F·F ATP synthases/ATPases (F·F) catalyze ATP synthesis by consuming energy of electrochemical potential of hydrogen ions (, or ATP hydrolysis resulting in the formation. It is generally accepted to consider F·F as a reversible chemomechanical-electrical molecular machine, however: (i) the mechanism of energy-dependent ATP synthesis is based only on the data on hydrolytic activity of the enzyme, (ii) F·F from a number of organisms effectively synthesize, but is unable to hydrolyze ATP, which indicates non-observance of the principle of microreversibility and requires development of a new hypotheses concerning the enzyme mechanism. Since 1980, the group of A. D. Vinogradov has been developing a concept according to which the elementary catalysis stages of ATP hydrolysis and ATP synthesis do not coincide, and there are two independently operating forms of F·F in the coupled membranes - -generating ATPase and -consuming ATP synthase. F·F of as a natural model of an irreversibly functioning enzyme is a convenient object for experimental verification of the hypothesis of unidirectional energy conversion. The review considers modern concepts of the molecular mechanisms of regulation of F·F ATP synthase/ATPase of and development of the hypothesis of two forms of F·F.

In eukaryotes, translation initiation occurs by the cap-dependent mechanism. Each translated mRNA must be pre-bound by the translation initiation factor eIF4E. All isoforms of this factor are combined into one family. The review considers natural diversity of the eIF4E isoforms in different organisms, provides structural information about them, and describes their functional role in the processes, such as oncogenesis, participation in the translation of certain mRNAs under stress, and selective use of the individual isoforms by viruses. In addition, this review briefly describes the mechanism of cap-dependent translation initiation and possible ways to regulate the eIF4E function.

Fibroblast activation protein alpha (FAPα) is a transmembrane serine peptidase and a well-known marker of activated fibroblasts that are formed during onco- and fibrogenesis and play an important role in the progression of cancer and fibrosis. Identification of FAPα-positive cells is widely used to visualize pathological changes in the stroma in the diagnosis and treatment of cancer diseases. Recent evidence suggests that FAPα itself contributes to the development of tumors and fibrosis-associated diseases through its enzymatic activity and other mechanisms. Various methods for visualization and evaluation of FAPα enzymatic activity are being developed, which are essential for deciphering the role of FAPα in the development of stromal pathologies. Here we discuss current approaches to visualization and regulation of FAPα enzymatic activity.

-adenosyl--methionine (SAM, AdoMet) is a ubiquitous biomolecule present in all living organisms, playing a central role in a wide array of biochemical reactions and intracellular regulatory pathways. It is the second most common participant in enzymatic reactions in living systems, following adenosine triphosphate (ATP). This review provides a comprehensive analysis of enzymatic reactions involving SAM, whether as a product, a reactant (cosubstrate), or as a non-consumable enzyme cofactor. The discussion encompasses various methods for SAM synthesis, including biotechnological, chemical, and enzymatic approaches. Particular emphasis is placed on the biochemical reactions where SAM functions as a cosubstrate, notably in trans-alkylation reactions, where it acts as a key methyl group donor. Beyond methylation, SAM also serves as a precursor for the synthesis of other molecular building blocks, which are explored in a dedicated section. The review also addresses the role of SAM as a non-consumable cofactor in enzymatic processes, highlighting its function as a prosthetic group for certain protein enzymes and its ability to form complexes with ribozymes. In addition, bioorthogonal systems involving SAM analogues are discussed. These systems employ engineered enzyme-cofactor pairs designed to enable highly selective interactions between target SAM analogues and specific enzymes, facilitating precise reactions even in the presence of other SAM-dependent enzymes. The concluding section explores practical applications of SAM analogues, including their use as selective inhibitors in clinical medicine and as components of reporter systems.

It was found out that when the patients with atherosclerosis are orally administered ubiquinone Q (CoQ), oxidation (lipid hydroperoxide content) of the low-density lipoprotein (LDL) particles sharply decreases, which confirms important role of this natural antioxidant in protecting LDL particles from free radical oxidation . Influence of the lipophilic natural antioxidants ubiquinol Q (CoQH) and α-tocopherol (α-TOH) on the kinetic parameters of Cu-induced free radical oxidation of LDL particles was investigated. In this model system, possible synergism of the antioxidant action of CoQH and α-TOH has been shown. Putative mechanisms of bioregeneration of lipophilic antioxidants in LDL particles, including regeneration of α-TOH from the tocopheroxyl radical (α-TO) with participation of CoQH and/or ascorbate, are discussed.

