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 2 (2025)
Molecular biophysics
Quantum-Chemical Modelling of Adenosine Triphosphate Hydrolysis in Water Medium
Abstract
The hydrolysis of adenosine triphosphate to adenosine diphosphate and orthophosphate has been modeled using the density functional method. Two systems were considered: adenosine triphosphate molecule in aqueous solution and reaction products (adenosine diphosphate, orthophosphate and H+) uniformly surrounded by water (nH2O = 80). Calculations showed that the hydrolysis of adenosine triphosphate is accompanied by a decrease in the total energy of the system, which is consistent with the ideas about the energydonor character of the reaction of adenosine triphosphate hydrolysis to adenosine diphosphate and orthophosphate. In the absence of divalent cations, the energy reduction resulting from the hydrolysis of adenosine triphosphate is ΔE = EADP+Pi − EATP ≈ −110 kJ/mol. Electrostatic interactions due to the presence of divalent cations (Mg2+ or Ca2+) increase the hydrolysis energy (ΔE ≈ −135 kJ/mol). The results obtained are discussed in the context of the energetic role of adenosine triphosphate in biological systems.
Biofizika. 2025;70(2):213-224
213-224
Processes of Thermal Aggregation and Autolysis of Cysteine Protease Molecules – Bromelain, Ficin, and Papain
Abstract
Among plant proteases, cysteine papain-like endopeptidases such as ficin, bromelain and papain occupy an important place due to their high proteolytic activity in the physiological pH range of the medium. The processes of thermal aggregation and autolysis of protease molecules can have a significant influence on their activity and, consequently, on the prospects of practical application. To date, the mechanisms of aggregation of protein molecules are still insufficiently studied, and it is still impossible to predict unambiguously their aggregation stability on the basis of amino acid sequence. In this connection, the aim of this work was to study the processes of thermal aggregation and autolysis of molecules of some cysteine proteases. It was found that despite similar structural and functional properties of ficin, bromelain and papain, their thermal aggregation processes proceed with different intensity. In particular, ficin and bromelain are approximately comparable in terms of their aggregation stability, whereas papain is significantly less susceptible to aggregation processes when exposed to elevated temperatures. It is suggested that the presence and configuration of internal structures of the molecule, such as cavities, tunnels, and pores, as well as the charge properties of its surface have a significant influence on the stability of these cysteine proteases to aggregation processes.
Biofizika. 2025;70(2):225-239
225-239
Spectral and Kinetic Characteristics of Tryptophan Fluorescence in Human and Bovine Serum Albumin at Different Temperatures
Abstract
The temperature dependence of the tryptophan fluorescence lifetime in human and bovine serum albumin in an aqueous solution and glycerol in the temperature range of –170°C to 20°C was studied. A model of forward and reverse electronic transitions in the tryptophan molecule from the excited state to the ground state and to the charge transfer state was constructed. Three main spectral regions of tryptophan fluorescence with different behavior of temperature dependences of transition rates from the excited state of tryptophan to the state with charge transfer were determined. It was found that the dynamics of the hydrogen bonding system in the selected spectral regions had a determining influence on the character of changes in the duration of tryptophan fluorescence. The nonlinear dependence of intramolecular transition rates on temperature found in the work is determined by the interaction of tryptophan molecules with its microenvironment. The rearrangements in the hydrogen bonding system of albumin protein containing tryptophan molecule have a determining influence on the processes of excitation deactivation in tryptophan.
Biofizika. 2025;70(2):240-250
240-250
Photoprotective Properties of Chitosan and Chitosan Succinate Against Trypsin at Different Methods of Enzyme Immobilization on Their Matrix
Abstract
UV irradiation at doses of 3020, 4510, and 6040 J/m2 was found to decrease the level of specific activity of free trypsin by 28, 32, and 49%, respectively. Adsorption immobilization on the matrix of chitosans with molecular masses of 200 and 350 kDa, inclusion of chitosan (<100 kDa) and chitosan succinate in the gel contribute to the preservation of trypsin molecule activity at the level of ~90% and higher. Under UV irradiation in the dose range of up to 6040 J/m2 in the presence of a photosensitizer, methylene blue, at a concentration of 10–4 mol/l, the activity of free trypsin decreases by 72%. After immobilization, the stability of the enzyme complex under the above conditions increases: the activity of trypsin immobilized on the matrix of chitosans with molecular masses of 200 and 300 kDa is maintained at the level of about 75%, after inclusion of the enzyme in the chitosan gel (<100 kDa) – up to ~50%, chitosan succinate – up to ~70%. The molecular docking method revealed that a number of tryptophan, tyrosine and phenylalanine residues, as well as two cystines, take part in the formation of bonds and interactions between the trypsin molecule and the matrices of chitosan and chitosan succinate, which probably predetermines the photoprotective properties of the named polysaccharides. IR spectroscopy showed that after UV irradiation in the presence of methylene blue and without it, no significant changes in the wave number values in the region of the amide I, II and III bands were detected in the spectra of trypsin immobilized on chitosan and chitosan succinate matrices, which indicates that the stability of the enzyme structure in the complexes with the named polysaccharides is maintained.
