Biofizika
“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 3 (2025)
Molecular biophysics
In vitro Interaction of Titin and Myosin-Binding Protein C
Abstract
The morphological and structural features of coaggregates of two muscle proteins of the sarcomeric cytoskeleton (titin and myosin-binding protein C) were studied using atomic force microscopy, FTIR spectroscopy, fluorimetry using the dye thioflavin T and X-ray diffraction. It was found that, depending on the ionic strength of the solution, coaggregation of these proteins occurs with the formation of structures with different morphologies. The data obtained in vitro expand the understanding of the peculiarities of aggregation of sarcomeric muscle proteins and are important for a better understanding of their interaction in sarcomeres in vivo.
Biofizika. 2025;70(3):421–429
421–429
Investigation of H1-Histamine Receptor Binding Patterns to Antidepressants and New Allergy Drugs
Abstract
Using the methods of computational chemistry – quantum–chemical methods and flexible docking – the peculiarities of the spatial organization of protein-ligand complexes formed as a result of binding of the H1-histamine receptor to a set of drugs were investigated. Representatives of antihistamine drugs of different generations, a drug belonging to the group of antiemetics, as well as several representatives of the class of tricyclic antidepressants with a pronounced antihistamine effect were chosen for the study. The results of the study can potentially be used for the development of new-generation antihistamines.
Biofizika. 2025;70(3):471-482
471-482
Molecular Dynamic Modeling of Pharmacological Vector-Receptor Pairs for Specific Drug Delivery to the Tumor: Atomic-Molecular Mechanisms of RGD-Peptide Embedding in the αvβ3-Integrin Receptor
Abstract
In this work, computer-based molecular dynamics studies of the interaction of the pharmacological pair “vector–receptor” have been carried out to model promising mechanisms and processes of specific drug delivery to the tumor. The purpose of these computational molecular dynamic calculations is to study the interaction processes and determine the spatial positions of the RGD peptide + αvβ3-integrin receptor system, which is solvated with water. The configuration positions of the RGD-peptide + αvβ3-integrin system in 100 ns relaxed states were obtained from molecular dynamic modeling. In this case, two RGD peptides were modeled located outside and inside the αvβ3-integrin receptor. One of the two RGDs is a peptide of the original PDB file localized inside the αvβ3-integrin receptor. The other RGD peptide is located outside the receptor in its initial position, freely diffuses throughout the entire area of the modeling cell, and naturally comes into contact and binds to αvβ3-integrin.
Biofizika. 2025;70(3):453-470
453-470
Identification of Potential SOX2 Binding Sites to Nucleosomes via Molecular Modeling
Abstract
The pioneer transcription factor SOX2 plays an important role in the regulation of gene expression by binding to condensed chromatin and inducing its decondensation. Experimental data on the preferred positions of SOX2 binding to DNA in the context of the nucleosome are contradictory: in some studies, binding to the inner segments of nucleosomal DNA is preferred, in others – to the edge segments. Within the framework of this work, all possible variants of SOX2 binding to nucleosomal DNA at different distances from the nucleosome center (determined by the superhelix position parameter – SHL) and different orientation of the binding site relative to the nucleosome center (determined by the SHL sign) were analyzed by molecular modeling. It was shown that on an intact nucleosome, binding is possible at positions SHL +2, SHL ±4 and SHL ±5, but if we assume a shift of nucleosomal DNA by one pair of nucleotides, binding becomes possible at positions corresponding to all integer values of SHL. This observation helps to explain part of the contradictions between the experimental data.
Biofizika. 2025;70(3):439-452
439-452
Analysis of Competitive Ligand Binding to DNA: Using Dyes as Fluorescent Sensors
Abstract
Determination of interaction parameters of low molecular weight compounds with DNA is difficult in cases where compounds do not exhibit appreciable fluorescence or their spectral changes are difficult to interpret. To solve this problem, an approach involving the use of known fluorescent dyes competitively binding on DNA is proposed. This approach uses a model describing the competitive binding of two extended ligands on a linear DNA matrix. This model allows approximation of experimental data and determination of binding parameters corresponding to two non-fluorescent types of ligands. The first type of ligands exhibits intercalation binding to DNA and competes with ethidium bromide, while the second type binds along a narrow groove and competes with Hoechst 33258 dye.
