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Volume 63, Nº 4 (2018)

Molecular Biophysics

Energy Landscapes of Macromolecules with Unique 3D Structures

Shaitan K.

Resumo

Abstract—A paradox of the convergence of the potential energy surface (PES) presented as a sum of pairwise interactions was formulated. Regularities of the formation of a multidimensional PES in the space of torsion (dihedral) angles were considered for the case of the macromolecules that form unique 3D structures. The presence of a single global minimum on the PES was shown to be impossible for nonchiral macromolecules. The chirality of the spatial structure of a macromolecule creates conditions for the formation of a single global minimum on the PES. The structure was studied for a model PES such that components of the multidimensional Fourier series exponentially damped with the increasing number of harmonics. It was proposed to describe the interaction between conformational degrees of freedom in the space of torsion angles by assigning distribution functions to linear combinations of harmonic numbers. A mathematical tool was developed for this purpose. The structure of the PES was studied for the cases of the Gaussian and Lorentzian distribution functions for the linear combinations of the Fourier series harmonic numbers. It was shown that the properties of such a PES can be described by introducing two generalized variables. A feature of the PES is the existence of a central funnel, which leads to a global energy minimum, and satellite funnels, which acts as traps during the folding process. Relatively rapid folding events (the achievement of the global energy minimum) may take place in the configuration space region that corresponds to the central funnel. This structure of the PES makes it possible to identify the configuration space areas that are important for the folding and to understand the basic difference between reversible (in solution) and irreversible (using an atomic force microscope) unfolding of unique 3D structures of biopolymers.

Biophysics. 2018;63(4):485-496
pages 485-496 views

The Effect of Single Deuterium Substitutions for Protium in a DNA Molecule on the Occurrence of Open States

Dzhimak S., Svidlov A., Basov A., Baryshev M., Drobotenko M.

Resumo

The data obtained by mathematical modeling of the occurrence of open states between nitrogenous bases in a D. melanogaster gene where a protium atom is replaced by deuterium are presented. It was shown that in the physiological range of deuterium concentrations substitution of deuterium for protium increases the probability of hydrogen-bond disruption between complementary bases by 0.22–0.60%. This result suggests that deuterium can decelerate the transcriptional reading of genetic information. At the same time, under conditions that weaken the hydrogen bonds between the strands of a DNA molecule, replacement of protium with deuterium facilitates the formation of open states, increasing the probability of base modification induced by damaging environmental factors.

Biophysics. 2018;63(4):497-500
pages 497-500 views

The Conformation of Chitosan Molecules in Aqueous Solutions

Davydova V., Yermak I.

Resumo

This paper presents a review focused on the study of the physicochemical properties of chitosans. The main attention is paid to the analysis of data on the conformation of the polymer molecules in aqueous solutions depending on the molecular weight and degree of N-acetylation of chitosan, as well as on external factors, such as the nature of the solvent, the pH, and the ionic strength of the solutions.

Biophysics. 2018;63(4):501-511
pages 501-511 views

Generation of Active Carboxyl Groups on the Surface of a Polyethylene Terephthalate Film and Their Quantitation by Digital Fluorescence Microscopy

Miftakhov R., Lapa S., Shershov V., Zasedateleva O., Guseinov T., Spitsyn M., Kuznetsova V., Mamaev D., Lysov Y., Barsky V., Timofeev E., Zasedatelev A., Chudinov A.

Resumo

A method to estimate the concentration of chemically accessible carboxylic groups on the surface of a polyethylene terephthalate (PET) film was developed using the fluorochrome cycanine Cy5 and digital fluorescence microscopy. A method was developed to activate the carboxylic groups on the PET surface and to allow covalent immobilization of amino group-containing molecular constructs.

Biophysics. 2018;63(4):512-518
pages 512-518 views

Properties of Bacterial Cellulose Composites with Silver Nanoparticles

Shidlovskiy I., Shumilova A., Shishatskaya E., Volova T.