Biofizika. 2025;70(2):251-264
251-264
Cell biophysics
Regulation of Electron Transport in Chloroplasts: Induction Processes in Tradescantia Leaves
Abstract
The results of a comparative study of electron transport in chloroplasts in situ in leaves of shade-tolerant and light-loving species of tradescantia (T. fluminensis and T. sillamontana) grown under conditions of strong (800–1000 μmol photons m−2s−1) or weak (moderate) illumination (50–125 μmol photons m−2s−1) are described. Electron transport processes were monitored by electron paramagnetic resonance and optical spectroscopy. Photoinduced redox transformations of the primary electron donor of photosystem I (Р700) and slow induction of chlorophyll a fluorescence were studied. It was shown that plants acclimated to high light intensity are characterized by more rapid processes of Р700 oxidation and attenuation of chlorophyll a fluorescence compared to plants grown at low light intensity. The data obtained are analyzed in the context of “short-term” mechanisms of pH-dependent regulation of electron transport in intact chloroplasts (non-photochemical quenching of excitation in photosystem II, retardation of plastoquinol oxidation by cytochrome b6f-complex, and activation of Calvin–Benson cycle reactions).
Biofizika. 2025;70(2):265-277
265-277
Study of the Distribution of Subcellular Structures in Algae Cells Using Optical Laser Tomography
Abstract
Using the developed method of optical laser tomography, the possibility of recording and analyzing the threedimensional distribution of subcellular organelles in eukaryotic algae (C. reinhardtii) was proved. The method allows analyzing the redistribution of subcellular organelles (nucleus, chloroplast) in consecutive slices of one cell in norm and under the influence of modifiers of its functional state. According to the authors, the proposed approach will allow not only to study the dynamics of distribution of intracellular structures (nucleus, thylakoids, mitochondria, etc.), but also changes of a single structure during cell functioning.
Biofizika. 2025;70(2):278-284
278-284
Changes in the Structure and Peroxidase Activity of Cytochrome C in Its Interaction with Phosphatidic Acid
Abstract
A comparative molecular investigation of the action of earlier little-studied phosphatidic acid and well-studied cardiolipin in their interaction with cytochrome C was carried out. Using spectrofluorimetry, close conformational changes in the cytochrome C active center were shown to occur during its interaction not only with cardiolipin, but also with phosphatidic acid. By means of an EPR assay, a significant enhancement of cytochrome C peroxidase activity during its interaction with cardiolipin and phosphatidic acid was demonstrated by formation of etoposide phenoxyl radical and luminol-dependent chemiluminescence. The assay indicated about 30% more pronounced changes in cytochrome C peroxidase activity in the presence of phosphatidic acid as compared to a similar effect of cardiolipin. At the same time, a close to intensity overwhelming recovery of the action of cardiolipin or phosphatidic acid was shown spectrophotometrically by cytochrome C reduction, which decreases by approximately 25% as compared to control phosphatidylcholinecontaining samples. Thus, phosphatidic acid can effectively change the cytochrome C confirmation and peroxidase activity as well effectively, and in peroxidase activity PA even surpasses cardiolipin. The obtained results may signify a high involvement of both cardiolipin and phosphatidic acid in the development of cytochrome С-mediated proapoptotic processes in mitochondria which, in its turn, may lay become foundation for a new direction in regulatory lipidomics.
