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In a solution of a given pH, a protein will have a negative or positive net charge dependent on the pKa values of the acidic and basic groups of the constituent amino acids. The isoelectric point, or pI, is the pH at which a protein has zero net charge. When the pH is higher than the isoelectric point, the protein has negative net charge, and when lower, positive net charge.
You can calculate the net charge of your protein easily at a given pH or over a range:
Calculating Net Charge Using Protein Calculator
- First, get the one-letter amino acid sequence of your protein of interest.
- See the Isoelectric point page for some methods.
- Or for a protein that has a 3D structure in Proteopedia, find the page for your structure named for PDB file code and click on OCA under the structure.
- At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).
- Click on the link for the one-letter amino acid sequence for one chain.
- Copy the sequence and paste it into the large box at Christopher Putnam's Protein Calculator.
- Check the first box under Charge at the right, and click Submit Query.
The calculation method was adapted from a class syllabus taught by Eric Martz.