Resumo

Composites of bacterial cellulose, which were synthesized in a culture of the strain of acetic acid bacteria Komagataeibacter xylinus VKPM B-12068, with silver nanoparticles were produced hydrothermally by varying the concentrations of AgNO3 in the medium. The presence of silver in the composites was confirmed by elemental analysis. An increase in the number of silver nanoparticles in the composite from 1.08 to 9.1 wt % (from 0.044 to 0.370 mg/cm2) was shown under increasing AgNO3 concentration in the medium from 0.0001 to 0.01 M. The structure, properties of the surface, and the physicochemical properties of the composites depending on the silver content were investigated using scanning electron microscopy, differential scanning calorimetry, X-ray diffraction, and a water contact-angle measurement system. Using the disk-diffusion method, it was shown that the resulting composites have a pronounced antibacterial activity against pathogenic microflora E. coli, Ps. eruginosa, and St. aureus.

Biophysics. 2018;63(4):519-525
pages 519-525 views

Cell Biophysics

The Kinetics of Thermal Denaturation of Acetylcholinesterase of the Rat Red Blood Cell Membrane during Moderate Hypothermia

Klichkhanov N., Dzhafarova A.

Resumo

The thermostability of acetylcholinesterase of rat erythrocyte membranes in the norm and moderate hypothermia was studied. It is shown that the kinetics of the thermal denaturation of acetylcholinesterase is nonlinear and corresponds to a model that involves two-step denaturation, fast and slow, of the enzyme’s native form. The rate constants of the fast phase, k1, are much higher than those of the slow phase, k2, while the energy of the fast phase activation is lower by only 19.4% compared to that of the slow one. Short-term moderate hypothermia is shown to increase k1 and decrease the index of relative activity of the intermediate form of acetylcholinesterase (parameter β), leading to significant lowering of the activation energies of both stages; parameter β becomes more temperature dependent. The prolongation of hypothermia up to 3 h mainly contributes to a decrease in k1 and k2 relative to short-term hypothermia and the activation energy of denaturation increases. These data support the hypothesis according to which the structure of acetylcholinesterase is labilized at the initial stages of the development of the hypothermic state and stabilized during prolonged hypothermia.

Biophysics. 2018;63(4):526-536
pages 526-536 views

Quercetin and its Complex with Cyclodextrin against Oxidative Damage of Mitochondria and Erythrocytes: Experimental Results in vitro and Quantum-Chemical Calculations

Ilyich T., Veiko A., Lapshina E., Zavodnik I.

Resumo

Abstract—In this work, we compared the efficacy of quercetin, one of the best known and widely investigated flavonoids, and the inclusion complex of quercetin and hydroxypropyl−β-cyclodextrin in prevention of disturbances in redox balance of rat liver mitochondria and erythrocytes during oxidative stress and regulation of the process of the mitochondrial permeability transition pore formations in vitro and theoretically calculated the structure of quercetin and its oxidative forms, as well as their molecular electronic properties. Quercetin (5–100 μM) inhibited membrane lipid peroxidation and reduced glutathione oxidation dose dependently in both rat liver mitochondria and erythrocytes during exposure to tert-butyl hydroperoxide (700 μM). Simultaneously, quercetin (25 μM) stimulated the Ca2+-induced mitochondrial permeability transition pore formations and inhibited this process at higher concentrations (100 mM). The incorporation of quercetin in the supramolecular complex with hydroxypropyl−β-cyclodextrin enhanced its antioxidative activity, first of all, in the cytoplasm of the cell and mitochondrial matrix. Molecules of quercetin, semiquinone radicals, and stable products formed in the oxidation, ortho- and p-quinone methide, have a planar structure. The calculated value of the dipole moment of the quercetin molecule is 4.34 D. The quercetin molecule is thermodynamically more stable than the products of its oxidation, among which p-quinone methide-III is the most stable form.

