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Vol 64, No 1 (2019)

Molecular Biophysics

An Adiabatic Calorimetry Method to Determine the Thermodynamic Characteristics of Cryoprotectants

Simonenko E.Y., Pryadun V.V., Ivanova A.A., Burmistrova E.V., Vasiliev A.N., Yakovenko S.A.

Abstract

Abstract—The efficiency of cryoprotectants used to protect cells from damage is usually evaluated by the changes in vital cell parameters after a freezing–thawing cycle. Certain physical parameters, such as the glass transition temperature, viscosity, toxicity, and the minimum concentration necessary for vitrification, are known for several components of cryoprotectants. However, it is impossible to provide physicochemical characteristics for a medium that contains both penetrating and nonpenetrating cryoprotective agents. An adiabatic calorimetry method adapted to studying liquid media was used to describe the temperature dependence of the heat capacity and to find the temperatures of the phase transition and changes in the state of aggregation for a glycerol-containing solution, which is commonly used as a basic component of cryoprotectants, and for a commercial cryoprotectant. Changes in entropy and enthalpy in the commercial cryoprotectant were 1.5 times higher than in aqueous solutions of glycerol.

Biophysics. 2019;64(1):1-6
pages 1-6 views

The Effect of Environmental Electromagnetic Radiation on Associate Formation in Aqueous Solutions

Avakyan S.V., Baranova L.A.

Abstract

Abstract—We present the results of studies of the nature of the features known in modern biophysics in the manifestation of the associative properties of aqueous solutions of biologically active substances. The phenomena observed during associate formation can be related with the effect of microwaves, primarily, of ionospheric origin. We take the results into account of earlier quantitative quantum mechanical analysis of the physical mechanism of formation of cluster associates in a liquid aqueous medium with the participation of water molecules, due to their high affinity for the proton. Comparison of the developed ideas and the experiments on electromagnetic shielding of biological solutions diluted to various degrees confirms the reality of the proposed relation of the phenomena in biological media with microwave radiation.

Biophysics. 2019;64(1):7-13
pages 7-13 views

The Relationship between Crystallization of Water Clusters Dispersed in Sephadex Resins in their Wet Form and the Polymeric Matrix Glass Transition Temperature

Tseretely G.I., Belopolskaya T.V., Grunina N.A., Smirnova O.I.

Abstract

Abstract—Differential scanning calorimetry (DSC) analysis was used to study the dependences of the main parameters of crystallization and melting of small water clusters dispersed in Sephadex resins on the amount of water (30–55%) in the wet polymer. The temperatures and heats of the processes were shown to depend on the frozen water (FW) concentration in Sephadex, with the dependence being considered as a manifestation of the size effect. Hysteresis between FW melting and crystallization was detected in a certain Sephadex humidity range; i.e., Tm was higher than Tcr and Qm higher than Qcr. The two findings reflected the basic properties of low-dimensional systems. Sephadex and amorphous starch, which was examined previously, were compared as two polysaccharide systems with different structural organizations, and a significant difference was observed in FW crystallization in the systems. Nucleation and crystallite growth, which determine water crystallization, were found to occur separately in time in Sephadex with a low humidity under these experimental conditions. Nucleation occurred during cooling, while growth was observed mainly during heating. Both of the processes occurred during cooling and partly overlapped only at a high humidity, far from Tg of Sephadex. In contrast, the two processes always occurred during cooling in amorphous starch regardless of its humidity. The difference in FW crystallization was assumed to arise because water mobility differs between the systems as a result of their difference in molecular mobility of the biopolymer matrix proper near the glass transition region.

Biophysics. 2019;64(1):14-22
pages 14-22 views

The Effect of Gold Nanoparticle Surface Modification with Polyethylene Glycol on the Absorbed Dose Distribution upon Irradiation with 137Cs and 60Co Photons

Belousov A.V., Morozov V.N., Krusanov G.A., Kolyvanova M.A., Shtil A.A.

