Biophysics
“Biophysics” is a peer-reviewed journal for publication of original experimental and theoretical data not being published elsewhere. Reviews at the request of the Editorial Board or Reviews on the initiative of researches subjected to evaluation by the editors are also encouraged. The scope of the journal covers following research areas: 1) Molecular Biophysics; 2) Cell Biophysics; 3) System Biophysics.
Periodicity – 6 issues per year. Russian ISSN: 0006-3029. English ISSN: 0006-3509 (printed version) and 1555-6654 (online version).
Media registration certificate: № 0110172 от 04.02.1993
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Vol 70, No 5 (2025)
Molecular biophysics
Analysis of Protein-Protein Interactions of Human Pioneer Transcription Factors Based on Predictions of the Structures of Their Complexes
Abstract
Pioneer transcription factors from the "Yamanaka cocktail" carry out cellular reprogramming. These proteins bind to heterochromatin, promote its opening and attract proteins to alter the epigenetic landscape and activate transcription. However, the literature lacks information on which chromatin proteins are attracted through direct protein-protein interactions with pioneer transcription factors. In this work, we predicted potential protein-protein complexes of three proteins from the "Yamanaka cocktail" (SOX2, OCT4, and KLF4) using neural network algorithms and performed structural and functional analysis of the resulting complexes.
Biophysics. 2025;70(5):837-853
837-853
Structure and Cooperative Interactions Between the Guanine Quadruplexes of the Promoter of Gallus gallus βA-Globin Gene
Abstract
Guanine quadruplexes are nucleic acid secondary structures present in the genomes of all eukaryotes, from yeast to mammals, where they play an important role in maintaining telomere integrity, creating TAD boundaries, and regulating transcription, alternative splicing, and translation. It was found that, contributing to the formation of a nucleosome-free region, guanine quadruplexes formed by two G-rich motifs inside the replication origin that is located within the βA-globin promoter in Gallus gallus, are necessary for the initiation of replication. In our work, circular dichroism spectroscopy was used to study the structures and dynamic properties of guanine quadruplexes formed by the βA-globin promoter/origin sequence in vitro. The data obtained show that quadruplexes located on the same DNA fragment are formed cooperatively, influencing the structures of each other and the entire DNA fragment on which they are located. These data suggest that the structures of guanine quadruplexes may be determined by their genomic environment, and also help explain some of the properties of quadruplexes observed in vivo.
Biophysics. 2025;70(5):854-863
854-863
Investigation of the Interactions of Methyl-β-Cyclodextrin and Amphotericin B with Erythrocyte Membrane Components by Molecular Docking
Abstract
The aim of this work was to analyze the interactions of methyl-β-cyclodextrin and amphotericin B (AmB) with spectrin, actin, and hemoglobin by the method of molecular docking. The protein structures were taken from PDB. The full-atom models of proteins were "cleaned" from water molecules and buffer components, surface charge arrangement was performed, and cells were selected for "blind" docking. The structural formula of methyl-β-cyclodextrin and amphotericin B were taken from PubChem and converted to HyperChem. Geometry optimization was performed using the MM+ model potential, rigid/fixed structures were optimized using the semi-empirical quantum chemical method PM3. The protein-ligand complex interactions were described using PLIP. The total binding energy for all complexes ranged from –4.4 to –10.3 kcal/mol. The complexes were formed due to hydrogen, van der Waals bonds, and salt bridges. Visualization of the most energetically advantageous positions confirmed that both amphotericin B and methyl-β-cyclodextrin localized in the central cavities of hemoglobin and actin, and in the distal sites of α- and β-subunits of spectrin. Amphotericin B formed more stable complexes with each of the proteins: the strength of hydrogen bonds and the number of hydrophobic contacts with the proteins were higher than for complexes with methyl-β-cyclodextrin.
Biophysics. 2025;70(5):864-876
864-876
Comparative Analysis of Sensitizing Activity and Biodistribution Characteristics of Chlorin e6 Derivatives: Influence of the Nature of Charged Groups
Abstract
New data have been obtained that expand the understanding of the role of the chemical structure and physico-chemical properties of photosensitizer molecules in determining the processes of their interaction with various biological objects, including serum proteins, biological membranes, cells and cellular systems. Changes in the side substituents in the chlorin e6 molecule significantly affect the physico-chemical properties of new compounds, the level of their accumulation in cells, and the rate of migration between cells, but do not significantly affect the intracellular localization of sensitizers. It is assumed that the increased photosensitizing activity of chlorin e6 derivatives is due to the influence of lateral substituents on their biodistribution processes.