Age is one of the key criteria of human health used in practical medicine to predict the risk of common chronic diseases. However, biological age, which reflects the state of an individual organism, functional capabilities, social well-being, and risk of premature death from various causes, often does not coincide with chronological age. To determine biological age of a particular individuals and the rate of their aging, specific panels of DNA methylation markers called "epigenetic clock" (EC) were proposed. This review summarizes the data about the main types of ECs developed to date and their key characteristics. We described the results of works studying individual aging rates in common age-associated diseases and outlined main directions, development of which could expand application of ECs in fundamental and practical medicine. There is no doubt that revealing complex mechanisms underlying interaction between the rate of epigenetic aging and the risk of age-associated diseases could play a key role for prediction and early diagnosis, as well as for the development of preventive measures that could delay onset of the disease.

is a non-tuberculosis fast-growing mycobacterium that has recently become a serious concern due to its rapidly increasing prevalence worldwide, mainly in individuals with a high susceptibility to pulmonary infections, for example, patients with cystic fibrosis, bronchiectasis, chronic obstructive pulmonary disease, and previous tuberculosis infection. According to present estimations, at least 20% of patients with cystic fibrosis are infected with . . This bacterium is extremely resistant to most drugs, leading to a severe and difficult-to-treat infection. That is why , previously classified as a low-virulent opportunistic pathogen, is now reconsidered as a true pathogenic bacterium. There are no effective drugs for successful infection therapy, as well as no vaccines to prevent its spread. This review focuses on the molecular mechanisms ensuring resistance to immune response and its ability to survive in the aggressive intracellular environment of human immune cells, and describes virulence factors that can serve as potential targets for the development of innovative therapeutic approaches to combat the spread of infections caused by .

Supraphysiological concentrations of calciprotein particles (CPPs), which are indispensable scavengers of excessive Ca and PO ions in blood, induce pro-inflammatory activation of endothelial cells (ECs) and monocytes. Here, we determined physiological levels of CPPs (10 μg/mL calcium, corresponding to 10% increase in Ca in the serum or medium) and investigated whether the pathological effects of calcium stress depend on the calcium delivery form, such as Ca ions, albumin- or fetuin-centric calciprotein monomers (CPM-A/CPM-F), and albumin- or fetuin-centric CPPs (CPP-A/CPP-F). The treatment with CPP-A or CPP-F upregulated transcription of pro-inflammatory genes (, , , , , , , ) and promoted release of pro-inflammatory cytokines (IL-6, IL-8, MCP-1/CCL2, and MIP-3α/CCL20) and pro- and anti-thrombotic molecules (PAI-1 and uPAR) in human arterial ECs and monocytes, although these results depended on the type of cell and calcium-containing particles. Free Ca ions and CPM-A/CPM-F induced less consistent detrimental effects. Intravenous administration of CaCl, CPM-A, or CPP-A to Wistar rats increased production of chemokines (CX3CL1, MCP-1/CCL2, CXCL7, CCL11, CCL17), hepatokines (hepassocin, fetuin-A, FGF-21, GDF-15), proteases (MMP-2, MMP-3) and protease inhibitors (PAI-1) into the circulation. We concluded that molecular consequences of calcium overload are largely determined by the form of its delivery and CPPs are efficient inducers of mineral stress at physiological levels.

Alginates are anionic unbranched plant and bacterial polysaccharides composed of mannuronic and guluronic acid residues. Alginates can form hydrogels under mild conditions in the presence of divalent cations (e.g., Ca). Because of their capacity to form gels, high biocompatibility, and relatively low cost, these polysaccharides are employed in pharmaceutical industry, medicine, food industry, cosmetology, and agriculture. Alginate oligomers produced by enzymatic cleavage of high-molecular-weight algal alginates are used as medicinal agents and dietary supplements. The global market for alginate-based products exceeds $1 billion. Alginates and their oligomers have attracted a special interest in biomedical sciences due to manifestation of various types of therapeutic activity. Across more than 50-year history of studies of alginates, over 60% scientific articles in this field have been published in the last 5 years. Unfortunately, the works dedicated to the mechanisms of biological activity of alginates and their oligosaccharides are still very scarce. This review analyzes the current state of research on the mechanisms (mainly biochemical) underlying biological and therapeutic activities of alginates (antioxidant, antibacterial, anti-inflammatory, antitumor, neuroprotective, antihypertensive, regenerative, and prebiotic). A comprehensive understanding of these mechanisms will not only improve the efficiency of alginate application in medicine and other traditional fields (cosmetology, food industry), but might also reveal their potential in new areas such as tissue engineering, nanobiotechnology, and bioelectronics.

