Biomedical Chemistry: Research and Methods, 2018, 1(2), e00009

pIPredict Version 2: New Features and PTM Analysis

V.S. Skvortsov*, N.N. Alekseychuk, Yu.V. Miroshnichenko, A.V. Rybina

Institute of Biomedical Chemistry, 8119121 Pogodinskaya Str., 10 bldg. 8, Moscow, Russia,*e-mail: vladlen@ibmh.msk.su

Key words: protein; peptide; isoelectric point; posttranslational modifications; property prediction

DOI: 10.18097/BMCRM00009

The whole version of this paper is available in Russian.

pIPredict was created as a tool for prediction of the isoelectric point of peptides and proteins. It can also generate virtual 2D electrophoresis maps. The method of pI prediction is based on the Henderson-Hasselbach equation. In a new version the ProMoST and our new scales of pKa values were added. The other added features included: correction of electrophoretic shift by analyzing amino acid composition of proteins and prediction of pI values for proteins with a new set of posttranslational and other chemical modifications. Prediction of pI for proteins with PTM can be used to predict position of modified proteoforms on the virtual 2D electrophoresis map or as the tool of identifying which particular proteoform was observed in the experiment.The program also includes several widely used pKa scales, that can partially calculate values for proteins with some post-translational modifications. pIPredict is created as JAVA application and is freely available at http://www.ibmc.msk.ru/LPCIT/pIPredict.

Figure 1. Example of the pIPredict 2 GUI. 277 proteins encoded by human chromosome XVIII were loaded. In the upper left frame - the sequence of the selected protein from the list of proteins (the lower left frame). In the right frame the virtual 2D map is shown.

Figure 2. Comparison of the experimental and predicted pI values for the set of 7390 peptides [5]. This set was obtained during analysis of peptides after isoelectric focusing and the experimental values were determined with accuracy ± 0.15 pH units, (or the "step" of 0.3 pH units). On the left side are shown values predicted by the widely used "Compute pI / Mw" service (https://web.expasy.org/compute_pi/). On the right side, the predictions by the new pIPredict 2 scale are shown.

Figure 3. Distribution of pI differences of predicted pI without and with elimination of N-terminal methionine (277 proteins encoded by human chromosome XVIII). The pKa’s scales ProMoST and pIPredict 2 were used. The group with insignificant changes (from 0 to 0.05) was removed.

Figure 4. An example of comparison of predicted pI values for the virtual proteoforms (probable PTMs include phosphorylation of threonine or serine residues and deamination of glutamine or asparagine residues, and their combination) with the experimentally observed proteoforms obtained by analysis of the Bos Taurus kidney tissues [9]. For these proteins several variants of the position (red points) were found. The y-axis is the shifts of proteoforms pI values (the most basic value is set as zero). The hypothesis about nature of detected variants can be made for the proteins: O02691, O77834, P10096, P14568, P41976, Q28035, Q95KZ6.

ACKNOWLEDGEMENTS

This work was performed within the framework of the Program for Basic Research of State Academies of Sciences for 2013-2020.

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