I have the peptide his-trp-pro-met-arg, which I've drawn accurately and everything. I calculated its pI to be 11 from its pKas (the approximate values we use anyway) which are 5, 6, 9.5, and 12.5.

I need to calculate the pH when the peptide has net charges of +2.52 and -0.21.

I have the Henderson-Hasselbach equation: pH = pKa + log ([conj base]/[conj acid]), but I'm not sure how to apply it in this case (I know how to do these calculations for a titration of acid by base just fine).

For the charge of +2.52, both (.52/.48) and (.48/.52) give me reasonable answers (5.03 and 4.97, respectively). From drawing the peptide, at a pH of 5.03, I would find that the net charge is +2 and at 4.97, it would be +3. That isn't very useful, but I'm not sure how else to check my answer.

For the charge of -0.21, I find these two, both of which give a net charge of 0 when I check.

pH = 9.5 + log (.79/.21) = 10.08

pH = 12.5 + log (.21/.79) = 11.92