Our review examines the key aspects of using polymeric carriers in biomedicine. The section "Polymers for Biomedicine" provides an overview of different types of polymers, their structural features and properties that determine their use as drug delivery vehicles. The section "Polymeric Carriers" characterizes the role of polymeric delivery systems in modern medicine. The main forms of polymeric carriers are described, as well as their key advantages for drug delivery. The section "Preclinical and Clinical Trials of Polymeric Drug Carriers" reviews the examples of clinical and preclinical studies of polymeric forms used for antitumor therapy, therapy for bacterial and infectious diseases. The final section "Targeted Drug Delivery Systems" is devoted to the discussion of approaches, as well as ligands that provide targeted drug delivery using polymeric carriers. We have paid special attention to modern approaches for increasing the efficacy of antibacterial therapy using vector molecules.

Protein phosphorylation is a pivotal mechanism for signal transduction, regulation of biochemical processes essential for reproduction, growth, and adaptation of organisms to changing conditions. Bacteria, which emerged more than 3.5 billion years ago, faced the need to adapt to a variety of ecological niches from the very beginning of their existence. It is not surprising that they developed a wide range of different types of kinases and target amino acid residues for phosphorylation. To date, many examples of phosphorylation of serine, threonine, tyrosine, histidine, arginine, lysine, aspartate, and cysteine have been discovered. Bacterial histidine kinases as part of two-component systems have been studied in most detail. More recently eukaryotic type serine-threonine and tyrosine kinases based on the conserved catalytic domain have been described in the genomes of many bacteria. The term "eukaryotic" is misleading, since evolutionary origin of these enzymes goes back to the last common universal ancestor - LUCA. Bioinformatics, molecular genetics, omics, and biochemical strategies combined provide new tools for researchers to establish relationship between the kinase abundance/activity and proteome changes, including studying of the kinase signaling network (kinome) within the cell. This manuscript presents several approaches to investigation of the serine-threonine protein kinases of cyanobacteria, as well as their combination, which allow to suggest new hypotheses and strategies for researchers.

Antibiotic resistance is a major challenge for public health systems worldwide. Rapid and effective identification of bacterial strains is critical for reducing the use of antibiotics and restricting the spread of antibiotic-resistant microorganisms. Various approaches have been developed in recent years for rapid bacterial identification and antibiotic susceptibility testing (AST), such as Raman spectroscopy, single cell image analysis, microfluidic techniques, mass spectrometry analysis, use of high-sensitive luminescent and fluorescent tags, impedance-based detection, and others. This review describes the methods developed for rapid bacterial identification and assessment of their antibiotic susceptibility, including general principles, specific problems, and future prospects.

Aging is associated with systemic changes in the physiological and molecular parameters of the body. These changes are referred to as biomarkers of aging. Statistical models that link changes in individual biomarkers to biological age are called aging clocks. These tools facilitate a comprehensive evaluation of bodily health and permit the quantitative determination of the rate of aging. A particularly promising area for the development of aging clocks is the analysis of cell-free DNA (cfDNA), which is present in the blood and contains numerous potential biomarkers. This review explores in detail the fragmentomics, topology, and epigenetic landscape of cfDNA as possible biomarkers of aging. The review further underscores the potential of leveraging single-molecule sequencing of cfDNA in conjunction with long-read technologies to simultaneously profile multiple biomarkers, a strategy that could lead to the development of more precise aging clocks.

This review presents materials on formation of the concept of moonlighting proteins and general characteristics of different similar proteins. It is noted that the concept under consideration is based on the data on the existence in different organisms of individual genes, protein products of which have not one, but at least two fundamentally different functions, for example, depending on cellular or extracellular location. An important feature of these proteins is that their functions can be switched. As a result, in different cellular compartments or outside the cells, as well as under a number of other circumstances, one of the possible functions can be carried out, and under other conditions, another. It is emphasized that the significant interest in moonlighting proteins is due to the fact that information is currently accumulating about their involvement in many vital molecular processes (glycolysis, translation, transcription, replication, etc.). Alternative hypotheses on the evolutionary origin of moonlighting proteins are discussed.

