Net Charge of Peptide Bond

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doshia9
Posts: 3
Joined: Tue Jan 14, 2020 11:07 am

Net Charge of Peptide Bond

Post by doshia9 » Tue Jan 14, 2020 11:15 am

When given the primary structure of a peptide bond, how do you find the net charge at a certain pH? I know that N-terminus, His, Lys, Arg are positively charged and C-terminus, Asp, and Glu are negatively charged. Are there any amino acids that we have to consider upon calculating that I'm missing?

Can you provide an example of the net charge above and below physiological pH? Thank you!
NS_Tutor_Mathias
Posts: 480
Joined: Sat Mar 30, 2019 8:39 pm

Re: Net Charge of Peptide Bond

Post by NS_Tutor_Mathias » Tue Jan 14, 2020 5:51 pm

At physiological pH your approach largely works, although Histidine will be overwhelmingly neutral.

For non-physiological pH, you are best served comparing the pKa of every relevant functional group (terminal amine, terminal carboxyl, all R-groups) with that of the environment.

For acidic residues, if pKa < pH, then the group will carry a negative charge.
For basic residues, if pKa < pH, then the group will carry a positive charge.
Apply this logic to the N and C termini too

(This slightly confusing change is because we give the pKa of the conjugate acid for all the basic residues - which is why the pKa of Histidine is given as ~6).

So, I have a peptide consisting of MHILPTTV at a pH of ~7.4, it would simply have a charge of ~0. At a pH of 5, I would expect a charge of +1 - now histidine is protonated, but the C terminus is still deprotonated. At a pH of 1, I would expect a charge of +2 - now the C terminus and histidine are both protonated (so +0 +1 +1).

Knowing all that, for an exercise tell me what the charge on DKKH would be at a pH of 14. Use this for reference: http://www.chem.ucalgary.ca/courses/351 ... 1-4-2.html
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