Abstract

Abstract—Modification of the surface of gold nanoparticles with polyethylene glycol (PEG) is widely used to investigate radiosensitization in vivo. This modification may lead to alterations in the spectral characteristics of secondary radiation emitted by gold nanoparticles under the influence of photons. Using a Monte-Carlo calculation, we found that upon irradiation of 17-nm gold nanoparticles coated with a 8.5-nm polyethylene glycol shell with 137Cs (Eav = 0.667 MeV) and 60Co (Eav = 1.25 MeV) photons, 53.9% (137Cs) and 51.3% (60Co) of ionization electrons (Auger, Coster–Kronig, and fluorescence), 7.1% (137Cs) and 0.9% (60Co) of the photoelectrons were absorbed, and 32.6% (137Cs) and 27.4% (60Co) of the Compton electrons; as well 0.4% (137Cs) and 9.7% (60Co) of the secondary photons were additionally generated in the polymer shell. The surface modification with polyethylene glycol led to shielding of the high-absorption dose area: the ratio of the absorbed doses for the unmodified and polyethylene glycol-coated gold nanoparticles differed by 1.3–9 times. Since the radiosensitizing efficacy of gold nanoparticles depends on the characteristics of the secondary radiation, the optimization of surface coatings is an important step in rational drug design.

Biophysics. 2019;64(1):23-30
pages 23-30 views

The Search for Ways to Improve the Catalytic Activity of Encapsulated Horseradish Peroxidase

Fomkina M., Minkabirova G., Montrel A., Ibadullaeva S.

Abstract

Abstract—We consider a previously proposed method for encapsulation of enzymes, which employs the layer-by-layer adsorption of oppositely charged polyelectrolytes onto composite spherulites (calcium carbonate/protein) followed by dissolution of the calcium carbonate support. The goal of this work is to choose conditions for encapsulation of the enzyme horseradish peroxidase by the method so that the catalytic activity of the encapsulated enzyme would be comparable with that of the soluble one. The steps of the fabrication of polyelectrolyte microcapsules with the studied enzyme have been tested. A protocol for obtaining composite spherulites of the desired size ranging from 2 to 10 µm has been developed. It is shown that the catalytic activity of horseradish peroxidase encapsulated in a microcapsule with a positively charged inner surface of the microcapsule envelope (the inner layer modified by polycation polyallylamine hydrochloride) is significantly higher than that of the enzyme encapsulated in a microcapsule with a negatively charged inner layer (modified by polyanion sodium polystyrene sulfonate). At the support dissolution step, ethylene glycol bis-(β-aminoethyl) tetraacetic acid (EGTA), a decalcifying agent used to dissolve CaCO3 from horseradish peroxidase microcapsules, is significantly less detrimental to enzymes than ethylene diamine tetraacetic acid. The catalytic activity of horseradish peroxidase encapsulated in polyallylamine hydrochloride/sodium polystyrene sulfonate/polyallylamine hydrochloride microcapsules (with positively charged inner surface of the microcapsule envelope) is 60–70% of the activity of the soluble enzyme (in experiments where the calcium-carbonate support of the composite spherulites is dissolved with EGTA).

Biophysics. 2019;64(1):31-37
pages 31-37 views

SASCUBE: An Updated Method of Cubes for Calculation of the Intensity of X-Ray Scattering by Biopolymers in Solution

Fedorov B.A., Smirnov A.V., Yaroshenko V.V., Porozov Y.B.

Abstract

Abstract—This work describes an updated method of cubes, which allows calculation of the SAS curves for biopolymers in solution on the basis of the coordinates of their atoms without introducing any fitting parameters. The efficiency of the method was checked on a number of model systems. For eight globular proteins, the scattering intensities that were calculated using the SASCUBE software (https://sourceforge.net/projects/sascube) were compared with the corresponding experimental curves. This work addresses the contentious issue of the nature of distortions of the electron density of water near a protein surface. Molecular dynamics simulations were used to show that the electron density distribution of water in a 0.3-nm thick near-border protein layer could not be considered uniform, while its mean value could be less than the average electron density of water. It was shown that the conformational mobility significantly influenced the scattering curve of proteins. The possibility of using the method of cubes (SASCUBE software) in combination with molecular dynamics is discussed in order to find the intensities of protein scattering taking all the factors that influence the scattering curve into account (conformational mobility of proteins, distortions of water structures, etc.).

