Calculating the net charge
The net charge Z of a peptide at a certain pH can be estimated by calculating
where Ni are the number, and pKai
the pKa values, of the N-terminus and the side chains of Arginine, Lysine,
and Histidine. The j-index pertain to the C-terminus and the Aspartic
Acid, Glutamic Acid, Cysteine, Tyrosine amino acids.
Innovagen's Peptide Property Calculator calculates the net charge for all pH values of 0.1 to 14 in increments of 0.1, and plots these producing a titration curve.
This algorithm has its limitations, some of which are:
- The residues are assumed to be independent of each other.
- Only free terminii and the 20 naturally occuring amino acids and their D-forms are considered, all others are ignored.
- The resulting net charge depends on what pKa values the algorithm uses. Innovagen's Peptide Property Calculator uses the values taken from the CRC Handbook of Chemistry and Physics, 87th edition.