Design of a software for calculating isoelectric point of a polypeptide according to their net charge using the graphical programming language LabVIEW

Abstract

A software to calculate the net charge and to predict the isoelectric point (pI) of a polypeptide is developed in this work using the graphical programming language LabVIEW. Through this instrument the net charges of the ionizable residues of the polypeptide chains of the proteins are calculated at different pH values, tabulated, pI is predicted and an Excel (-xls) type file is generated. In this work, the experimental values of the pIs (pI) of different proteins are compared with the values of the pIs (pI) calculated graphically, achieving a correlation coefficient (R) of 0.934746 which represents a good reliability for a p < 0.01. In this way the generated program can constitute an instrument applicable in the laboratory, facilitating the calculation to graduate students and junior researchers.

Accurate Estimation of pKb Values for Amino Groups from Surface Electrostatic Potential (VS,min) Calculations: The Isoelectric Points of Amino Acids as a Case Study

“…The same principle holds true for a peptide. As a descriptor in proteomics, it has become an important part of protein characterization and study. , Isoelectric points for peptides can be determined indirectly from physicochemical measurements, such as the ζ-potential, or group contribution-based algorithms. − …”

An idea to explore: Visualization of ionization of amino acids using Mathematica

“…Therefore, the discussion of percentage of ionization (protonation or deprotonation) of an acidic or basic functional group is found in many articles. [3][4][5][6] However, the discussion often obscures the fact that AA ionization is a cooperative phenomenon (ionization of one group influences the ionization of another) and that experimental pK a values available in the literature do not in fact correspond to any particular acidic/basic functional group as Darvey had pointed out. 3,4 Ionic interactions between acidic and basic functional groups can occur between different molecules or within the same molecule.…”

“…Mathematica software has been used previously to present pedagogically accessible models of metabolic cycles. 6 The novelty of our approach is in using probabilistic concept to describe AA ionization 7 and using exact general formulas which correlate concentrations of ionic species with pH of solution. 8,9 We did not rely on approximation which considers ionizations of functional groups to take place independently.…”

“…Weakly acidic or basic functional groups are ubiquitous in biomolecules, especially in AA and related peptides and proteins. Therefore, the discussion of percentage of ionization (protonation or deprotonation) of an acidic or basic functional group is found in many articles 3–6 . However, the discussion often obscures the fact that AA ionization is a cooperative phenomenon (ionization of one group influences the ionization of another) and that experimental p K a values available in the literature do not in fact correspond to any particular acidic/basic functional group as Darvey had pointed out 3,4 …”