Biophysics. 2019;64(1):38-48
pages 38-48 views

The Topology of the Contacts of Potential Ligands for the UxuR Transcription Factor of Escherichia coli as Revealed by Flexible Molecular Docking

Purtov Y.A., Tutukina M.N., Nikulin A.D., Ozoline O.N.

Abstract

UxuR is a transcription factor that controls the expression of genes involved in hexuronate utilization. Its ability to bind to the promoters of regulated genes is dependent on sugar ligands. Two regions of the preferred interaction with D-glucuronate and D-galacturonate were found on the surface of the UxuR monomer earlier, one of which was located in the flexible linker connecting the N- and C-terminal domains of the protein. Binding of a ligand in this region may change the mutual orientation of the domains, thereby affecting the interaction of UxuR with DNA. The second binding region was found within the pocket of the C-terminal domain from where the regulatory effect may be explained either by conformational changes in the domain, or by influence of sugar ligands on the protein dimerization. Here, a 3D-model of the UxuR dimer was obtained and molecular docking of a range of sugars on its surface was performed. Additional platform for carbohydrate binding was found in the junction of the two C-terminal domains in the UxuR dimer. Interdomain linkers were occupied by different sugars including those that were able to penetrate into the pockets of the C-terminal domains from the side of interdomain space. Potentially, this allows transposing regulatory signal derived from the pocket loading into the conformation transition that changes mutual orientation of the domains.

Biophysics. 2019;64(1):49-56
pages 49-56 views

Cell Biophysics

The Role of Erythrocyte Receptors in Regulation of the Conformation and Distribution of Hemoglobin

Maksimov G.V., Slatinskaya O.V., Tkhor E.S., Anisimov N.A., Mamaeva S.N., Shutova V.V.

Abstract

Abstract—Using Raman spectroscopy, atomic force microscopy, and laser interferometry we found that variations in insulin-like growth factor (IGF-1) and purinergic compounds such as ATP in the blood influence the hemoglobin distribution and hematoporhyrin conformation in hemoglobin in erythrocytes. Our results suggest that receptor activation promotes changes in conformation of cytoskeletal protein molecules and hemoglobin.

Biophysics. 2019;64(1):57-61
pages 57-61 views

The Effect of Mobile Phone Radiation on in vitro Platelet Aggregation in Patients with Polycythemia Vera and Ischemic Stroke

Olkhovskiy I., Stolyar M., Lagutinskaya D., Zakhvataev V., Khlebopros R.

Abstract

Abstract—The influence of exposure to mobile phone radiation on in vitro platelet aggregation has been studied. It has been shown that a 30-min exposure of blood samples to mobile phone radio frequency waves increases ADP-induced platelet aggregation in groups of healthy volunteers and patients with stroke, whereas platelet aggregation in JAKV617F-positive patients with polycythemia vera is significantly suppressed and is eventually completely inhibited. The mechanisms that underlie this phenomenon may be associated with cell oxidative stress and anomalies the JAK2 signal transduction pathway in malignized blood cells. The results indicate that it is important to set safety standards for the use of mobile devices by patients with various diseases.

Biophysics. 2019;64(1):62-66
pages 62-66 views

Changes in the Dendrite Morphology of Mauthner Neurons in Goldfish under the Conditions of Monocular Deprivation and Sensory Stimulation

Mikhailova G.Z., Shtanchaev R.S., Bezgina E.N., Kashirskaya N.N., Pen’kova N.A., Tiras N.R.

