Question

1. What sorts of residues (i.e. what amino acid side chains) would one expect to find on the surface of a protein with an unusually high isoelectric point (e.g. 9.5). What if the pI were unusually low (e.g. 3.4)?

2. When one talks about “protein-ligand” interactions, what sorts of molecules can be “ligands?”

3. How would you explain the conformational selection model of protein-ligand interactions to an educated lay person?

Answer 1

1) Isoelectric point is average of pKa1,pKa2 and pKa3(if there is basic or acidic side chain on amino acid). Isoelectric point will be higher when side chain is basic in nature because bacis side chain adds extra positive charge so it will neutralize under more basic pH so isoelectric point( pH at neutralization ) will be higher

2)In protein -ligend interactions ligend is a molecule which produces a signal by binding to a site on target protein. Some ligends are protein other ligends are some hydrophobic molecules like steroids and some ligends are gases like nitric oxide ,oxygen etc.

3) ligends interact with protein in same way as key interacts with lock. So only a selected key can fit in the lock and open it in the same way there are many receptors on surface of proteins these receptors form a complementary shape for the shape of ligends binding site .not all receptors can fit a perticulaf ligend so protein have different binding sites in different conformations for different ligends that's why for a successful interactions of ligends onprotein both must be in favourable conformations.because different conformations create different environment which either repel or attract ligends differently by structure hibderence and many other ways.