Biofizika. 2025;70(3):430-438
430-438
Cell biophysics
Quenching with Oxygen of the Triplet State of Spheroiden in the Reaction Centers of C. sphaeroides in the Temperature Range 0–45°C
Abstract
The efficiency of quenching with dissolved oxygen of the triplet state of the carotenoid spheroiden ([T]Car) in the photosynthetic reaction center of purple bacteria Cerebacter (Rhodobacter) sphaeroides in the temperature range from 0°C to +45°C was investigated. For the possibility of [T]Car formation during light excitation of the reaction center, o-phenanthroline (10[−][2] M) was added to the preparations, partially displacing the primary quinone acceptor from the structure of reaction center. The activation energies of the process of [T]Car quenching under normal aerobic conditions and with partial degassing of the studied samples were determined.
Biofizika. 2025;70(3):483-490
483-490
Effect of Light Intensity and Spectral Composition on Electron Transport in Chloroplasts in situ and in silico
Abstract
Light-induced redox transformations of P700, the reaction center of photosystem I, were studied by EPR method depending on the illumination conditions of plant leaves (intensity and spectral composition of the active light). Within the framework of a mathematical model, the key stages of electron transfer along the noncyclic electron transport chain containing photosystems I and II and mobile transporters (plastoquinone, plastocyanin, ferredoxin) and the processes of trans-thylakoid proton transfer associated with ATP synthesis were considered. The mechanisms of pH-dependent regulation of electron transport in chloroplasts at the acceptor and donor sites of photosystem I have been analyzed. The modeling results are in agreement with experimental data on the kinetics of light-induced transformations of P700 in chloroplasts of higher plants. The results obtained are discussed in the context of "short-term" pH-dependent mechanisms of electron transport regulation in chloroplasts in situ.
Biofizika. 2025;70(3):491–503
491–503
Interaction of Iron (II) Ions with Lipids of Lecithin Liposomes in Aqueous Medium
Abstract
The interaction of divalent iron ions in a wide range of concentrations with lipids of soybean lecithin liposomes in aqueous medium has been studied. Using methods of thin-layer chromatography and dynamic light scattering, as well as mathematical processing of UV spectra of lecithin and its mixtures with iron ions by Gauss method, it was found that the participation of iron ions at different stages of the oxidation process, their interaction with lipids of liposomes and influence on spontaneous aggregation of lecithin in aqueous medium are determined by the following factors: the initial degree of oxidation of lipids, their composition, the ratio of concentrations of lecithin and iron ions in the medium. The ratio of these factors either leads to the incorporation of iron ions into the hydrophobic sites of membranes, initiating oxidation processes, or causes the formation of complexes with N- and P-containing fragments of phospholipids and disruption of the relationship between primary and secondary oxidation products. The absence of linear dependence of the size of liposomes and their zeta potential on the concentration of iron ions in the medium was revealed.
Biofizika. 2025;70(3):504–511
504–511
The Role of Metabolites of the Phosphoinositide Cycle in the Regulation of Excitation Conditions and Regeneration of Damaged Somatic Nerves under the Action of Insulin-Like Growth Factor-1
Abstract
Changes in the qualitative composition and quantitative content of metabolites of the phosphoinositide cycle have been studied and their participation in the process of excitation conduction along nerve conductors and regeneration of damaged somatic nerves under the action of insulin-like growth factor-1 have been established. It was shown that during nerve excitation there is a decrease in the level of phosphatidylinositol and phosphatidylinositol-4,5-diphosphate and an increase in the content of phosphatidylinositol-4-monophosphate and phosphatidylinositol-3,4,5-triphosphate, which indicates the intensification of phosphoinositide metabolism under conditions of depolarization of the nerve fiber membrane, and there is also a redistribution of fatty acids in the composition of phosphatidylinositol, diacylglycerol and free fatty acid fractions. Nerve transection is accompanied by accumulation of all forms of phosphoinositides and a decrease in the level of diacylglycerol in both proximal and distal sections of the nerve conductor, apparently as a result of inactivation of phosphoinositide-specific phospholipase C. Against the background of intramuscular injection of insulin-like growth factor-1 at a concentration of 100 ng/kg, intensification of phosphoinositide metabolism, accumulation of diacylglycerol and decrease in the level of free fatty acids were observed. The methods of Raman spectroscopy, registration of action potentials and growth cones revealed the restoration of the physico-chemical state of the lipid bilayer and functional activity in the proximal segment of somatic nerves using insulin-like growth factor-1, which correlates with the data we obtained on the changes in the composition of the lipid fraction of damaged nerve conductors against the background of the drug action. We believe that insulin-like growth factor-1 is one of the factors of axonal regeneration and restoration of functioning of damaged nerve conductors, exerting its effect as a result of activation of phosphoinositide-specific phospholipase C and phosphatidylinositol-3-kinase signaling pathways.