Biophysics. 2025;70(5):877-890
877-890
Protein Adsorption on Polymeric Nanoparticles: Impact of Polyvinyl Alcohol
Abstract
The protein corona has a significant impact on the biodistribution, pharmacokinetics and therapeutic functionality of nanosystems, which determines the need for an in-depth study of the factors influencing its formation. The auxiliary substances included in the nanoparticles, in particular polyvinyl alcohol, can affect their physico-chemical properties, thereby affecting the formation of a protein corona. In this work, nanoparticles based on a copolymer of lactic and glycolic acids loaded with paclitaxel were synthesized by single emulsification using various concentrations of polyvinyl alcohol. The obtained nanoparticles were characterized by dynamic and electrophoretic light scattering methods. The adsorption models of Langmuir, Freundlich, Langmuir-Freundlich, and Brunauer, Emmett and Teller were used to describe the process of protein adsorption on the surface of nanoparticles. The obtained data indicate that the concentration of adsorbed proteins decreases when the residual polyvinyl alcohol concentration on the particle surface is increased. The revealed relationship will allow optimizing the design of nanosystems based on a copolymer of lactic and glycolic acids in order to increase the effectiveness of therapy.
Biophysics. 2025;70(5):891-900
891-900
Cell biophysics
Study of the Structure and Function of Musculature in Planarians (Platyhelminthes)
Abstract
The functional activity and morphological characteristics of the musculature of planarians have been studied. A physiological study conducted on isolated muscle cells of the planarian Procerodes littoralis (Turbellaria, Platyhelminthes) showed that caffeine in concentrations of 1–10 mM and depolarization caused by a high content of potassium ions (20–75 mM) had a dose-dependent stimulating effect on the musculature of planarians. Tapsigargin and cycloplazonic acid, calcium reuptake blockers in the sarcoplasmic reticulum store, reduced the number of muscle responses induced by both caffeine and depolarization. In addition, contractions of single P. littoralis muscle fibers induced by a medium with a high content of potassium ions were inhibited by ryanodine, which in mM concentrations is a blocker of the ryanodine calcium channels of the sarcoplasmic reticulum. The data obtained suggest that intracellular calcium store, as an intracellular source of calcium ions, play a role in the mechanism of contractile muscle response in flatworms. Histochemical examination using frozen sections and staining with fluorescently labeled phalloidin demonstrated the conservative organization of the body wall musculature of Schmidtea mediterranea planarians. The musculature of the body wall contains circular, diagonal and longitudinal muscle fibers. The thinnest circular fibers are densely packed in the outer layer of the musculature. The longitudinal fibers are the thickest and are mostly assembled in pairs. The diagonal fibers extend in two directions at an angle of 110–115 degrees to each other. Dorso-ventral muscle bundles penetrate the planarian body. The intestinal lumen is surrounded by thin longitudinal muscle fibers. Experiments have shown that planarians can be successfully used as a model object for studying the mechanisms of muscle contraction in flatworms.
Biophysics. 2025;70(5):901-912
901-912
Features of Smooth Muscle Cells of the Thoracic Aorta of SHR Rats in the Early Stages of Arterial Hypertension
Abstract
Proliferation, contraction and migration of vascular smooth muscle cells of thoracic aortic of SHR were studied at the age of 1-, 2- and 3-week-old rats. Real-time PCR was used to assess proliferation by comparing the relative amounts of genomic DNA between the control and experimental conditions; wound healing assay was used to determine migration; and collagen gel compression assay was used to assess cell contraction. An increased proliferation (by ~20%, p ≤ 0.01) and decreased migration (by ~47%, p ≤ 0.01) and contraction (by ~43%, p ≤ 0.01) were found in aortic smooth muscle cells from 1-week-old SHR compared to normotensive rats. In 2-week-old SHR, the proliferation and migration of aortic smooth muscle cells did not differ from normotensive rats, while the contraction of cells in SHR of this age group was reduced (by ~69%, p ≤ 0.01). In aortic smooth muscle cells of 3-week-old SHR, a decreased proliferation (by ~54%, p ≤ 0.01) and migration (by ~47%, p ≤ 0.01) were observed. Thus, the obtained changes in the studied parameters of thoracic aortic smooth muscle cells of SHR compared to such activities in normotensive rats are observed already in 1-week-old animals in the early neonatal period of development.