Abstract

Abstract—The effects of sensory stimulation on the model of paired Mauthner neurons of monocularly deprived goldfish have been studied by light- and electron microscopy. Three-dimensional reconstruction was performed using serial semi-thin sections in order to determine the volumes of soma and dendrites for the right and left Mauthner neurons. These data suggested that long-term stimulation of some fish caused a decrease in the volume of the lateral dendrites of neurons contralateral with respect to the side of the enucleated eye. As a result, the morphological homeostasis in the dendrites of Mauthner neurons, which was observed in the control fish, was disturbed after the effect of stimulation upon this group of fish. The main mechanism of this effect of stimulation, according to ultrastructural analysis, is the compaction of the cytoskeleton in the lateral dendrite of a neuron and a reduction in the number of synaptic vesicles in the region of afferent synapses. In contrast, stimulation of the remaining fish induced the resistance of the contralateral Mauthner neuron to prolonged stimulation, as well as the hypertrophy of its lateral and shortening of the ventral dendrites. These results suggest that the homeostasis of the dendrites of Mauthner neurons essentially depends on the state of the visual inputs, the load on which increased as a result of the doubled impact.

Biophysics. 2019;64(1):67-74
pages 67-74 views

Internal Hydrodynamics in the Cytoplasm of Normal and Cancer Cells; a Principle of Live Tissue Engineering from the Cells: Hypotheses, Physical and Mathematical Models; Approximate Calculation of the Frequency Characteristics of the Cell

Koltcova N.A.

Abstract

Abstract—A proposed model of internal hydrodynamics of the cells of the body is considered. Extracellular fluid flows around the cell elements under the regular action of the osmotic “pump.” The flow around the nucleus of the cell is considered without taking the flow around its other elements into account. This flow is similar to a viscous stationary flow around a sphere at small values of the Reynolds number (the Stokes theorem). Two types of the mechanism of such a flow are suggested: a uniform flow around and a shear flow around. In the first case, a vorticity occurs behind the nucleus, the distribution of which is determined by solving the Stokes theorem. In the second case, in addition to vorticity, there is a vortex flow around the nucleus. In a cancer cell, the internal movement of the cytoplasm is absent, the metabolism is almost stopped, which corresponds to the transition of the cell in such conditions to continuous division. When a normal cell divides (mitosis), the newly formed cells have a distribution of vortex flow around the nucleus, which is opposite to the original vortex flow in the parent cells; this allows the cells to be at a close constant distance to each other and to form tissue in the future. Such a mechanism makes it possible to create further organic connections between the cells of the tissue. There may be a movement of the cytoplasm to the nucleus in the cell under the influence of electrostatic forces formed between the elements of the negatively charged cytoplasm and the positively charged nucleus. The reasons for the “failure” of the normal activity of the cell and its transformation into a cancer cell are discussed.

Biophysics. 2019;64(1):75-82
pages 75-82 views

Mitochondrial Lipofuscin and Thermomitochondrial Lipofuscin in Homogenates of Rat Organs

Chaplygina A.V., Vekshin N.L.

Abstract

Abstract—The amounts of lipofuscin (age pigment) were compared in four organs of rats: the liver, the kidney, the heart muscle, and the brain, as well as in a suspension of ghosts of hepatic mitochondria. It was shown that liver lipofuscin, which absorbs UV light at 360 nm and fluoresces at 460 nm, is predominantly formed due to mitochondrial processes. The lowest lipofuscin content was observed in the heart muscle; in the other organs studied, the levels of lipofuscin calculated per mg of protein were approximately the same. The spectral data and the lifetime of the excited state suggest that a considerable contribution to the fluorescence of lipofuscin in various organs belongs to mitochondrial lipofuscin. Along with lipofuscin, a fluorescent pigment, all organs were shown to contain non-fluorescent protein aggregates: their level was the highest in the heart muscle and the lowest in the liver. Among them, a significant portion were covalently cross-linked aggregates that were not destroyed by detergent treatment. Moderate heating of the organ homogenates caused the formation of thermolipofuscin. The level of thermolipofuscin production was the highest in the brain and the lowest in the heart. Apparently, a significant portion of the thermolipofuscin that formed in organ homogenates was thermomitochondrial lipofuscin from the membranes of damaged mitochondria. The formation of thermolipofuscin strongly involved aromatic residues: tyrosine and tryptophan.