Biofizika. 2025;70(3):512-526
512-526
Complex systems biophysics
Hybrid Models of Epidemic Waves Including Assessment of Changes in Cellular Receptor Binding Affinity
Abstract
Purposeful development of special modeling methods for specific modern epidemic situation at accumulation of collective immunity but preservation of mutant pathogen in the population is continued. The evolution of SARS-CoV-2 is not halted by the problem of Long COVID disease chronicization. We propose an evolution of the modeling method to include tracking of the affinity index for ad hoc redefinition of hybrid computational structures according to monitoring of current mutations and estimation of the frequency of strains occurrence.
Biofizika. 2025;70(3):554–577
554–577
Mild Toxic Effect of Dinitrosyl Iron Complexes During Inhalation of Syrian Hamsters in a "Nose-Only" Chamber
Abstract
Using methods of general and biochemical blood analysis and histological analysis of the lungs, liver, heart and kidneys of Syrian hamsters, it was checked whether aerosol treatment of these animals with binuclear dinitrosyl iron complexes with glutathione, alone or followed by similar treatment of the same animals with diethyldithiocarbonate, as well as aerosol treatment of Syrian hamsters with dinitrosyl iron complexes with mercaptosuccinate, leads to negative, toxic effects at the level of the whole organism. The detected weak, reversible toxic effect in the form of nephrotoxicity of such treatment allows us to assert that such an effect, which ensures the suppression of COVID infection in these animals, is due to the selective in vivo action of dinitrosyl iron complexes and diethyldithiocarbonate on the SARS-CoV-2 virus, without affecting other tissues and organs of the animal.
Biofizika. 2025;70(3):527-538
527-538
Application of Granulocyte Colony-Stimulating Factor in the Form of Pegfilgrastim in Fractionated Irradiation of Mice
Abstract
The radioprotective efficacy of granulocyte colony-stimulating factor in the form of pegfilgrastim at fractionated irradiation was evaluated on male ICR (CD-1) mice. Mice were exposed to five daily exposures to X-rays at a dose of 2.5 Gy. Three hours after each exposure, pegfilgrastim was injected subcutaneously into mice at a dosage of 0.5 μg/g. The drug was also administered daily 3–7 days after the last irradiation. The efficacy of this therapeutic regimen was evaluated on the basis of the degree of DNA damage in spleen cells 30 min after the last irradiation, hematologic parameters – after 30 min and 3 days, Schiffbases, trieno and oxodiene conjugates in the liver – after 30 min, thymus and spleen weight, the number of karyocytes in the femur, the content of thiobarbiturate-reactive products in the liver – after 3 days, as well as on the basis of 30-day survival. The application of the therapeutic regimen under study contributed to a significant correction of irradiation-induced oxidative stress: according to the criteria of the content of Schiff bases, trieno and oxodieno conjugates, the group receiving pegfilgrastim corresponded to the intact mice, the content of thiobarbiturate-reactive products in the liver decreased relative to the irradiated control, but the parameters of intact mice were not reached. Pegfilgrastim administration did not compensate for the irradiation-induced bone marrow cell death 3 days after the last irradiation and could eventually ensure the survival of only 3 mice out of 14 individuals receiving the drug. Thus, for effective application of pegfilgrastim during fractionated irradiation at a total dose of 12.5 Gy it is necessary to increase the number of irradiation sessions with decreasing dose of each session, or to decrease the total radiation dose. Joint use of pegfilgrastim with other radioprotective drugs with other mechanisms of action is also promising.