Biophysics. 2025;70(5):913-922
913-922
Modification of the Extracellular Matrix of the Umbilical Cord Mesenchymal Stromal Cells during Long-Term Modeling of Microgravity Effects
Abstract
It is known that microgravity leads to significant changes in the functioning of human physiological systems. In vitro, mechanosensitive cells also adapt to microgravity, demonstrating a rearrangement of cytoskeletal elements and functional activity. The effect of long-term microgravity simulated on a randomization position device (Gravite®) was studied on cultured multipotent mesenchymal stromal cells of umbilical cord tissue. After 21 days of exposure, the cells retained high viability and a characteristic stromal phenotype. The expression of CD90 and CD105 markers involved in cell-to-cell and cell-to-matrix adhesion increased on their surface. The cytokine profile changed, and the concentration of pleiotropic cytokines MCP-3, GM-CSF, and PDGF-AA, which potentiate metalloproteinase activity, increased. The expression of the genes encoding MMP1 and osteocalcin increased, and decreased in case of osteopontin. The main extracellular matrix proteins — fibronectin, collagen, and osteopontin — were visualized in both experimental groups, while collagen was more pronounced in microgravity. The described changes indicate adaptive changes in the local microenvironment and remodeling of the extracellular matrix in response to prolonged exposure to simulated microgravity while the functional activity of mesenchymal stromal cells is maintained.
Biophysics. 2025;70(5):923-932
923-932
Complex systems biophysics
Immutable and Variable Mechanisms in Synaptic Modulation of Various Types of Skeletal Muscles
Abstract
An overview of data on studies of multi-vector, as well as the persistence of unidirectional synaptic modulation in various types of motor units is presented. As is known, modulators of synaptic transmission are numerous. These include: the main mediator directly involved in this synapse, neuropeptides (endorphins and enkephalins, calcitonin, substance P, etc.), fatty acid derivatives (arachidonic acid and eicosanoids), gaseous mediators (NO, CO, and H2S), as well as purines and pyrimidines (extracellular ATP, adenosine, etc.). Using the example of data analysis based on the results of the action of the most effective neuromodulators, purines, both their constant and variable effects in the synaptic modulation of various types of skeletal muscles were revealed.
Biophysics. 2025;70(5):933-943
933-943
Antitumor Efficacy of Combined Use of Drugs Containing Precious Metals – Gold and Silver Polyacrylates and Cisplatin
Abstract
The possibility of combined use of compounds containing precious metals – gold and silver polyacrylates, and cisplatin, in experimental animal tumor models has been investigated. An additive effect has been established with the combined use of cisplatin and aurumacryl (Acatol adenocarcinoma, Lewis lung carcinoma) and the therapeutic synergism of the combination of cisplatin with argacryl (Lewis lung carcinoma). A tumor that recurs after exposure to cisplatin retains the sensitivity inherent in the original tumor to both cisplatin and argacrylate (Lewis lung carcinoma).
Biophysics. 2025;70(5):944-951
944-951
Activation of the Angiotensin Converting Enzyme Significantly Contributes to Oxidative Stress in the Aorta of Rats with Alloxan-Induced Diabetes
Abstract
Changes in the activity of the angiotensin converting enzyme and the production of reactive oxygen species in the rat aorta during diabetes induction by alloxan have been studied. The activity of the angiotensin converting enzyme in the aortic segments was determined by the hydrolysis of hippuryl-L-histidyl-L-leucine, and the formation of reactive oxygen species was determined by the oxidation of dichlorodihydrofluorescein. It has been shown that the activity of the angiotensin converting enzyme increases with an increase in blood glucose concentration to a maximum value at a glucose concentration of 12 mM and does not increase with a further increase in glucose levels. In contrast to the activity of the angiotensin converting enzyme, the formation of reactive oxygen species increases with increasing glucose concentration over the entire studied concentration range (up to 24 mM). Experiments with enalapril, an angiotensin converting enzyme inhibitor, have shown that it completely prevents an increase in the rate of formation of reactive oxygen species up to glucose concentration of 12 mM (100% contribution of activation of angiotensin converting enzyme to an increase in the formation of reactive oxygen species), but further the effectiveness of enalapril decreases (about 30% contribution of activation of angiotensin converting enzyme to an increase in formation of reactive oxygen species).