Biophysics. 2018;63(4):537-548
pages 537-548 views

The Hypoxia Signal as a Potential Inducer of Supercomplex Formation in the Oxidative Phosphorylation System of Heart Mitochondria

Byvshev I., Murugova T., Ivankov A., Kuklin A., Vangeli I., Teplova V., Popov V., Nesterov S., Yaguzhinskiy L.

Resumo

A correlation between the transition of the oxidative phosphorylation system into a supercomplex state and a change of the functional state of mitochondrial energetics upon the transition from aerobic respiration to hypoxic conditions has been established for the first time. The effect was observed by two different methods in liver and heart mitochondria. The occurrence of highly ordered structures in the membranes of heart mitochondria under hypoxic conditions has been detected by small-angle neutron scattering and electron microscopy during the transition of oxidative phosphorylation into the supercomplex state. The structural parameters of cristae inferred from the data of small-angle neutron scattering and electron microscopy have been compared. The results of measurements using the two methods coincided. Successive exposure to hypoxia and weak osmotic stress signals showed a qualitative difference between these signals. Successive exposure to two signals, with hypoxia as the first one and weak osmotic stress as the second one, was shown to cause impairment of mitochondrial integrity. The effect was observed by small-angle neutron scattering and electron microscopy. Thus, we demonstrated the existence of two qualitatively different signals (hypoxia and osmotic stress), which altered the oxidative phosphorylation system and induced its transition into the supercomplex state.

Biophysics. 2018;63(4):549-560
pages 549-560 views

A Study of the Mechanism of the FeCl3-Induced Aggregation of Human Erythrocytes

Sheremet’ev Y., Popovicheva A., Levin G.

Resumo

Abstract—Aggregation of intact and ATP-depleted human erythrocytes, which was induced by FeCl3 at a final concentration of 200 μM, was studied. The shape of erythrocytes and the stability of their cytoskeleton, the effect of shear flow on erythrocyte deformation, and the content of anionic sites in cell membranes were investigated. It is shown that the ATP depletion of erythrocytes led to a change in their shape: discocytes were transformed into echinocytes. This was accompanied by a decrease in the membrane cytoskeleton stability, disturbance in the deformation of erythrocytes, and reduction in the content of anionic sites in the membrane of ATP-depleted erythrocytes. Aggregation of such erythrocytes significantly decreased. A possible mechanism of FeCl3-induced aggregation of human erythrocytes is discussed.

Biophysics. 2018;63(4):561-565
pages 561-565 views

Regulation of Action Potential Frequency and Amplitude by T-type Ca2+ Channel During Spontaneous Synchronous Activity of Hippocampal Neurons

Teplov I., Tuleukhanov S., Zinchenko V.

Resumo

In this paper, the changes in the frequency and amplitude of action potentials (AP) were investigated depending on the depolarization caused by the Ca2+ channels activity during the spontaneous synchronous activity (SSA) of hippocampal neurons in culture. It is known that the pacemaker neuronal electrical activity can be both tonic and bursting. Using the image analysis to measure [Са2+]i and patch-clamp to register the membrane potential we show that depolarization caused by the GABA(A) receptor inhibitor results in a pattern of SSA in which tonic APs frequency of 2−3 Hz are generated by a neuron without any changes in cytosolic free Ca2+ concentration, ([Ca2+]i). The tonic mode is interrupted by bursts activity, which is accompanied by slow depolarization and calcium pulses. The inhibitor of T-type calcium channels, ML218, suppresses this process. The frequency and amplitude of the AP are regulated by slow depolarization pulses as follows: on the depolarization front, the APs frequency increases. At the same time, the amplitude decreases due to Na+ channels inactivation. The higher is the depolarization rate, the higher is the APs frequency. If slow depolarization amplitude exceeds Na+ channels reactivation potential, the neuronal impulse activity stops. As the [Ca2+]i increases and Ca2+-dependent K+ channels are activated, depolarization amplitude decreases slowly, and Na+ channels are reactivated, which leads to a gradual increase in the amplitude of APs against the background of depolarization decrease. The frequency of APs on the backside of depolarization pulse slows down to 3–4 Hz due to the occurrence of the faster Ca2+-potential oscillations (micro bursts of AP). Under these conditions, only one AP can be generated due to rapid depolarization at the leading edge. After that, APs generation is suppressed due to Na+ channel inactivation. The frequency of APs in this case coincides with the Ca2+ channel activation frequency (3−4 Hz). The burst firing is terminated due to [Ca2+]i increase, Ca2+-dependent K+ channels activation, and voltage-gated Ca2+ channels (VGCC) inactivation. As a result, the membrane is hyperpolarized even more (10 mV lower than the critical potential), that suppress AP generation, activate HCN-like channels and reactivate Na+ and VGCC. The activity of HCN-like channels increases, the membrane slowly depolarizes and reaches the threshold potential. The generation of tonic APs begins, and then, the Ca2+ channels opens, and Ca2+ potential and Ca2+ signal induced again. Thus, the Ca2+-channels, is determining the pulse of slow depolarization, control the frequency and the amplitude of APs during SSA, regulating the activation and inactivation conditions of Na+ channels. The T-type channels inhibitors reduce the duration of burst firing and Ca2+ impulse in neurons in vitro, stimulating their survival during hyperexcitation and ischemia. Thus, reducing the Ca2+ pulse duration caused by the inhibitors of T-type Ca2+-channels, can be one of the reasons for the known neuroprotective effect of these compounds.

