Isoelectric point

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 charge, and when lower, positive charge. You can calculate the isoelectric point of your protein easily using on-line resources:

• First, get the one-letter amino acid sequence of your protein. To do this for a solved structure, get to the page for the PDB ID at the RCSB Protein Data Bank. There in the upper right under 'Dsiplay files', click the 'FASTA Sequence' link and download all chains in FASTA format. Open the text file and block the sequence of the chain of interest (excluding the comment line beginning >) and copy it to the clipboard. Alternatively go to the OCA browser-database and enter your PDB code in search. or use the link to the OCA on the Proteopedia page of each solved structure. And then at the OCA scroll down to Sequence-derived information (near the bottom), click on the link for the one-letter amino acid sequence for one chain and copy the sequence of the chain to the clipboard.

• Second, go to the EMBL WWW Gateway to Isoelectric Point Service, paste your sequence in the box, and press the button.

• Warning: the sequence you paste in must be in UPPER CASE one letter code. If you paste in a lower case sequence, you'll get pI = 6.014999, which is for the backbone only, because it doesn't recognize lower case amino acids!

Alternative to calculate Isolelectic point using Protein CalculatorAlternative to calculate Isolelectic point using Protein Calculator

• 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 the Protein Calculator.
• Check the first box under Charge at the right, and click Submit Query.

Content AttributionContent Attribution

The first method was adapted from the Glossary that accompanies Eric Martz's Protein Explorer. The second was adapted from a class sylabus taught by Eric Martz.