Biophysics. 2025;70(5):952-957
952-957
Effect of Antiorthostatic Suspension on Sperm Parameters of Mus musculus Mice
Abstract
The effect of 30-day antiorthostatic hanging of male Mus musculus mice on spermogram parameters, including the use of essential phospholipids, was studied. The concentration and motility of spermatozoa were measured, the fertilizing ability, the content of cholesterol, calcium ions and cytoskeletal proteins in spermatozoa were assessed. To assess the specificity of changes in spermatozoa, the content of cholesterol and cytoskeletal proteins was determined using buccal epithelial cells. It was shown that anti-orthostatic hanging led to a decrease in the proportion of fertilized oocytes and the absence of 2–4-cell embryos, but the use of essential phospholipids prevented these changes. The observed increase in the cholesterol content in spermatozoa, which is non-specific due to similar changes in buccal epithelial cells, in response to anti-orthostatic hanging, as well as the accumulation of calcium ions, could change the effectiveness of capacitation and cause a decrease in fertilizing capacity, which requires further research.
Biophysics. 2025;70(5):958-968
958-968
Medical biophysics
Mitochondrial DNA Deletions in Peripheral Blood of Offspring of Workers Occupationally Exposed to Chronic Ionizing Radiation
Abstract
Deletions in mitochondrial DNA are recognized factors in mitochondrial disorders and aging. The aim of this study was to investigate the prevalence of large-scale mtDNA deletions in peripheral blood samples of offspring whose parents, "Mayak" PA workers, were exposed to combined external γ- and internal α-radiation during the preconception period. Using long-extension PCR, deletions of 4977 bp and sizes ranging from 7436 to 8044 bp were detected. It was found that the prevalence of deletions in the studied groups of these offspring tended to increase, but no statistically significant differences were found compared to the control group.
Biophysics. 2025;70(5):969-975
969-975
Collagen Peptides Made of Pork Hyaline Cartilages for Nutritology and Biomedicine
Abstract
The difficulty of obtaining collagen peptides from connective tissues is due to the high mechanical strength of collagen fibrils. Collagen hydrolysates were obtained after ultrasonic homogenization of hyaline cartilages. Homogenization was performed at temperatures denaturing collagen and under conditions of enzymatic hydrolysis. The particle sizes were determined by photon correlation spectroscopy. According to spectral studies, the particles in the samples obtained at a karpazim concentration of 10% have the smallest size. Karpazim at a concentration of 10% is preferred for the enzymatic hydrolysis of hyaline cartilage and the production of low-molecular-weight type II collagen peptides. The peptides were distributed in the range from 180 to 600 Da. Collagen peptides containing 2–5 amino acid residues are convenient in size for use in biomedicine.
Biophysics. 2025;70(5):976-984
976-984
A Method for Obtaining Covalent Conjugates of QD Particles with Enzymes Involved in Thrombosis and Thrombolysis
Abstract
Covalent complexes of prourokinae, miniplasmin, and thrombin with QD nanoparticles containing aldehyde, amino, and carboxyl groups on the surface were obtained. It was shown that under the selected immobilization conditions, the listed enzymes immobilized on QD nanoparticles fully retained their enzymatic activity, and the formed complexes were stable colloids. The coating density of nanoparticles with enzymes reached 50–100 molecules per a particle. The immobilization of enzymes on carboxylic nanoparticles was performed using carbodiimide. Unlike the technology with carboxyl groups, the immobilization of enzymes on aldehyde nanoparticles does not require the use of carbodiimide to form a covalent complex and does not require a procedure for washing reagents before adding enzymes to nanoparticles, which improves the reproducibility of the immobilization procedure. It has been shown that particles with immobilized thrombin, when incubated with fibrinogen or blood plasma, form microemboli, which in vitro are completely destroyed by plasmin in the physiological concentration of the latter.
