Isoelectric plots the charge as a function of pH for any peptide sequence.
Isoelectric calculates the isoelectric point of a protein from its amino acid composition assuming no electrostatic interactions occur that perturb ionization. Isoelectric makes a plot of the total positive and negative charges and the net charge of a protein as a function of pH. The isoelectric point (pH at which the net charge is zero) is indicated on the plot.
Here is part of the output file (if you are reading the Program Manual, you can see the plot from this session following the output file):
ISOELECTRIC of: pir1:Kihua Check: 1665 from: 1 to: 194 August 29, 1998 16:44
P1;KIHUA - adenylate kinase (EC 2.7.4.3) 1 - human
N;Alternate names: myokinase
C;Species: Homo sapiens (man)
C;Date: 23-Oct-1981 #sequence_revision 23-Oct-1981 #text_change 05-Sep-1997
C;Accession: A33508; A00679
R;Matsuura, S.; Igarashi, M.; Tanizawa, Y.; Yamada, M.; Kishi, F.; Kajii, T.;
Fujii, H.; Miwa, S.; Sakurai, M.; Nakazawa, A
Amino Acid Number of
Residues
----------------- -----------
Arginine 13
Lysine 19
Histidine 2
Tyrosine 7
Cysteine 2
Glutamic Acid 20
Aspartic Acid 9
Amino Terminus 1
Carboxyl Terminus 1
Number of Hydrogen Ions Bound
---------------------------------------------------------- Net
pH Arg Lys His Tyr Cys Glu Asp NH2 COOH Total Charge ..
1.0 13.0 19.0 2.0 7.0 2.0 20.0 9.0 1.0 1.0 74.0 34.97
1.5 13.0 19.0 2.0 7.0 2.0 20.0 9.0 1.0 1.0 73.9 34.92
///////////////////////////////////////////////////////////////////////////
12.5 6.5 0.4 0.0 0.2 0.0 0.0 0.0 0.0 0.0 7.1 -31.94
13.0 3.1 0.1 0.0 0.1 0.0 0.0 0.0 0.0 0.0 3.3 -35.70
Isoelectric Point
9.1 13.0 18.6 0.0 6.9 0.3 0.0 0.0 0.2 0.0 39.0 0.00
Isoelectric accepts a single protein sequence as input. If Isoelectric rejects your protein sequence, turn to Appendix VI to see how to change or set the type of a sequence.
PeptideSort shows the peptide fragments from a digest of an amino acid sequence. It sorts the peptides by position, putative molecular weight, and relative HPLC retention at pH 2.1, and shows the composition of each peptide. It also prints a summary of the composition of the whole protein. PeptideSort lists the isoelectric points of the peptide fragments resulting from the digest of an amino acid sequence as well as the isoelectric point of the entire protein sequence.
The isoelectric point must exist and lie between pH 1.0 and 13.0.
The isoelectric point is the pH at which the protein has no net charge. The net charge of a protein is calculated as the sum of the number of positively charged residues (protonated lysine, arginine, histidine), minus the number of negatively charged residues (deprotonated tyrosine, cysteine, glutamate, aspartate), plus the number of protonated amino termini, minus the number of deprotonated carboxyl termini. The net charge calculation does not take into account any electrostatic interactions within the protein that may perturb ionization. For each amino acid of interest, the number of protonated residues is determined by the following equation:
where N(p) = number of protonated residues, N(t) = total number of residues of a specific amino acid, [H(+)] = hydrogen ion concentration, K(N) = dissociation constant for the amino acid of interest that is equal to the following:
By default, the vertical axis of the plot (Net Charge) is scaled from -50 to +50. For some proteins, particularly large ones, the charge may be much less than -50 or much greater than +50 at pH's close to the isoelectric point. For those proteins, you can expand the vertical scale with Minimum net charge to plot and Maxmimum net charge to plot.
Isoelectric was originally written by L. L. Houston. Frank J. Manion rewrote this program to work with the Wisconsin Package(TM), and Irv Edelman revised and enhanced this version for inclusion with Version 6.0 of the Package.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.