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 off 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. Answer A and B Calculate the average charge on the peptide at pH 7.4Show your working 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

Que 1

Ala-Cys-Phe-Gly-Leu-Val-Pro-His-Gln

6.1 -5.2 -5.9-6.0 -6.0-6.0-6.3-7.4----

At physiological pH,         Asp & Glu have                  2 -ve charges

                                                Lys, Arg & His have          3+ve charges

Therefore, overall all charges shall be

Charges =0+0+0+0+0+0+0+(3+)+0=3+ve charges

Que 2

Ab binding site is largely hydrophobic and contains

1-Lys3+-1-Asp2- oriented towards cys0 and His3+

For acidic amino acid side chain, If, pH >pKa à amino acid shall exist more as acidic form

While, for basic amino acid pH<pKa àalso cause it to be in ionic form.

Therefore, on increasing pH from 7.4 to 11, cause less polarization of His3+ (pKa=6) on antigen, and more polarization of Asp2- on Ab. However, Lys of Ab will nearly unaffected. Thus, the binding will be comparatively stronger at pH-11.

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