Biophysics. 2025;70(5):985-1001
985-1001
Evaluation of the Possibility of Using the Registration of Fluorescence of Stained Cells Isolated from the Skin to Study the Severity of Oxidative Stress
Abstract
Oxidative stress is a key link in the development of many pathological processes. Fluorescent dyes sensitive to reactive oxygen species, in particular dichlorofluorescein and its derivatives, are widely used for its evaluation. These dyes are actively used in works on cell cultures, but there is very little data on their use for the analysis of cells isolated directly from animal tissues. The present study was devoted to the investigation of the possibility of using 6-carboxy-dichlorofluorescein to register oxidative stress in cells isolated from rat skin flaps. To induce reactive oxygen species, skin fragments were incubated in a medium with hydrogen peroxide, after which cell suspensions were prepared from them. The cells were stained with 6-carboxy-dichlorofluorescein and Hoechst 33342, which allowed the fluorescent signal to be normalized by the number of cells in the sample. In separate experiments, the precursor of 6-carboxy-dichlorofluorescein was injected intradermical to live animals. Evaluation of the fluorescence ratio of 6-carboxy-2',7'-dichlorofluorescein and Hoechst 33342 showed the possibility of registering only pronounced oxidative stress, while it was not possible to distinguish its degree or record low-intensity changes. Additionally, microscopic analysis revealed the presence of cellular aggregates and fragments of the intercellular matrix, which reduced the reliability of the results. The data obtained indicate the limitations of the method of staining skin cells with dichlorofluorescein derivatives to assess the intensity of oxidative stress in native tissue.
Biophysics. 2025;70(5):1002-1010
1002-1010
Oxidized Disulfiram Derivatives Activate an Integrated Stress Response and Cause Paraptosis of Human Cancer Cells BT474
Abstract
Disulfiram, a well-known anti-alcohol drug with minimal side effects, as well as other dithiocarbamates are being investigated as part of the Drug Repurposing program in order to expand their use, including in oncology. In this work, using the example of human tumor cells BT474, it was found that the action of oxidized disulfiram metabolites generated by aerobic oxidation of diethyldithiocarbamate in the presence of the catalyst cobalamin (vitamin B12b) causes stress in the endoplasmic reticulum, and the integrated stress leads to cell death by paraptosis. The ability of substances of this class to cause non-apoptotic types of cell death is of interest for the development of new approaches in oncotherapy.
Biophysics. 2025;70(5):1011-1021
1011-1021
Piezopulsometric Analysis of the Functional State of the Cardiovascular System in Patients with Metabolic Syndrome
Abstract
The results of using the differential pulsometry method for non-invasive screening and analysis of the functional state of the cardiovascular system and the nature of its autonomous regulation in patients with metabolic syndrome are presented. The indicators characterizing the general cardiohemodynamics, as well as the variability of the VmaxPP and PP parameters of cyclic waves of blood pulse pressure, reflecting the regulatory effect of peripheral mechanisms of the autonomic nervous system and endocrine systems on the cardiovascular system of patients with metabolic syndrome, are evaluated. The involvement and role of myocytes of the wall of left ventricle as a universal muscle effector providing both the main pumping function of the cardiovascular system and the possibility of regulating the strength and speed of contractions of the left ventricle is considered. The prognostic significance of a comprehensive piezopulsometric examination of the cardiovascular system of patients for early noninvasive detection of signs of metabolic syndrome and its treatment is discussed.
Biophysics. 2025;70(5):1022-1032
1022-1032
Brain Biopotentialsas a Factor of Automatic Modulation of Therapeutic Sensory Stimulation Parameters
Abstract
The development of new personalized approaches to non-drug treatment of functional disorders and impairments is a priority area of scientific and technological development in Russia. This review analyzes innovative research line using automatic modulation of non-invasive sensory stimuli (transcranial magnetic and electrical stimulation, acoustic, optical, and audiovisual stimuli) by rhythmic components of a subject's electroencephalogram for therapeutic purposes. When considering numerous examples of successful therapeutic use of sensory stimulation automatically modulated by feedback signals from rhythmic components of the electroencephalogram, an analysis of the observed effects is undertaken depending on the conditions and parameters of the organization of these electroencephalogram-controlled stimulations. The main advantages of the approach under consideration are considered, such as the optimal involvement of neuroplasticity mechanisms and resonance mechanisms of the brain in the therapeutic process. Prospects for the development of this line of research are outlined using the example of the author's own research.
Biophysics. 2025;70(5):1033-1040
1033-1040