Question

Examine the tripeptide below:

Lys-Glu-Asp

Calculate the isoelectric point (pI) of this tripeptide. You can assume that the pKa of the amino terminus is 9.06 and the pKa of the carboxy-terminus is 1.99.

a. 2.95

b. 3.99

c. 5.53

d. 6.48

e. 7.31

Answer 1

Question) How do we calculate the isoelectric point (PI) of peptides?

1. estimate the pH at which the net charge on the protein would be zero
2. find the average of the 2 pKa values directly above and directly below the estimate

so here the given peptide contains 3 aminoacids- (lysine-glutamate-aspartate)

so first we have to estimate the pH at which the net charge on the protein is zero. for that we have to consider the pKa values of alpha- carboxyl group (here it is 1.99), alpha-amino group (given, 9.06) as well as the pKa values of the side chains of the aminoacids. (for that refer the image)

so lets assume the pH as 7, and find out which side chains are protonated (+ve value) and deprotonated (-ve value)

protonated if pKa value is greater than pH value

deprotonated if pKa value is lesser than pH value

aminogroup of lysine (Lys)	side chain of lysine (Lys)	side chain of glutamate (Glu)	side chain of aspartate (Asp)	carboxyl group of aspartate (Asp)
pKa 9.06(given)	pKa 10.5	pKa 4.2	pKa3.9	pKa1.99 (given)
+ve	+ve	-ve	-ve	-ve

so, +1+1-1-1-1 = -1 (so the net charge on the protein is not zero)

lets assume the pH value as 4.2 . So the side chain of glutamate will be neutralised.

aminogroup of lysine (Lys)	side chain of lysine (Lys)	side chain of glutamate (Glu)	side chain of aspartate (Asp)	carboxyl group of aspartate (Asp)
pKa 9.06 (given)	pKa 10.5	pKa 4.2	pKa 3.9	pKa1.99 (given)
+ve	+ve	0	-ve	-ve

so, +1+1+0-1-1= 0 (so at pH 4.2 the net charge on the protein is zero)

next step is to calculate the average of the two pKa values directly above and directly below the estimated pH.

that is 9.06 and 3.9 which are directly above and directly below the estimated pH 4.2

so the average or the isoelectric point of the given peptide Lys-Glu-Asp is = (9.06+3.9)/2

   = 6.48

Option d (6.48) is the right answer