An important aspect of medical microbiology is identification of the causes and mechanisms of reactivation (resuscitation) of dormant non-sporulating bacteria. In particular, dormant () can cause latent tuberculosis (TB), which could be reactivated in the human organism to the active form of the disease. Analysis of experimental data suggested that reactivation of mycobacteria and reversion of the growth processes include several stages. The initial stage is associated with breakdown of the storage substances like trehalose upon the action of trehalase and with peptidoglycan hydrolysis. Demethylation of tetramethyl porphyrins accumulated in hydrophobic sites (membranes) of the dormant cell also occur in this stage. Metabolic reactivation, starting with cAMP synthesis and subsequent activation of metabolic reactions and biosynthetic processes take place at the stage two as has been shown in the omics studies. Mechanisms of cell reactivation by exogenous free fatty acids via activation of adenylate cyclase and cAMP production have been also suggested. Onset of the cell division is a key benchmark of the third and final stage. Hydrolysis of peptidoglycan as a result of enzymatic action of peptidoglycan hydrolases of the Rpf family is an important process in reactivation of the dormant mycobacteria. Two possible mechanisms for participation of Rpf proteins in reactivation of the dormant bacteria are discussed. On the one hand, muropeptides could be formed as products of peptidoglycan hydrolysis, which could interact with appropriate receptors in bacterial cells transducing activating signal via the PknB phosphotransferase. On the other hand, Rpf protein could presumably change structure of the cell wall, making it more permeable to nutrients and substrates. Both hypotheses were examined in this review. Upon reactivation, independent enzymatic reactions resume their functioning from the beginning of reactivation. Such activation of the entire metabolism occurs rather stochastically, which concludes in combining all biochemical processes in one. This review presents current knowledge regarding biochemical mechanisms of the dormant mycobacteria reactivation, which is important for both fundamental and medical microbiology.

14-3-3 is a family of small regulatory proteins found exclusively in eukaryotic organisms. They selectively bind to phosphorylated molecules of partner proteins and regulate their functions. 14-3-3 proteins were first characterized in the mammalian brain approximately 60 years ago and then found in plants, 30 years later. The multifunctionality of 14-3-3 proteins is exemplified by their involvement in coordination of protein kinase cascades in animal brain and regulation of flowering, growth, metabolism, and immunity in plants. Despite extensive studies of this diverse and complex world of plant 14-3-3 proteins, our understanding of functions of these enigmatic molecules is fragmentary and unsystematic. The results of studies are often contradictory and many questions remain unanswered, including biochemical properties of 14-3-3 isoforms, structure of protein-protein complexes, and direct mechanisms by which 14-3-3 proteins influence the functions of their partners in plants. Although many plant genes coding for 14-3-3 proteins have been identified, the isoforms for and studies are often selected at random. This rather limited approach is partly due to an exceptionally large number and variety of 14-3-3 homologs in plants and erroneous   assumptions on the equivalence of certain isoforms. The accumulated results provide an extensive but rather fragmentary picture, which poses serious challenges for making global generalizations. This review is aimed to demonstrate the diversity and scope of studies of the functions of plant 14-3-3 proteins, as well as to identify areas that require further systematic investigation and close scientific attention.

The review discusses the influence of various factors (e.g., post-translational modifications and chaperones) on the pathological transformation of amyloidogenic proteins involved in the onset and development of neurodegenerative diseases (Alzheimer's and Parkinson's diseases) and spongiform encephalopathies of various origin with special focus on the role of α-synuclein, prion protein, and, to a lesser extent, beta-amyloid peptide. The factors investigated by the authors of this review are discussed in more detail, including posttranslational modifications (glycation and S-nitrosylation), cinnamic acid derivatives and dendrimers, and chaperonins (eukaryotic, bacterial, and phage). A special section is devoted to the role of the gastrointestinal microbiota in the pathogenesis of amyloid neurodegenerative diseases, in particular, its involvement in the transformation of infectious prions and possibly other proteins capable of prion-like transmission of amyloidogenic diseases.

The proposed approach for determining catalytic activity of the SARS-CoV-2 main protease (M) is based on registration of the peak area of electrochemical oxidation of tyrosine residue in the model peptide substrate CGGGAVLQSGY immobilized on the surface of a graphite screen-printed electrode (SPE) modified with gold nanoparticles (AuNP). The AuNP were obtained by electrosynthesis. Steady state kinetic parameters of M in the reaction with the model peptide were determined: catalytic constant () was (3.1 ± 0.1) × 10 s; Michaelis constant () was (358 ± 32) × 10 M; catalytic efficiency (/) was 8659 s/M. The limit of detection (LOD) determined for M using the proposed electrochemical system was 44 nM. The proposed approach is a promising tool to search for new M inhibitors as drugs for treatment of coronavirus infections.

