Question

To the nearest hundredth of a unit, what is the net charge of the peptide AIGNECK at pH 4.4? Use the following set of pKa values:

Group pKa N-ter 8.0

C-ter 3.1

Asp or Glu 4.0

Lys 10.5

Arg 12.4

His 6.0

Tyr 10.5

Cys 8.4

Also, use the approximation that if the separation between the pH and pKa of a group in question is 2 units or greater, then consider the group completely protonated or unprotonated as the case might be.

Answer 1

The peptide AIGNECK has the following amino acids: alanine (A), isoleucine (I), glycine (G), asparagine (N), glutamic acid (E), cysteine (C), and lysine (K). Among these alanine, isoleucine, and glycine are nonpolar amino acids. Asparagine, glutamic acid, cysteine are polar and uncharged whereas lysine is polar and positively charged amino acid.

The Ka is the acid dissociation constant which is a quantitative measure of the strength of an acid in the solution. The more the value of pKa, the smaller is the extent of dissociation. In the given peptide, only the N-terminal, C-terminal, Glutamic acid (E), and Lysine (K) can determine the net charge on the peptide at the given pH. The charge on each residue can be calculated using the Henderson-Hasselbalch equation for acid and base.

The sum of charge on the acidic residues will contribute to the total –ve charge at the specific pH and the sum of charge on the basic residues will contribute to the total +ve charge on peptide.

([A-] + [HA]) = 1 + ([A-] / [HA])
Net (-ve) = ([A-] / [HA]) / ([A-] + [HA])
([B] + [BH+]) = 1 + ([B] / [BH+])
Net (+ve) = 1 / ([B] + [BH+])

Net charge on the peptide = (Total –ve charge residues) – (total +ve charge residues)

Net charge = 1.6674 – 1.999

= 0.33

Therefore, the net charge of the peptide AIGNECK at pH 4.4 is 0.33