Biofizika. 2025;70(2):285-294
285-294
Endolysins T5 and PlyG Dynamics: Comparative Analysis in silico
Abstract
Bacteriophage endolysins are part of a lytic enzymes complex responsible for the destruction of the bacterial cell wall peptidoglycan. In this paper, the dynamic properties of bacteriophage T5 single-domain endolysin and the multi-domain endolysin PlyG of gamma phage are studied using molecular dynamics and normal mode analysis. The mechanism of activation of bacteriophage T5 endolysin by calcium and the discovery of a fundamental difference in the dynamic features of single-domain and multi-domain endolysins are explained.
Biofizika. 2025;70(2):295-304
295-304
Effects of Macromolecular Crowding in Erythrocyte Cytoplasm
Abstract
Using Raman spectroscopy, fluorescence spectroscopy, and time-correlated single-photon counting, it was shown that increasing the incubation temperature of human erythrocytes enhances the homogeneity of hemoglobin distribution in the cytoplasm and reduces globin molecule packing density. This likely results from the cellular “macromolecular crowding” effect. Observed conformational changes are specific to intracellular Hb and independent of the plasma membrane surface potential. Multiple pools of hemoglobin with varying structure and dynamics are proposed, they form clusters, creating heterogeneous hemoglobin distribution. The role of these effects in oxygen transport and regulatory signaling is discussed.
Biofizika. 2025;70(2):305-313
305-313
M-Cholinergic Brain Reaction in Dependence on the Environmental Temperature for Cold-Blooded and Warm-Blooded Animals
Abstract
During artificial incubation of slices of the sensorimotor cortex of guinea pigs and the telencephalon of turtles, microionophoretic application of acetylcholine to neurons revealed a significantly lower frequency of spike responses in the nerve cells of turtles compared with guinea pig cells. This difference was attributed to the different rate of M-cholinergic response in the temperature ranges of 27–29°C and 34–36°C, as found previously in hypothermic experiments. Although experiments on guinea pig and turtle neurons were performed in the same temperature range (32–34°C), the genetically determined structure of neuronal membranes reflects the natural temperature dependence of both species: guinea pig membranes with a constant habitat temperature of 38°C have a higher density of К+ channels than turtles with a preferred temperature of 28–32°C. The difference in К+ channel representation was determined by a significantly longer activation aftereffect in turtle neurons in response to glutamate-induced spike activation. The low density of К+ channels on membranes and the low rate of the M-cholinergic response, which closes them at the onset of any adaptive act, prevent neurons from forming high-frequency and long-lasting impulse sequences to regulate behavior over a wide range in turtles with a preferred temperature of 28–32°C.
Biofizika. 2025;70(2):314-327
314-327
Measuring LINE-1 Activity and ATP Amount in Human Cell Cultures
Abstract
DNA demethylation makes closed regions of the genome available for transcription and thus causes increased activity of mobile genetic elements (transposons) in the genome. The study of the influence of abnormal activity of transposons on cell energy attracts attention due to the potential possibility of using this effect to create an energy deficit with subsequent launch of cell death programs, which may be relevant for the development of anti-cancer strategies. The paper presents the results of experimental measurements of the ATP amount in HEK-293 cells obtained from human embryonic kidneys and the MCF-7 breast cancer cell line under normal and demethylation conditions. The HEK-293 line was transfected with a plasmid containing the LINE-1-EGFP genetic construct, and active insertion of the LINE-1 transposon in the transfected cells was shown. Transposon expression in demethylated MCF-7 cells was shown using real-time PCR. The results of ATP measurements demonstrate an increase in energy stores in cells upon both demethylation and transfection with LINE-1-EGFP. The observed effect suggests that the energy load expected from transposon activation is overwhelmed by the energy release from other cellular processes that occur during demethylation and transfection.
Biofizika. 2025;70(2):328-332
328-332
Octacalcium Phosphate Doped with Barium Cations for Application in Tissue Engineering
Abstract
The objective of the study was to investigate the impact of barium cation doping on the phase and structural properties of octacalcium phosphate powder synthesized via a low-temperature method, along with its biocompatibility, particularly under in vitro circumstances that mimic inflammation. It was revealed that doping with Ba2+ cations in the concentration range used (1, 5 and 10 calculated %) does not interfere with the lowtemperature chemical transformation of DPCD and its transformation into OCP, however, the percentage of real substitution is at a maximum of 6.7 at.%. The results of in vitro studies confirm that the substitution of Ca2+ for Ba2+ in the structure of OCP does not affect its cytotoxic properties and all the studied variants of low-temperature OCP and its Ba-substituted variants at the recommended concentration of 1 mg/ml do not have a cytotoxic effect and are biocompatible. The effects revealed for OCP-Ba10, namely the absence of an effect on the content of lysosomes and ROS in human macrophages under normal conditions and a significant decrease in ROS production under inflammatory conditions, as well as a significant increase in the constitutive activation of T-lymphocytes, indicate that these processes are directly and dose-dependently associated with Ba2+ cations in the composition of OCP. The proposed approach of low-temperature chemical transformation of Ba2+-substituted variants of OCP is promising and is of interest for obtaining CPC materials with specified properties. The obtained Ba2+-substituted variants of OCP are safe and biocompatible, and the most effective variant of OCP with a maximum degree of Ca2+ substitution by Ba2+ 10% (OCP-Ba10) is bioactive and has potential antioxidant and immunomodulatory effects.
