Question

To the nearest hundredth of a unit, what is the net charge of the peptide AIGNECK at pH 4.3? 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

Ans. Calculation of EXACT Charge on peptide:

Note: Only the N-ter, C-ter, acidic (E) and basic residues (K) are used for calculating charge. Ignore rest of the values.

Method 1: Use Henderson-Hasselbalch equation

Net Charge (exact value) at pH 4.7 = + 0.393

#I. The residues with acidic side chain and C-terminal are written in RED/BOLD. Their corresponding charge is written in columns of “Acidic residues”. Ignore all other charge/values in “black ink”. The sum of charge in “RED ink” is the total –ve charge on the peptide at specified pH.

#II. The residues with basic side chain and N-terminal are written in Blue/BOLD. Their corresponding charge is written in columns of “Basic residues”. Ignore all other charge/values in “black ink”. The sum of charge in “Blue ink” is the total +ve charge on the peptide at specified pH.

#III. The charge on each residue/ group is calculated using Henderson-Hasselbalch equation as shown in respective column. That is, the charge on acidic residue is calculated using pH = pKa + log ([A^-] [AH]).

The charge on basic residues in calculated using HH equation for base pOH = pKb + log ([BH⁺] / [B]); Where   B = Base , BH⁺ = Conjugate acid