Discussion:
Ionization State and Cooperative Ligand Binding
1. The active site of lysozyme contains two amino acid residues essential for catalysis: Glu35 and Asp52. The pka values of the carboxyl side chains of these low residues are 5.9 and 4.5 respectively.
a) What is the ionization state (protonated or deprotonated) of each residue at pH5.2? What is the pH optimum of lysozyme?
b) How can the ionization states of these residues explain the pH-activity profile of lysozyme?
2. which set of binding data is likely to represent cooperative ligand binding in an oligomeric protein? Explain.
A.[ligand] Y(fractional saturation) B.[ligand] Y(fractional saturation)
(mM) mM
0.1 0.3 0.2 0.1
0.2 0.5 OR 0.3 0.3
0.4 0.7 0.4 0.6
0.7 0.9 0.6 0.8