Biofizika. 2025;70(2):333-346
333-346
Complex systems biophysics
Effect of Vernalization on the Expression of Flowering Time Genes in Chickpea
Abstract
Vernalization, or prolonged exposure to cold, significantly accelerates flowering and increases yields in many crops. The mechanisms of the effect of vernalization on the transition to flowering are well studied in the model organism Arabidopsis thaliana, but have not yet been uncovered in legumes. We examined the effect of vernalization on flowering gene expression in one of the most important legumes, chickpea. The response to vernalization is characteristic of wild chickpea species, while this property is largely lost in the cultivated varieties. We compared expression of orthologs of the main Arabidopsis flowering regulators in wild and cultivated chickpea with and without vernalization. The expression levels of FTa1 and FTa3 gene products increased significantly after vernalization, regardless of species. At the same time, the response to vernalization of FT-activated genes differed between cultivated and wild chickpea, suggesting different regulatory mechanisms in the gene network.
Biofizika. 2025;70(2):347-353
347-353
Purinergic Modulation of Ocular Muscle Contraction
Abstract
The problem of purinergic regulation in synapses of phasic and tonic muscles of warm-blooded animals was investigated. For this purpose, the effect of the cotransmitter of the main mediator, ATP, and its persistent metabolite, adenosine, on the contraction of various oculomotor systems of the rat, the lateral rectus (tonic) and circular (phasic) muscles of the eye, was evaluated. ATP potentiated the carbacholine-evoked contraction of the rat lateral rectus muscle by a quarter, while this purine, on the contrary, significantly inhibited the carbacholine-evoked contraction of the circular eye muscle. No significant manifestation of the modulatory effect of adenosine on the carbacholine-evoked contraction of the muscles under study was revealed. The results obtained indicate a multidirectional postsynaptic effect of ATP on phasic and tonic oculomotor systems.
Biofizika. 2025;70(2):354-358
354-358
Simplified Model of Skeletal Muscle Contraction Dynamics
Abstract
The skeletal muscle contraction model as a complex of active motor units (sarcomeres) is discussed. The sarcomere model takes into account that forces are generated by myosin bridges interacting with actin filaments in muscle myofibrils. The input of the model is the rate of calcium ion influx into muscle cells, which is assumed to be proportional to the motor neurons potential. The description of the muscle force as a whole uses averaging over an ensemble of motor units. The parameters of the model are adapted to describe contraction of a skeletal muscle sarcomere. The transition from contraction of a single sarcomere to slow contraction of the whole muscle is constructed using motion separation methods. The model of “slow” contraction of a single muscle fiber excited by a single nerve impulse has no independent value because the characteristic time of change of the impulse potential is short. Nevertheless, for description of tetanic muscle contraction, when the change in the total action on the muscle is smooth enough, it seems acceptable to use such an approximate model. Approximate numerical estimates of the error of the constructed model for a simplified example are given.
