[Structural-functional diversity of p53 proteoforms]

Bioinformatic identification of proteins with altered PTM levels in a mouse line established to study the mechanisms of the development of fibromuscular dysplasia

Data from a mass spectrometry experiment of a mouse line developed to study the mechanisms of fibromuscular dysplasia and deposited by d'Escamard et al. in ProteomeXchange (PXD051750) have been analyzed. Identification of peptides with post-translational modifications (PTMs) was repeated using more stringent conditions than in the original work. The following modifications were considered during analysis of changes in the PTM levels in experimental and control groups of mice: acetylation of lysine residue and N-terminal protein peptide, ubiquitination of lysine residue, phosphorylation of serine, threonine and tyrosine residues, and deamination of asparagine and glutamine residues. The multistage analysis resulted in selection of 23 proteins with PTMs for which different levels of modification between experimental and control groups could be assumed. These included six proteins with N-terminal protein acetylation, which were particularly interesting: P80318 (T-complex protein 1 subunit gamma), P43274 (Histone H1.4), P97823 (Acyl-protein thioesterase 1), P63242 (Eukaryotic translation initiation factor 5A-1), Q3UMT1 (Protein phosphatase 1 regulatory subunit 12C), Q9D8Y0 (EF-hand domain-containing protein D2). Thus, repeated bioinformatic analysis of the data deposited in the specialized databases resulted in detection of changes in the level of N-terminal acetylation of proteins that might be functionally significant in the mechanisms underlying the development of fibromuscular dysplasia.

Puzzle of Proteoform Variety-Where Is a Key?

One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.

Variability of haptoglobin beta-chain proteoforms

Existing knowledge on changes of the haptoglobin (Hp) molecule suggests that it may exist in multiple proteoforms, which obviously exhibit different functions. Using two-dimensional electrophoresis (2DE) in combination with mass spectrometry and immunodetection, we have analyzed blood plasma samples from both healthy donors and patients with primary grade IV glioblastoma (GBM), and obtained a detailed composite 2DE distribution map of β-chain proteoforms, as well as the full-length form of Hp (zonulin). Although the total level of plasma Hp exceeded normal values in cancer patients (especially patients with GBM), the presence of particuar proteoforms, detected by their position on the 2DE map, was very individual. Variability was found in both zonulin and the Hp β-chain. The presence of an alkaline form of zonulin in plasma can be considered a conditional, but insufficient, GBM biomarker. In other words, we found that at the level of minor proteoforms of Hp, even in normal conditions, there was a high individual variability. On the one hand, this raises questions about the reasons for such variability, if it is present not only in Hp, but also in other proteins. On the other hand, this may explain the discrepancy between the number of experimentally detected proteoforms and the theoretically possible ones not only in Hp, but also in other proteins.

[The bioinformatic identification of proteins with varying levels of post-translational modifications in experimental ischemic stroke in mice]

The experimental data obtained by Simats A. et al. (Molecular and Cellular Proteomics, 2020, 19(12), 1921-1936) was analysed using a bioinformatic approach. Original experimental results available in the ProteomeXchange database were obtained using a comprehensive multidomain approach to identify potential blood biomarkers in ischemic stroke in mice. The identification of peptides with post-translational modification (PTM) was performed by us using the raw data (accession code PXD016538). Only phosphorylation and deamination were considered as PTMs. Different combinations of data sets (ischemic tissue with intact tissue, ischemic tissue with control taken from mice after sham surgery, etc.) were compared both in terms of the ratio of abundance for the modified peptide to the unmodified variant and in terms of absolute values of abundance. The most likely change in precisely PTM levels was shown for 27 proteins, which include dynamin, glycogen phosphorylase and 70 kDa heat shock protein.