the amino acid such that the new amino acid could now form hydrogen bond or electrostatic interaction with ligand. Moreover, another possibility could be that the new amino acid altered the pKa of the adjacent amino acids such that their extent of interaction with ligand now increased drmatically.