Isoelectric point

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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:


Calculating Isolelectric Point Using EMBL WWW Gateway to Isoelectric Point Service

The EMBL Gateway to pI appears to be out of service in May, 2013. Use the alternative below.

  • First, get the one-letter amino acid sequence of your protein of interest.
    • An easy way to do this for a protein that has 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 for a protein with a solved structure, 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.
    • For going from a nucleotide sequence, a number of tools are available for 'virtual' translation:
      • At the ExPASy - Translate tool choose 'Compact' for the output format below the box where you paste in your sequence.
      • Another online site lists several tools that may be useful depending on the state of the nucleotide sequence you have available.
  • 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!

Alternatively, Calculating Isolelectric Point Using Protein Calculator

  1. First, get the one-letter amino acid sequence of your protein of interest.
    1. See above for some methods.
    2. Or for a protein structure published in the PDB, find the page in Proteopedia titled with the PDB code and click on OCA in the Resources section under the structure.
      1. At your PDB code in OCA, scroll down to Sequence-derived information (near the bottom).
      2. Click on the link for the one-letter amino acid sequence for one chain.
  2. Copy the sequence and paste it into the large box at Christopher Putnam's Protein Calculator.
  3. Check the first box under Charge at the right, and click Submit Query.

See Also

Content Attribution

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

Proteopedia Page Contributors and Editors (what is this?)

Wayne Decatur, Eric Martz

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