You are examining the binding of a short peptide antigen to the antigen-binding

Question

You are examining the binding of a short peptide antigen to the antigen-binding site of an antibody.

The amino acid sequence of the peptide is: Ala-Cys-Phe-Gly-Leu-Val-Pro-His-Gln

The binding site on the antibody is composed of a largely-hydrophobic surface but with the side chains of a lysine residue and an aspartic acid residue oriented towards the cysteine and histidine residues of the peptide antigen respectively.

A) Calculate the average charge on the peptide at pH 7.4 Show your working.

B) Will increasing the pH of the solution containing antigen and antibody from 7.4 to 11 make it easier or harder to dissociate the antigen from the antibody? Explain your answer.

Explanation / Answer

Answer A) The amino acid sequence of the peptide can be written as

NH3+-Ala-Cys-Phe-Gly-Leu-Val-Pro-His-Gln-COO-

While solving such questions, remember that only 7 amino acids have an ionizable group that contributes to the charge on the peptide. These are tyrosine, cysteine, arginine, lysine, histidine, aspartic acid, and glutamic acid. Only the alpha-amino group on the amino-terminus and alpha-carboxyl group on the carboxy-terminus are the ionizable groups in the peptide. The other alpha-amino and alpha-carboxyl groups are used to form polypeptide bonds.

Ionizable groups and their respective pKa values
Amino-terminus (NH3+) - 9.7
Cysteine (Cys) - 8.4
Histidine (His) - 6.0
Carboxy-terminus - 2.0

At pH 7.4, the groups whose pKa values are less than 7.4 are mostly deprotonated, and the groups with pKa values greater than 7.4 are mostly protonated. Therefore, the average charge on the peptide is +1.
Ionizable group and their respective charge
Group Charge

Amino-terminus +1
Cysteine +1
Histidine 0
Carboxy-terminus -1
Net charge: (+1 +1 + 0 -1) = +1

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