Binding site affinity?
I am confused, because my professor said that if the concentration of a single ligand is high, there will likely be increased affinity of the binding site. Im having trouble understanding how this would affect affinity. I kind of thought that if there's a high concentration of a ligand, it would actually be lower affinity like how it is with sodium potassium pumps where the transporter has a higher affinity for sodium when its on the site of the pump with less sodium and a higher affinity for potassium when its on the site of the pump with less potassium. Does anyone understand?
- hcbiochemLv 74 weeks agoFavorite Answer
If a protein has a single binding site for a particular ligand, the concentration of the ligand has no effect on the affinity of that site for the ligand. The affinity of a binding site for a ligand is essentially a property of the binding site and its conformation, and is not determined by or affected by the presence of the ligand.
If the concentration of a ligand is very low, regardless of the affinity of the site, relatively few binding sites will be occupied by the ligand. As the concentration of the ligand is increased, more and more binding sites will be occupied by the ligand, until eventually at some high concentration of ligand, all of the binding sites are occupied.
In the case of the Na/K pump, the binding of Na+ to the protein drastically changes the conformation of the protein. That change in conformation causes a large change in the shape of the active site and this decreases the affinity of the binding site for Na+ and increases the sites affinity for K+. Binding of K+ induces a different conformation change which reduces the binding site's affinity for K+ and again increases its affinity for Na+. It is the conformation change in the protein induced by binding the ligand that causes a change in the affinity.
Now, in something like hemoglobin, the four polypeptide chains of the protein exhibit "cooperativity" because of their interactions with each other. When oxygen is bound by one low affinity site, the binding again induces a conformational change in the hemoglobin protein. This conformational change results in an increased affinity of the remaining oxygen binding sites. This kind of affect only occurs in proteins that have multiple subunits with binding sites for the ligand in each subunit.
Does this help some?