Comparing Complex Protein Samples Using Two-Dimensional Polyacrylamide Gels

Gel-Based and Gel-Free Phosphoproteomics to Measure and Characterize Mitochondrial Phosphoproteins

The mitochondrion is a key intracellular organelle regulating metabolic processes, oxidative stress, energy production, calcium homeostasis, and cell survival. Protein phosphorylation plays an important role in regulating mitochondrial functions and cellular signaling pathways. Dysregulation of protein phosphorylation status can cause protein malfunction and abnormal signal transduction, leading to organ dysfunction and disease. Investigating the mitochondrial phosphoproteins is therefore crucial to better understand the molecular and pathogenic mechanisms of many metabolic disorders. Conventional analyses of phosphoproteins, for instance, via western blotting, can be done only for proteins for which specific antibodies to their phosphorylated forms are available. Moreover, such an approach is not suitable for large-scale study of phosphoproteins. Currently, proteomics represents an important tool for large-scale analysis of proteins and their post-translational modifications, including phosphorylation. Here, we provide step-by-step protocols for the proteomics analysis of mitochondrial phosphoproteins (the phosphoproteome), using renal tubular cells as an example. These protocols include methods to effectively isolate mitochondria and to validate the efficacy of mitochondrial enrichment as well as its purity. We also provide detailed protocols for performing both gel-based and gel-free phosphoproteome analyses. The gel-based analysis involves two-dimensional gel electrophoresis and phosphoprotein-specific staining, followed by protein identification via mass spectrometry, whereas the gel-free approach is based on in-solution mass spectrometric identification of specific phosphorylation sites and residues. In all, these approaches allow large-scale analyses of mitochondrial phosphoproteins that can be applied to other cells and tissues of interest. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Mitochondrial isolation/purification from renal tubular cells Support Protocol: Validation of enrichment efficacy and purity of mitochondrial isolation Basic Protocol 2: Gel-based phosphoproteome analysis Basic Protocol 3: Gel-free phosphoproteome analysis.

Performance of nanoparticles for biomedical applications: The in vitro/in vivo discrepancy

Nanomedicine has a great potential to revolutionize the therapeutic landscape. However, up-to-date results obtained from in vitro experiments predict the in vivo performance of nanoparticles weakly or not at all. There is a need for in vitro experiments that better resemble the in vivo reality. As a result, animal experiments can be reduced, and potent in vivo candidates will not be missed. It is important to gain a deeper knowledge about nanoparticle characteristics in physiological environment. In this context, the protein corona plays a crucial role. Its formation process including driving forces, kinetics, and influencing factors has to be explored in more detail. There exist different methods for the investigation of the protein corona and its impact on physico-chemical and biological properties of nanoparticles, which are compiled and critically reflected in this review article. The obtained information about the protein corona can be exploited to optimize nanoparticles for in vivo application. Still the translation from in vitro to in vivo remains challenging. Functional in vitro screening under physiological conditions such as in full serum, in 3D multicellular spheroids/organoids, or under flow conditions is recommended. Innovative in vivo screening using barcoded nanoparticles can simultaneously test more than hundred samples regarding biodistribution and functional delivery within a single mouse.

[Expression levels and activity of rat liver lactate dehydrogenase isoenzymes in alloxan diabetes]

A significant decrease in the activity of lactate dehydrogenase (LDH, EC 1.1.1.27) in liver cells of rats with alloxan diabetes was found due to a decrease in the expression of the corresponding genes. The decrease in the activity of the enzyme under study in experimental type I diabetes was associated with inactivation of the cytoplasmic isoform of LDH. It was found that the level of ldha and ldhb gene transcripts in the liver of healthy rats was higher than in animals with alloxan diabetes. The ldha gene expression demonstrated almost 9-fold decrease, while a decrease in the ldhb gene expression was less pronounced (just 1.25-fold). Probably, the decrease in the rate of functioning of the enzyme under study is associated with a decrease in the intensity of glucose uptake by cells, which leads to inhibition of glycolysis and intensification of all stages of gluconeogenesis, particularly, reversed glycolysis reactions. Thus, the data obtained by us indicate an important role of LDH in the adaptive response of cellular metabolism in the development of type I diabetes mellitus.

[Effect of jerusalem artichoke extract on the functioning of malate dehydrogenase in the liver of rats with alloxan diabetes]

An increase in the activity and the appearance of a new isoform of NAD-dependent malate dehydrogenase (MDH; EC 1.1.1.37) has been detected in the liver of rats with alloxan diabetes was revealed. This confirms the possibility of MDH involvement in the adaptive reaction of the body under oxidative tress caused by biochemical changes in diabetic animals. The increase in the hepatic MDH activity in rats with experimental type I diabetes mellitus (T1DM) is associated with the formation of an additional MDH isoform in peroxisomes. Data on the expression of the MDH encoding genes mdh1 and mdh2 confirm that in T1DM the increase in MDH activity occurs at the level of transcription of MDH encoding genes. The use of the extract of Helianthus tuberosus led to a marked decrease in the blood glucose concentration of rats with alloxan diabetes, abolished by the change in transcriptional activity of the studied genes and blocked the formation of new MDH isoforms in rats with experimental alloxan diabetes. This suggest that extract of H. tuberosus may be of considerable interest from the point of view of pharmacological correction of metabolic changes during the development of pathologies of this kind.

Target Protein Identification on Photocatalyst-Functionalized Magnetic Affinity Beads

Although various affinity chromatography and photoaffinity labeling methods have been developed for target protein identification of bioactive molecules, it is often difficult to detect proteins that bind the ligand with weak transient affinity using these techniques. We have developed single electron transfer-mediated tyrosine labeling using ruthenium photocatalysts. Proximity labeling using 1-methyl-4-aryl-urazole (MAUra) labels proteins in close proximity to the photocatalyst with high efficiency and selectivity. Performing this labeling reaction on affinity beads makes it possible to label proteins that bind the ligand with weak transient affinity. In this article, novel protocols are described for target protein identification using photocatalyst proximity labeling on ruthenium photocatalyst-functionalized magnetic affinity beads. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of ruthenium photocatalyst Basic Protocol 2: Synthesis of azide- or desthiobiotin-conjugated labeling reagents Basic Protocol 3: Preparation of photocatalyst and ligand-functionalized affinity beads Basic Protocol 4: Target protein labeling in cell lysate Basic Protocol 5: Enrichment of labeled proteins with MAUra-DTB for LC-MS/MS analysis Basic Protocol 6: 2D-DIGE analysis of fluorescence-labeled proteins.