Two-Dimensional Gel Electrophoresis as an Information Base for Human Proteome

The main intricacy in the human proteome is that it is tremendously complex and composed of diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances should be performed. The approaches that allow disclosing and keeping the information about human proteome using two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) or immunodetection in combination with bioinformatics and 2DE can be used for the development of a comprehensive knowledge base of the human proteome

Proliferating cell nuclear antigen in the cytoplasm interacts with components of glycolysis and cancer

AbstractProliferating cell nuclear antigen (PCNA) is involved in a wide range of functions in the nucleus. However, a substantial amount of PCNA is also present in the cytoplasm, although their function is unknown. Here we show, through Far-Western blotting and mass spectrometry, that PCNA is associated with several cytoplasmic oncoproteins, including elongation factor, malate dehydrogenase, and peptidyl-prolyl isomerase. Surprisingly, PCNA is also associated with six glycolytic enzymes that are involved in the regulation of steps 4–9 in the glycolysis pathway.Structured summaryMINT-7995351: G3P (uniprotkb:P04406) and PCNA (uniprotkb:P12004) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7995334: ENOA (uniprotkb:P06733) and PCNA (uniprotkb:P12004) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7995368: ALDOA (uniprotkb:P04075) and PCNA (uniprotkb:P12004) colocalize (MI:0403) by fluorescence microscopy (MI:0416)MINT-7995141: G3P (uniprotkb:P04406) binds (MI:0407) to PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995182: ENOA (uniprotkb:P06733) binds (MI:0407) to PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995132: G3P (uniprotkb:P04406) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995228: PRDX6 (uniprotkb:P30041) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995220: CAH2 (uniprotkb:P00918) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995114: Triosephosphate isomerase (uniprotkb:P60174) binds (MI:0407) to PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995244: K2C7 (uniprotkb:P08729) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995252: ANXA2 (uniprotkb:P07355) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995122: Triosephosphate isomerase (uniprotkb:P60174) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995093: ALDOA (uniprotkb:P04075) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995148: PGK1 (uniprotkb:P00558) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995158: PGAM1 (uniprotkb:P18669) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995166: PGAM1 (uniprotkb:P18669) binds (MI:0407) to PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995105: ALDOA (uniprotkb:P04075) binds (MI:0407) to PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995260: PPIA (uniprotkb:P62937) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995173: ENOA (uniprotkb:P06733) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995268: EF1A (uniprotkb:P68104) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995236: MDHM (uniprotkb:P40926) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995189: RSSA (uniprotkb:P08865) physically interacts (MI:0915) with PCNA (uniprotkb:P12004) by far western blotting (MI:0047)MINT-7995282: PCNA (uniprotkb:P12004) physically interacts (MI:0915) with ALDOA (uniprotkb:P00883) and G3P (uniprotkb:P46406) by anti bait coimmunoprecipitation (MI:0006)

Towards the Full Realization of 2DE Power

Here, approaches that allow disclosure of the information hidden inside and outside of two-dimensional gel electrophoresis (2DE) are described. Experimental identification methods, such as mass spectrometry of high resolution and sensitivity (MALDI-TOF MS and ESI LC-MS/MS) and immunodetection (Western and Far-Western) in combination with bioinformatics (collection of all information about proteoforms), move 2DE to the next level of power. The integration of these technologies will promote 2DE as a powerful methodology of proteomics technology

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

Proteomics and Its Applications in Cancers

Cancer is a system malignant transformation that covers a wide group of diseases and can affect any organ of the human body [...

Empowering Shotgun Mass Spectrometry with 2DE: A HepG2 Study

One of the major goals of the Chromosome-Centric Human Proteome Project (C-HPP) is to catalog and annotate a myriad of heterogeneous proteoforms, produced by ca. 20 thousand genes. To achieve a detailed and personalized understanding into proteomes, we suggest using a customized RNA-seq library of potential proteoforms, which includes aberrant variants specific to certain biological samples. Two-dimensional electrophoresis coupled with high-performance liquid chromatography allowed us to downgrade the difficulty of biological mixing following shotgun mass spectrometry. To benchmark the proposed pipeline, we examined heterogeneity of the HepG2 hepatoblastoma cell line proteome. Data are available via ProteomeXchange with identifier PXD018450

Dataset of protein species from human liver

This article contains data related to the research article entitled “Zipf׳s law in proteomics” (Naryzhny et al., 2017) [1]. The protein composition in the human liver or hepatocarcinoma (HepG2) cells extracts was estimated using a filter-aided sample preparation (FASP) protocol. The protein species/proteoform composition in the human liver was determined by two-dimensional electrophoresis (2-DE) followed by Electrospray Ionization Liquid Chromatography-Tandem Mass Spectrometry (ESI LC-MS/MS). In the case of two-dimensional electrophoresis (2-DE), the gel was stained with Coomassie Brilliant Blue R350, and image analysis was performed with ImageMaster 2D Platinum software (GE Healthcare). The 96 sections in the 2D gel were selected and cut for subsequent ESI LC-MS/MS and protein identification. If the same protein was detected in different sections, it was considered to exist as different protein species/proteoforms. A list of human liver proteoforms detected in this way is presented

A semi-virtual two dimensional gel electrophoresis: IF–ESI LC-MS/MS

A method for increasing the productivity of ESI LC-MS/MS (electrospray ionization-liquid chromatography-tandem mass spectrometry) was proposed and applied. After IF (isoelectric focusing) of the sample using IPG (immobilized pH gradient) strip, the strip was cut to sections, and every section was treated according to trypsinolysis protocol for MS/MS analysis. The peptides produced were further analyzed by ESI LC-MS/MS. The procedure allows to: • identify many more proteins and proteoforms compared to shotgun analysis of extracts. • build a semi-virtual 2DE map of identified proteins

Variety and Dynamics of Proteoforms in the Human Proteome: Aspects of Markers for Hepatocellular Carcinoma

We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their proteoforms from normal (liver) and cancer (HepG2) cells. This allowed us to detect, in a single proteome, about 20,000 proteoforms coded by more than 4000 genes. A set of 3D-graphs showing distribution of these proteoforms in 2DE maps (profiles) was generated. A comparative analysis of these profiles between normal and cancer cells showed high variability and dynamics of many proteins. Among these proteins, there are some well-known features like alpha-fetoprotein (FETA) or glypican-3 (GPC3) and potential hepatocellular carcinoma (HCC) markers. More detailed information about their proteoforms could be used for generation of panels of more specific biomarkers