Keywords: spontaneous synchronous activity of neurons, calcium signal, T-type calcium channels, voltage-gated calcium channels, action potential, genesis of bursting activity, action potential bursts, depolarization shift, critical potential

Biophysics. 2018;63(4):566-575
pages 566-575 views

The Role of Peroxiredoxins in Various Diseases Caused by Oxidative Stress and the Prospects of Using Exogenous Peroxiredoxins

Sharapov M., Fesenko E., Novoselov V.

Resumo

This review summarizes the recent achievements in studying the functions of peroxiredoxins (Prxs) in socially significant diseases and considers possible applications of research outcomes. Prxs are an evolutionarily ancient family of peroxidases that perform diverse functions in the cell. Prxs are involved in maintaining cell redox homeostasis and prevent oxidation and aggregation of many important regulatory proteins, thereby affecting the expression levels of a huge number of genes. Prxs play a role in intracellular and intercellular signal transmission and modulate the cell response in normal conditions and in stress accompanied by elevated levels of reactive oxygen species (ROS). Because of their versatility and abundance in all tissues and organs, Prxs contribute to the development or suppression of many pathological conditions. Understanding the molecular mechanisms of these processes will help to design new means to prevent and to treat many socially significant diseases.

Biophysics. 2018;63(4):576-589
pages 576-589 views

Complex Systems Biophysics

Analysis of the Recurrence of Noisy Time Series

Rusakov A., Medvinsky A., Nurieva N.

Resumo

Abstract—A method based on the use of recurrence plots was proposed for numerical evaluation of the character of the dynamics of noisy time series under conditions where external noise transforms recurrence plots that correspond to qualitatively different dynamic modes such that they become virtually indistinguishable. As demonstrated using the difference logistic map as an example, the method makes it possible to distinguish random fluctuations from deterministic oscillations, including both regular and chaotic oscillations, even when the signal-to-noise ratio is relatively high. An increase in noise level was additionally shown to lead to a convergence of the recurrent properties of regular and chaotic oscillations.

Biophysics. 2018;63(4):590-595
pages 590-595 views

Investigation of the Class of One-Dimensional Unimodal Mappings Obtained in the Modeling of the Lemming Population

Kamenev G., Sarancha D., Polyanovsky V.

