Isoelectric point: Difference between revisions
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The isoelectric point, or pI, is the pH at which a protein has zero [[Net charge|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 | The isoelectric point, or pI, is the pH at which a protein has zero [[Net charge|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. | ||
== | |||
==Getting the one-letter sequence of your protein== | |||
*First, get the one-letter amino acid sequence of your protein of interest. | *First, get the one-letter amino acid sequence of your protein of interest. | ||
** | **Go to [https://uniprot.org UniProt.Org], find your protein, click on Sequence, then on Download to get the one-letter sequence in FASTA format. Copy {{font color|red|only the sequence, excluding the header line that begins ">".}} | ||
**Another way to do this for a protein that has a solved structure: get to the page for the PDB ID at [http://www.pdb.org 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 [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain 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. | **Alternatively for a protein with a solved structure, go to the [http://www.ebi.ac.uk/msd-srv/oca/oca-bin/ocamain 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: | **For going from a nucleotide sequence, a number of tools are available for 'virtual' translation: | ||
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***[http://molbiol-tools.ca/Translation.htm Another online site] lists several tools that may be useful depending on the state of the nucleotide sequence you have available. | ***[http://molbiol-tools.ca/Translation.htm Another online site] lists several tools that may be useful depending on the state of the nucleotide sequence you have available. | ||
==Protein Calculator== | |||
= | |||
#First, get the one-letter amino acid sequence of your protein of interest. | #First, get the one-letter amino acid sequence of your protein of interest. | ||
##See above for some methods. | ##See above for some methods. | ||
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#Copy the sequence and paste it into the large box at Christopher Putnam's [http://protcalc.sourceforge.net/ Protein Calculator]. | #Copy the sequence and paste it into the large box at Christopher Putnam's [http://protcalc.sourceforge.net/ Protein Calculator]. | ||
#Check the first box under Charge at the right, and click Submit Query. | #Check the first box under Charge at the right, and click Submit Query. | ||
==Prot-pi== | |||
"Prot pi | Protein Tool calculates isoelectric point and net charge of proteins, as well as the exact mass and the absorption coefficient using the amino acid sequence." | |||
*Go to [https://www.protpi.ch/Calculator/ProteinTool Prot-pi]] and follow instructions. | |||
==EMBL WWW Gateway to Isoelectric Point Service== | |||
<font color='red'>The EMBL Gateway to pI appears to be out of service in May, 2013. Use the alternative below.</font> | |||
*Go to the [http://www.embl-heidelberg.de/cgi/pi-wrapper.pl 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! | |||
==See Also== | ==See Also== | ||