JaMBW Chapter 3.1.6
Given a sequence of aminoacids, this program computes and plots the
average net charge of the entire peptide, as function of the pH.
Mode of operation
The program uses 3 windows: the top one should be filled from the user, with the sequence of interest,
the small window beneath is used by the program to return messages to
the user, while the bottom one visualizes the results of the analysis. The following steps must
be performed to use this program:
- Sequence input
- Symbols used
Either paste or type in the top area the sequence of interest, using the one letter notation. Any
character or symbol that does not belong to the IUPAC-IUB set is
- removal of header information
Only the sequence must be placed in the top window:
heading comments must be removed
- long sequences and small window
In order to allow users with small screens to still be able of use this
program, the size of each window had been made rather small. Therefore,
use the scroll-bars in order to move around in the input and output windows.
The suggested strategy is to double click in the specified area and then
do copy/paste from/to the text-editor of choice or across different
Once the sequence is placed in the top window, by pressing the "COMPUTE"
button the Net Charge of the entire protein is computed as function
of the pH, at 0.5 unit interval and then visualized. The Isoelectric point
is searched by computing the Net Charge at very fine grade. Its value,
that is the pH at which the Net Charge of the entire polypeptide is zero,
is displayed with red cross-bars and numerically is returned in the
text window above the chart.
How to understand its output
- The pI
The textual information that is returned in the middle window indicates
the value of pH at which the Net Charge of the polypeptide would be neutralized,
if the polypeptide would have a conformation with each aminoacid fully exposed
to the solvent. That is the usual definition of "Isoelectric Point".
- The chart
The chart displays the evolution of the Net Charge of the protein as function of the pH. One would
generally notice that at lower pH the polypeptide is more highly charged, and vice-versa. The
red lines are used to identify the pH at which all the charges are neutralized. The horizontal
red line is used to mark the charge neutrality level.
- IUPAC-IUB Joint Commission on Biochemical Nomenclature (1984)Nomenclature and symbolism for Amino Acids and Peptides, Eur.J.Biochem., 138, 9-37
- Lehninger A., (1972) Biochimie Ed: Flammarion
- http://www-biol.univ-mrs.fr/d_abim/d_docs/doc-tab-pk.htmlTables of pK values.
Author:Luca I.G. TOLDO,
Edition date: 28 February 1997