Resumo

A model that describes periodic changes in the lemming population size as a function of the physical characteristics of ecologically significant parameters of the habitat is analyzed. Earlier studies on modeling of the population size dynamics for tundra animals substantiated a new class of one-dimensional unimodal mappings of a state space into itself. The dependence of trajectory stability on parameter variation and the bifurcation and asymptotic properties of the trajectories are in the focus of attention when this class of mappings is studied. Methods for approximating implicitly defined sets are used for numerical analysis of the maps: trajectory tubes, attractors, and bifurcation diagrams are constructed. An example of a bifurcation diagram construction along the contour in the parameter space is given for this class of mappings; the diagram enables the analysis of the dependence of trajectory behavior on changes of the modeling map parameters. Thus, the use of the mapping of the type considered for the model description of the lemming population enabled the study of the effect of long-term biospheric rhythms, which include time intervals with extreme living conditions. The study showed that such impacts do not cause degeneration of the population: the periods with chaotic dynamics that emerge under extreme conditions are replaced by well-ordered behavior in the form of small-period population cycles.

Biophysics. 2018;63(4):596-610
pages 596-610 views

A Study of the State of Photosynthetic Pigments of Hybrid Maize Seeds Exposed to Ultraviolet and Radiation

Slatinskaya O., Protopopov F., Seifullina N., Matorin D., Radenovic C., Shutova V., Maksimov G.

Resumo

Abstract—We investigated the state of the pigments of inbred (zpp1225) and hybrid (zp341) maize (Zea mays L.) seeds exposed to ultraviolet radiation and α-irradiation using spectral methods. Exposure to different ultraviolet radiation doses from 5 to 13.39 kJ/m2 and α-irradiation from 1.5 to 3 kGy stimulated plant growth and seed germination. Exposure of seeds to a high dose of α-irradiation (15 kGy) led to inhibition of plant growth and development. Irradiation of seeds can change the state and function of the pigments present in the leaves. Irradiation of seeds induced conformational changes of carotenoid modules (increase of the length of the polyene chain and amount of molecules in 15-cis-conformation); the effect depends on the type of irradiation (the effect was larger when seeds were exposed to α-irradiation). It was shown that the photosynthetic apparatus in hybrid (zp341) maize is characterized by a relatively increased I–P phase on the induction curve of fast fluorescence and a higher degree of oxidation of the P700 reaction center, indicating a higher acceptor pool on the acceptor side of the photosystem I in the hybrid maize. Seed exposure to ultraviolet radiation and α-irradiation caused inhibition of reactions in photosystem II in leaves, observed as a decrease in the quantum yield of electron transport (φEo), an increase of non-photochemical quenching (DI0/RC and φDo) and a decrease of the energy of thylakoid membranes (higher Δψ). The highest decease caused by radiation was determined for the generalized index of photosystem II performance (PIABS). The PIABS production index can be recommended for assessing the status of plants in selection studies.

Biophysics. 2018;63(4):611-620
pages 611-620 views

The Influence of Nanoparticles of Biogenic Ferrihydrite on the Rooting of Lignified Cuttings of the Ledebour Willow

Bopp V., Mistratova N., Petrakovskaya E., Gurevich Y., Teremova M., Khlebopros R.

Resumo

The influence of nanoparticles of biogenic ferrihydrite on the root formation of lignified cuttings of the Ledebour willow (Salix ledebouriana Trautv.) was investigated. The rooting of stem cuttings was performed in water using a phytohormone (indoyl-3-acetic acid) and nanoparticles. In comparison with the variants of incubation of cuttings in water and in a solution containing indolyl-3-acetic acid, the number and total length of the adventitious roots after 5 and 15 days of rooting were greatest in the cuttings treated with nanoparticles. In the early period of root development, increased levels of free radicals and intensities of the hyperfine structure lines of Mn2+ cleavage were recorded in the EPR spectra of plant tissues (lenticels of cuttings of treated with nanoparticles). The latter is related to the activity of manganese-containing superoxide dismutase. The response of cuttings to the treatment with nanoparticles was recorded by EPR before manifestation of adventitious root primordium initiation and development.

Biophysics. 2018;63(4):621-628
pages 621-628 views

The Lamé Problem Applied to a Blood Vessel with an Active Wall

Shadrina N.