Biofizika. 2025;70(2):359-373
359-373
The Effectiveness of Biomedical and Other Applications by the Utilization of Gold Nanoparticles Manufactured Utilizing an Environmentally Safe Method: A Review
Abstract
This review will examine recent studies on the utilization of gold nanoparticles produced through the environmentally friendly green synthesis method. These nanoparticles are derived from extracts of plants with medicinal significance, such as leaves, peels, or seeds, and are subsequently loaded onto gold nanoparticles or other types of nanoparticles. The studies referenced in this review are sourced from reputable platforms including Google Scholar, ResearchGate, PubMed, and Scopus. We will ascertain whether these research have demonstrated the presence of nanoparticle-induced impacts on tissues. Multiple studies have consistently demonstrated that the toxicity of gold nanoparticles produced using environmentally sustainable methods is minimal. To mitigate environmental risks, it is imperative to prioritize the development of eco-friendly methods for synthesizing nanomaterials. Consequently, researchers are exploring green synthesis methods to address the gaps and alleviate the challenges. Biological synthesis processes are economically efficient, nontoxic, comparatively uncomplicated, and environmentally benign. The green synthesis process involves obtaining biological compounds from plant extracts, bacteria, and algae. The capacity to manipulate the morphological characteristics (such as size, form, and crystalline structure) of AuNPs during their creation plays a significant role in several sectors of application. Biological molecules derived from plants are appropriate for synthesizing metal nanoparticles. Numerous studies have demonstrated the potential of utilizing nanoparticles, including gold and other types, to administer treatment with minimal impact on healthy tissues. Additionally, these nanoparticles possess the capability to repair damage.
Biofizika. 2025;70(2):374-389
374-389
Magnetic Biological Effect: Quantum Constraints
Abstract
The spin-chemical mechanism of radical pairs is considered today as the most probable molecular mechanism explaining the observed biological effects of weak magnetic fields. The magnitude of these effects depends on the spin relaxation rate, but no explicit functional relationship has been proposed yet. In the present work, an analytical solution of the Liouville−Neumann equation for a system of two electrons and a nucleus has been found taking into account spin relaxation and chemical kinetics. A relation has been obtained linking the magnitude of the magnetic response with the rate of relaxation due to thermal fluctuations. This effect obeys a general quantum constraint. At plausible relaxation rates, the calculated effects are small and cannot explain the observations. It can be concluded that today, despite the attractiveness of the radical pair mechanism and the increased theoretical understanding, the problem of magnetobiology still lacks a coherent conceptual solution.
Biofizika. 2025;70(2):390-397
390-397
Medical biophysics
Evaluation of the Effect of Riboxin, Copper Chlorophyllin, Indralin and Combined Application of Glutathione and Ascorbic Acid on the Degree of DNA Damage in the Spleen of Mice under Fractionated Irradiation
Abstract
Using alkaline gel electrophoresis of single cells of the spleen of male ICR (CD-1) mice exposed to five daily exposures to X-ray radiation at a dose of 1.4 Gy, DNA damage was studied on the day of the last irradiation against application of riboxin, or inosine (200 μg/g), copper chlorophyllin (20 μg/g), indralin (50 μg/g) and antioxidants: glutathione (350 μg/g) and ascorbic acid (150 μg/g) together. The 30-day survival of groups of 10 mice was evaluated in parallel.The level of DNA damage when using indralin and riboxin did not differ significantly from the intact mice. However, 1 mouse each from the riboxin and antioxidant groups died to evaluate survival. There were no deaths of mice from other groups, including the irradiated control. The use of antioxidants protected DNA to a small extent. Copper chlorophyllin did not protect DNA compared to the irradiated controls.
Biofizika. 2025;70(2):398-403
398-403
Influence of Smoking on the State of the Thiol-Disulphide System in Blood Plasma and the Frequency of TCR-Mutant Lymphocytes in Healthy Individuals and Cancer Patients
Abstract
A comparative study of indicators of somatic mutagenesis and the thiol-disulfide system in the peripheral blood of cancer patients before treatment and healthy individuals with different smoking status (n = 95) was carried out. All studied parameters including the content of reduced (GSH), oxidized (GSSG) glutathione and their ratio (GSH/GSSG), the frequency of lymphocytes with mutations at T-cell receptor (TCR) locus were found to be significantly increased by 1.5–2.7 times in the general group of patients as compared to those in the general group of healthy individuals (p < 0.01 in all cases). After smoking cessation, a decrease in the frequency of mutant cells and the ratio of reduced and oxidized glutathione was observed in patients (p < 0.05). At the individual level, strong correlations were found between the frequency of TCR-mutant cells and the content of GSH and GSSG only in the subgroup of smoking patients with a high level of mutagenesis. Thus, the correlation coefficient between the frequency of TCR-mutant lymphocytes and the GSH content in this subgroup was 0.82 (p < 0.001), for GSSG – r = 0.68 (p < 0.01). The results obtained indicate the contribution of the thiol disulfide system to the formation of a high frequency of gene mutations in a part of smokers with cancer.
Biofizika. 2025;70(2):404-416
404-416