Biofizika. 2025;70(3):539–553
539–553
Medical biophysics
Macroerg Adenosine Triphosphoric Acid in BioMedical Research (Review)
Abstract
The dual role of ATP molecule – macroergic compound and neurotransmitter – is considered. As a signaling molecule, ATP participates in the formation of the embryonic visual system and the development of the inner ear; in mediating pain and taste sensations. In cardiovascular diseases, the release of ATP into the intercellular medium serves as a signal for the organism to activate repair mechanisms. ATP is involved in the maintenance of normal function of many organs and tissues. This suggests the possibility of its application for the treatment of a number of disorders: kidney, bone, bladder, skin, neurological and psychiatric pathologies, cardiovascular diseases. Some new trends in the development of new drugs, which have emerged on the basis of expanding knowledge about the functions of ATP in the body, are indicated. Tetranitrosyl iron complexes – NO donors – are a new class of potential anticancer and cardioprotective drugs. Their reactions with ATP, rates and formed products are considered in detail. It is concluded that the interaction of these NO-donor iron complexes with glycolytic macroergic ATP and/or neurotransmitter ATP contributes significantly to the therapeutic effects of these compounds.
Biofizika. 2025;70(3):578-601
578-601
Cycloastragenol Exerts Antiapoptotic Effect on Human Lymphocytes under UV-Irradiation
Abstract
Changes in the level of some markers of apoptosis (lipid asymmetry of plasma membranes, production of reactive oxygen species, nitric oxide, concentration of ionized calcium) of human blood lymphocytes modified by exposure to hydrogen peroxide (10−5 mol/l) and UV light (254 nm, 1510 J/m2) in the presence of cycloastragenol (10−8–10−4 mol/l) were studied. The intensity of apoptotic lymphocyte death processes was found to decrease after UV-light exposure in the presence of cycloastragenol (10−8 mol/l). The cytoprotective effect of cycloastragenol on lymphocytes was found to be due to a decrease in the level of intracellular reactive oxygen species and calcium ions, an increase in the activity of catalase and glutathione reductase and nitric oxide production. Possible mechanisms of cycloastragenol action as a regulator of apoptotic death of lymphocytes induced by UV radiation and hydrogen peroxide exposure are discussed.
Biofizika. 2025;70(3):602–612
602–612
Biochemical Indicator of Isometric Exercises Effectiveness in Early Rehabilitation of Elderly Patients after Hip Arthroplasty
Abstract
Improving the effectiveness of early rehabilitation of elderly patients after hip arthroplasty remains an urgent task. The aim of the study was to evaluate the effectiveness of isometric exercises in early (2 weeks) rehabilitation of elderly patients after hip replacement using blood parameters. The randomized study included 10 elderly patients in the groups of control (n = 5) and experimental (n = 5), supplemented with isometric exercises, rehabilitation techniques performed daily from 1 to 12 days after total cement hip arthroplasty. The effectiveness of rehabilitation was assessed by the indices of muscle traumatization (myoglobin, creatine phosphokinase, aspartate aminotransferase, lactate dehydrogenase concentration) and systemic inflammation (erythrocyte sedimentation rate, CRP concentrations, and interleukins IL-6, IL-8, and IL-1β) in the blood of patients on the 12th day after surgery. The indices of muscle traumatization, concentration of C-reactive protein and leukocytes in blood, as well as erythrocyte sedimentation rate did not reveal any significant difference between the groups of patients. The difference between the control and experimental groups in terms of restoration of interleukin IL-6, IL-8, and IL-1β concentrations in the blood to the normal range was statistically reliable according to Fisher’s exact criterion (p = 0.042). In general, the obtained results showed that additional isometric exercises provided more effective early rehabilitation of elderly patients after endoprosthesis in comparison with the standard set of exercises, and normalization of the concentration of proinflammatory interleukins, primarily IL-6 and IL-8, can be considered as an objective indicator in assessing the effectiveness of methods of early rehabilitation of elderly patients after hip arthroplasty.
Biofizika. 2025;70(3):613–622
613–622
Cronicle
Vadim Ivanovich Bruskov
Biofizika. 2025;70(3):623-624
623-624