Alzheimer's disease (AD), a severe neurodegenerative disease of the central nervous system, is the most common cause of cognitive impairment in people over the age of 60. The etiology and pathogenesis of Alzheimer's disease are still unclear despite decades of active research. Numerous studies have shown that neurodegenerative processes in AD are associated with the mitochondrial dysfunction. In this review, we briefly discuss the results of these studies and present the reported evidence that mitochondrial dysfunction in AD is associated with mitochondrial DNA (mtDNA) variations. The results of association analysis of mtDNA haplogroups and individual polymorphic variants, including those whose combinations define haplogroups, with AD are described in detail. These data clearly indicate the role of variations in the mitochondrial genome in the susceptibility to AD, although the problem of significance of individual mtDNA variants is far from being resolved.

Biallelic mutations in the gene encoding lysosomal enzyme glucocerebrosidase (GCase), lead to the development of the Gaucher disease (GD) and also represent a significant risk factor for the Parkinson's disease (PD). In most cases, mutations in the gene are located outside the region coding for the enzyme active site and cause a decrease in the GCase activity due to the reduction in the efficiency of transport of conformationally altered enzyme to the lysosomes. Drugs used to treat GD (enzyme replacement therapy) cannot cross the blood-brain barrier and, therefore, are not effective in the treatment of neuronal forms of GD or PD associated with mutations in the gene (GBA1-PD). Currently, inhibitors of the leucine-rich repeat kinase 2 (LRRK2) are undergoing clinical trials for the treatment of PD. It was previously shown that inhibition of LRRK2 leads to the increase in the GCase activity in patient-specific GBA1-PD cells. We assessed the effect of the LRRK2 inhibitor MLi-2 on the GCase activity in the primary culture of peripheral blood macrophages from patients with type 1 GD. The activity of GCase and the levels of its substrate in cells cultured with and without MLi-2 was assayed by high-performance liquid chromatography coupled with tandem mass spectrometry (HPLC-MS/MS). No effect of LRRK2 inhibition on the activity GCase in a group of patients with GD was found.

The mechanisms of development of autoimmune, neurological, and viral diseases and the possibilities of immune response to various antigens in these pathologies still pose many questions. Human immune system is theoretically capable of synthesizing about a million antibodies with very different properties against the same antigen. It remains unclear how many antibodies and with what properties can form in healthy people and patients with autoimmune diseases (AIDs). The capabilities of traditional approaches, such as enzyme immunoassay or affinity chromatography of Abs on specific sorbents, in answering these questions and analyzing the diversity of antibodies formed against external and internal antigens, as well as their role in the pathogenesis of various diseases, are very limited. Analysis of monoclonal antibodies in the blood of patients with systemic lupus erythematosus (SLE) using phage display revealed that the number of autoantibodies against DNA and myelin basic protein (MBP) can exceed 3-4 thousand, and approximately 30-40% of them are abzymes capable of hydrolyzing DNA and MBP. However, this approach does not allow to investigate the variety of properties of such antibodies, in particular their catalytic activity. Abzymes can play either positive or negative role in the development of various diseases. For example, in HIV-infected patients, abzymes against viral polymerase and integrase cleave these proteins, thus slowing down the development of immunodeficiency syndrome. Other antibodies play a negative role in the pathogenesis of viral, neurological, and autoimmune diseases. Thus, antibodies capable of hydrolyzing DNA and histones can penetrate through the cellular and nuclear membranes, stimulate cell apoptosis, and, as a result, trigger autoimmune processes in many pathologies. Antibodies against MBP cleave this protein in the membranes of cells in nerve tissues, leading to the development of multiple sclerosis (MS). In this case, abzymes against individual histones were able to hydrolyze each of these histones, as well as MBP, while Abs against MBP hydrolyzed MBP and all five histones. It has also been established that the substrate specificity of abzymes in the hydrolysis of histones and MBP varied greatly depending on the stage of MS or SLE development. Here, we used this example to analyze in detail the role that abzymes against various antigens play in their expanded involvement in the pathogenesis of some AIDs. The review also describes the impact of defects in the bone marrow stem cell differentiation characteristic of AIDs in the formation of B lymphocytes producing harmful abzymes and summarizes for the first time the data on the exceptional diversity of autoantibodies and abzymes, their unusual biological functions, and involvement in the pathogenesis of autoimmune pathologies.