Isoelectric Point

This app is a part of Bio- Chemistry and Chemical Engineering Lab Pack including several apps dealing with chemical solutions, reaction equilibrium and kinetics, acid base neutralisation reaction, titration, and liposome and monolayer preparation.

This application calculates a relative charge of macromolecule (proteins, peptides etc.), consisting of basic and acidic residues as a function of pH value of solution. The application graphically represents the relative charge (actual charge divided by the molar concentration of macromolecule) through the whole range of pH values and finds out the isoelectric point value.

Layout of "IEP". The “Chain” menu lets to choose the various chains from the uploaded FASTA file for further analysis. The sequence of polymer molecule is inserted into the “Sequence” field in the single letter format (YHRK…). The sequence can be typed or uploaded from the local FASTA file (for polypeptides). Long press on “Sequence” field calls for file finder dialog that let the user to upload the FASTA file from local SD. The next “Analyse” button, when clicked, analyses the sequence, calculates the total molar weight and counts and fills the number of recognized acidic and basic residues into the appropriate cells in the amino acid info table. Cells for acidic residues are coloured red and for basic are blue. The table comprised of nine sets of three cells per each amino acid. The three cells provide the charge contributing amino acid acronym, pKa value and number of this particular residue in the macromolecule, respectively. The “-C” and “-N” cells represent C- and N-terminus respectively. The “Calculate” button initiates the analysis of the table data (including customized input) and outputs the IEP value. Important! Table data can be fully customized after or without any sequence analysis! IEP calculation uses table values, whatever their origin.

Application features.

• The application can extract the protein sequence (chain by chain) from FASTA files.

• Estimates the isoelectric point of macromolecule based on pKa values provided.

• Application plots relative charge curve as function of pH and export it as an image or a data file to the “Isoelectric point” directory on local SD drive.

• Application provides data for most common acidic and basic amino acid residues, but every cell can be updated! Sequence analysis reverts the table back to its original state.

The preparation of the desired solutions may be facilitated by using Chemical Solution Wizard app and deprotonation kinetics may be followed by using Chemical Kinetics app. On the other hand, pH values of simple acids, bases and their titrations through neutralization reactions can be calculated and plotted by means of Acid Base pH app.