Resumo

Abstract—In this paper we consider a two-dimensional problem of the stress distribution in the wall of a blood vessel with a lumen size that may vary depending on activation of smooth-muscle cells. Based on experimental data, the dependence of the circumferential stress on the parameter of smooth-muscle activation was obtained and the dependence of the latter on the cell membrane potential was described. It has been shown that contractile activity in smooth muscles (myogenic reaction) produces a significant decrease in the stresses. The maximum value of circumferential stress is achieved at the outer vessel wall, whereas the maximum value of the radial stress is reached at the inner wall. The contractions of the smooth-muscle cells reduce the circumferential stretch and smooth out the heterogeneity of its distribution in the vessel wall.

Biophysics. 2018;63(4):629-636
pages 629-636 views

Ultrasonic Monitoring of Blood Coagulation and Fibrinolysis under Intensive Blood Flow

Ivlev D., Shirinli S., Uzlova S., Guria K.

Resumo

An acoustic study of the processes of coagulation and fibrinolysis in intense blood flows under the influence of several drugs was carried out. The processes of blood coagulation and fibrinolysis have been observed in vitro in real time using optical and acoustical tools. When fibrin microclots formed in the flow, an automatic injector provided an input of a fibrinolytic drug. The experiments have shown that the method allows the monitoring of fibrinolysis in blood plasma as well as in whole blood and could be applied for the effective control of the injection of fibrinolytics. Acoustic registration was shown to be sufficient to estimate the efficiency of the fibrinolysis. The developed software-hardware complex allows one to test fibrinolytic drugs and could be used to develop protocols for their administration. The prospects for creating new classes of portable devices for hemostasis correction have been opened up.

Biophysics. 2018;63(4):637-643
pages 637-643 views

Substantiation of a New Method for Diagnosing Ciliary Body Microcirculatory Ischemia by Determining a Decreased Level of Diastolic Perfusion Pressure in its Metarterioles

Kovalchouk A.

Resumo

Abstract—The ability to diagnose ciliary body microcirculatory ischemia by determining a decreased (below 35.0 mm Hg) level of diastolic ocular perfusion pressure in its metarterioles was theoretically substantiated. This corresponds to the level of an increase in the intraocular pressure induced by local vacuum compression of the eye, during which a decrease in the amplitude of the blood filling pulse fluctuations is registered rheographically. According to the utility model, by applying a perilimbal vacuum-compression ring of original construction (pat. UA 112192) with rheographic electrodes mounted in the base, the diastolic ocular perfusion pressure is determined only in arterioles included in the regional system of the ciliary body microcirculation. The aqueous secretion and outflow of moisture briefly proportionally decreases with the preservation of an unchanged eye volume. The calculation of the level of the increase in the intraocular pressure by the degree of the applied vacuum VAC and the eye diameter D is carried out according to the formula \(K\frac{{VAC}}{{{{D}^{4}}}}\), where the coefficient K is determined by the size of a particular vacuum-compression ring.

Biophysics. 2018;63(4):644-654
pages 644-654 views

Lanomax as a Drug in Cataract Treatment: A Case Study

Balashova L., Namiot V., Kolesnichenko I., Novoderyozhkin V., Udaltsov S.

Resumo

The possibility of determining lanosterol, the active ingredient of the drug Lanomax, in the lacrimal fluid by a new electrochemical method of multisensory stripping voltammetry was studied. The measurements were carried out using a planar solid-state electrode. The test-system solution was a 0.05 М KCl solution, which contained the Zn2+, Cd2+, Pb2+, Cо2+ and Hg2+ metal cations at the concentration of 5 · 10–5 M. It was shown that the method is effective for the determination of lanosterol; the dynamics of the change in its concentration in time was considered. It was also shown that the lanosterol concentration in the lacrimal fluid remains constant for 12 h. The possibility of nonsurgical dissolution of cataracts in humans using Lanomax was investigated. In the course of the dynamic observation of this process for 8 months, the stabilization of rapidly progressive cataract was found.

Biophysics. 2018;63(4):655-661
pages 655-661 views