Biophysics. 2019;64(1):83-88
pages 83-88 views

Complex Systems Biophysics

The Biological Effect of Dinitrosyl Iron Complexes with Glutathione upon Nitric Oxide Hyperproduction Induced by Endotoxin Shock

Timoshin A.A., Lakomkin V.L., Abramov A.A., Vanin A.F., Ruuge E.K.

Abstract

Abstract—The objective of this work was to study the biological effect of dinitrosyl iron complexes (DNICs) with the glutathione ligand (GSH−DNICs) as a stabilized form of nitric oxide in a rat model of nitric oxide hyperproduction induced by inflammation. Administration of GSH−DNICs in endotoxin shock did not increase the total nitric oxide levels in rat organs, but exerted a protective effect by suppressing nitric oxide hyperproduction in the liver and led to an accumulation of the complexes with protein ligands in the kidney.

Biophysics. 2019;64(1):89-94
pages 89-94 views

Time-Resolved Tryptophan Fluorescence as an Indicator of Alterations in Serum Proteins in Melancholic Depression

Syrejshchikova T.I., Smolina N.V., Brilliantova V.V., Syromyatnikova E.D., Uzbekov M.G., Dobretsov G.E.

Abstract

Abstract—The goal of this work was to search for blood serum parameters that would be associated with the state of patients with mental disorders. Such indicators are needed for an objective assessment of this state versus the prevailing subjective evaluation methodologies. The kinetics of tryptophan fluorescence decay in the serum albumin fraction was compared in patients with melancholic depression (before treatment) and in healthy volunteers. Albumin fluorescence is mainly due to the tryptophan 214 residue, which is located in the immediate vicinity of the first drug-binding center of the molecule. The decay kinetics were described as a sum of three exponential functions with lifetimes τi (in the 6.5, 2.8 and 1.0 ns region) and the amplitudes Ai. The τi values were similar in both groups of individuals. In contrast, there was a significant difference between patients and controls in the A1/A3 amplitude ratio. It is suggested that the A1/A3 value can be considered as a potential marker indicating the presence or absence of melancholic depression in patients before treatment.

Biophysics. 2019;64(1):95-99
pages 95-99 views

Nature Reduces the Energy Costs of Water Flow in the Capillary System of Plants and Blood Vessels of Animals

Khodakov G.S.

Abstract

Abstract—Nature is known to minimize the energy costs of water flow in the vascular bundles of plants and the blood vessels of animals. However, until recently, the mechanisms of this phenomenon remained unknown. The superfluidity of aqueous solutions that was recently discovered made it possible to develop a scientific basis and overcome many problems concerning this phenomenon. Vascular systems, which carry vital biological fluids, penetrate literally through all of the plants and animals on Earth. A variety of minerals are dissolved in soil water and blood plasma, which results in electrically charged conducting systems. All this enables manifestation of superfluidity in vascular systems of plants and animals. Superfluidity is an equivalent of viscosity reduction in fluids to values that are much lower than it can be expected.

Biophysics. 2019;64(1):100-108
pages 100-108 views

The Influence of Weak Geomagnetic Disturbances on the Rat Cardiovascular System under Natural and Shielded Geomagnetic Field Conditions

Kuzmenko N.V., Shchegolev B.F., Pliss M.G., Tsyrlin V.A.

Abstract

Abstract—This work was aimed at studying the effects of weak geomagnetic disturbances on systolic blood pressure, the R–R interval, the low-frequency and high-frequency components, and its ratio of heart rate variability spectrum under natural and shielded geomagnetic field conditions. All tests were performed with male Wistar rats placed in simulation and shielded chambers. In the simulation chamber, significant shifts in the parameters under study were observed on the days of geomagnetic disturbances: an increase in systolic blood pressure, as well as in the ratio of low- to high frequency components of the heart rate variability spectrum. In the shielded chamber, the parameters were not considerably different under quiet and disturbed geomagnetic field. In addition, in the stimulation chamber, the value of the mean daily barometric pressure was inversely correlated with systolic blood pressure; this relationship was significantly weakened under shielded geomagnetic field conditions. It was concluded that weak geomagnetic disturbances affect cardiovascular and autonomic nervous system functions. The authors hypothesize that the enhanced effect of a slight decrease in barometric pressure on systolic blood pressure in the natural geomagnetic field could be associated with the effect of geomagnetic activity on the mechanisms of blood oxygenation.

