Vol 89, No 8 (2024)

The current stage of development of proteomic research in the field of biology, medicine, development of new drugs, population screening, or personalized approaches to therapy dictates the need to analyze large sets of samples within the reasonable experimental time. Until recently, mass spectrometry measurements in proteomics were characterized as unique in identifying and quantifying cellular protein composition, but low throughput, requiring many hours to analyze a single sample. This was in conflict with the dynamics of changes in biological systems at the whole cellular proteome level upon the influence of external and internal factors. Thus, the low speed of whole proteome analysis has become the main factor limiting the developments in functional proteomics, where it is necessary to annotate the intracellular processes not only in a wide range of conditions, but also over a long period of time. The enormous level of heterogeneity of tissue cells or tumors, even of the same type, dictates the need to analyze the biological system at the level of individual cells. These studies involve obtaining molecular characteristics for tens, if not hundreds of thousands of individual cells, including their whole proteome profiles. The development of mass spectrometry technologies providing high resolution and mass measurement accuracy, predictive chromatography, new methods for peptide separation by ion mobility and processing proteomic data based on artificial intelligence algorithms have opened a way for significant, if not radical, increase in the throughput of whole proteome analysis and led to the implementation of the novel concept of ultrafast proteomics. Work done just in the last few years has demonstrated proteome-wide analysis throughput of several hundred samples per day at a depth of several thousand proteins, levels unimaginable three or four years ago. The review examines the background of these developments, as well as modern methods and approaches that implement ultrafast analysis of the entire proteome.

The proper functioning of the cardiovascular system is one of the most important goals of the body. The physiological processes in myocardium is regulated by the balance of cardioprotective and pathological mechanisms. The system of insulin-like growth factors (IGF system, IGF signaling pathway) plays pivotal role in regulating the growth and development of various cells and tissues. In the myocardium, the IGF system provides both cardioprotective and pathological effects. This review summarizes recent data on the role of IGF signaling in the realization of cardioprotection from one side and the pathogenesis of various cardiovascular diseases from the other side, as well as analyzes the severity of these effects in various conditions.

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

Hepatic encephalopathy (HE) is a prevalent neuropsychiatric syndrome occurring in patients with severe liver dysfunction and/or portocaval shunt. Despite more than a one hundred year history of study on interrelationships between liver failure and brain pathology, pathogenetic mechanisms leading to development of encephalopathy in liver diseases have not been fully elucidated yet however, it is generally accepted that the main trigger of neurological complications of HE is a neurotoxin – ammonia, the concentration of which in the blood increases to toxic levels (hyperammonemia, HA) when the detoxification function of the liver is impaired. Seamlessly penetrating into brain cells and affecting NMDA receptor-mediated (NMDA-R) signaling, ammonia triggers a pathological cascade leading to dramatic inhibition of aerobic glucose metabolism, oxidative stress, cerebral hypoperfusion, nerve cell damage, and the formation of neurological deficits. Brain hypoperfusion, in turn, may be associated with impaired oxygen transport function of erythrocytes, associated with impaired metabolic/energetic processes occurring in the membranes and inside erythrocytes and controlling the affinity of hemoglobin to oxygen, which determines the degree of oxygenation of blood and tissues. We recently confirmed the above causal relationship and identified a novel NMDA-R hyperactivation-mediated ammonium-induced prooxidant effect on erythrocytes that impairs their oxygen transport function. For a more complete assessment of “erythrocytic” factors that impair brain oxygenation and lead to encephalopathy, in this study we determined enzyme activity and concentration of metabolites of glycolysis, Rapoport-Lubering shunt, and morphological characteristics of erythrocytes from rats with acute HA. To assess the role of NMDA-R in the said processes, the study was conducted using MK-801, a non-competitive NMDA receptor antagonist. The results obtained allow us to conclude that morphofunctional disorders of erythrocytes and hemoglobinemia resulting from ammonium-induced disruption of a highly integrated system of metabolic pathways should be considered as an additional systemic “erythrocytic” pathogenetic factor leading to the progression of cerebral hypoperfusion in HE accompanied by HA.

The lipoxygenase cascade of plants is a source of oxidized fatty acid derivatives, oxylipins, which play an important role in regulatory processes, as well as in the formation of responses to stress factors. One of the most common enzymes of the lipoxygenase cascade are 13-specific hydroperoxide lyases (HPL, synonym “hemiacetal synthase”) of the CYP74B subfamily. This work described the discovery and cloning of the CYP74B34 gene of the carrot (Daucus carota), as well as a description of the biochemical properties of the corresponding recombinant enzyme. The CYP74B34 enzyme was active towards 9- and 13- hydroperoxides of linoleic (9-HPOD and 13-HPOD, respectively) and α-linolenic acids (9-HPOT and 13-HPOT, respectively). CYP74B34 specifically converted 9-HPOT and 13-HPOT into aldoacids (HPL products). The transformation of 13-HPOD led to the formation of aldoacids (as main products) and epoxyalcohols (as minor products). Epoxyalcohols are products of the epoxyalcohol synthase (EAS) activity. At the same time, 9-HPOD conversion resulted in the formation of the epoxyalcohols as main products and aldoacid as the minor one. Thus, the CYP74B34 enzyme is the first enzyme with double HPL/EAS activity described in carrot. The presence of corresponding catalytic activities was confirmed by the results of analyses of oxylipin profiles of roots of young seedlings and mature plants. In addition, the work describes the results of substitution of amino acid residues in one of the catalytically essential sites.