Biophysics. 2019;64(1):109-116
pages 109-116 views

The Impact of Stochastic Perturbations upon the Hydrodynamic Relationship between the Activity of Human Cardiac Ventricles and Low-Frequency Blood Flow Oscillations in the Microcirculatory Bed

Grinevich A.A., Tankanag A.V., Chemeris N.K.

Abstract

Abstract—The experimentally revealed high phase coherence between low-frequency oscillations in the cutaneous blood perfusion signal at the contralateral skin sites indicates the existence of a central mechanism of its regulation. The vascular bed can be such a regulatory mechanism because it is a closed hydrodynamic system. It has been shown in this study using a mathematical model of the human cardiovascular system that the impact of low-intensity stochastic perturbations on the stiffness of the cardiac ventricles leads to the formation of low-frequency oscillations in microvascular blood flow. The results show that there is a relationship between the activity of the heart and low-frequency oscillations of microcirculatory skin blood flow, which is due to the hydrodynamic properties of the vascular bed without the involvement of autonomous control from autonomic nervous system.

Biophysics. 2019;64(1):117-128
pages 117-128 views

Modeling the Main Physical Processes in Beehives

Oskin S.V., Ovsyannikov D.A.

Abstract

Abstract—A winter bee community of 15 000 bees housed in wooden beehive boxes with 12 frames was used to analyze the physical processes that occur in beehives. The most important specific feature of this study is assessment of the changes in the size of the bee cluster during overwintering and the relationship between temperature, humidity, and air flows in the beehive. The physical processes in hives were simulated using the Comsol 5.3 software package. The temperature fields confirm the high heat insulating ability of bees. The temperature on the external surface of winter cluster was +12°C. Despite the changes in the temperature outside the cluster, the temperature inside it was stably maintained at +25 to +32°C. The inside temperature of the winter cluster was nonuniform, with some local foci of up to but not exceeding +34°C, which is safe for the bees. Analysis of the air flows showed a velocity of 0.03–0.1 m/s at the entrance to the hive and of 0.12–0.17 m/s at the central opening. The highest velocity was recorded inside the cluster (over 0.19 m/s). The moisture distribution in the hive was as follows: the moisture content in the incoming air was 0.04 mol/m3 and in the outgoing air it was 0.5–0.6 mol/m3, which is explainable by elimination of the moistened air from the bee cluster. The images of the moisture distribution in hive elements prove the agreement between the saturation rate of wooden walls and the humidity of the boundary air.

Biophysics. 2019;64(1):129-136
pages 129-136 views

A Multiparametric Equation for Calculation of the Animal Lifespan

Vekshin N.L., Frolova M.S.

Abstract

Abstract—We propose a multiparametric equation for calculation of the average natural lifespan of various vertebrate species, including well-known mammalian “outliers,” such as the naked mole rat and bat. This equation includes body and brain weights; durations of puberty, sleep, and hibernation; daily food intake; oxygen consumption; and body temperature. We infer that aging is the result of protein and DNA damage that accumulate during animal life cycles rather than a genetic program that underlies phenoptosis.

Biophysics. 2019;64(1):137-142
pages 137-142 views

Letters to the Edition

Organization of Mobile Flowering Signals in ICCV 96029 Chickpea Cultivar

Gursky V.V., Kozlov K.N., Nuzhdin S.V., Samsonova M.G.

Abstract

ICCV 96029 is the earliest flowering chickpea cultivar. We analyzed the model of the gene network controlling floral transition and hypothesized that this chickpea cultivar is significantly different from other legumes in organization of mobile flowering signals related to the expression of the FT (FLOWERING LOCUS T) gene paralogs. Unlike pea and other legumes, that according to previously obtained data could demonstrate cross-regulation between FT-like genes and different nature of the associated flowering signals, the simulation results for chickpea suggest that the FT paralogs play additive roles in the promotion of flowering.

Biophysics. 2019;64(1):143-144
pages 143-144 views