Том 62, № 6 (2017)

Secondary RNA structures play an important role in transposition, in particular, in RNA recognition by transposon proteins. Previously, we found a conserved structure at the 3′-end of human transposons and proposed a hypothesis about the role of this structure in transposition. Although there is no similarity at the sequence level, the conserved position of this structure points to the fact that structural properties occur that are under positive natural selection. In this paper, the physical and geometric properties of stem-loop structures at the 3′-end of human transposons are identified and compared with properties of the structures of other genome regions. Each stem-loop structure was characterized by a set of ten characteristics: the Gibbs free energy, enthalpy, entropy, hydrophilicity, Shift, Slide, Rise, Tilt, Roll, and Twist. A model has been built using machine-learning methods, which recognizes stem-loop structures according to their physical and geometric characteristics with 94% accuracy. The most important parameters in the recognition model are hydrophilicity, enthalpy, Rise, and Twist. These properties of transposon structure are thought to be under positive natural selection.

Molecular-modeling methods have been used to perform energy analysis of dimeric complex formation between lexitropsins and double-stranded DNA. Stabilization of dimeric complexes by hydrophobic and van der Waals interactions has been demonstrated. Electrostatic interactions and the contributions of hydrogen bonds and changes in the number of degrees of freedom had a destabilizing influence. The energy of monomeric and dimeric binding has been compared.

This article discusses some basic problems of structural biology and molecular dynamics simulation methods that need to be taken into account when considering, the protein folding problem, and prediction of 3D-structures for biopolymers. A multidimensional Fourier series expansions were formulated for the energy landscapes of the systems with conformational mobility, These energy landscape representations are correct from the viewpoint of the topology of the macromolecule configuration spaces. The problem of the single global minimum on the energy landscape for proteins is discussed and is formulated in tems of phase rules for the component of Fourier expansions. This rule is formally similar to the problem of diffraction on a multidimensional cubic lattice. The calibration of biopolymer force fields and their correspondence to topologically correct energy landscapes are discussed. Equations of motion were obtained in a matrix form for the relaxation of a representative point position on a multidimensional potential energy surface. The solutions of the equations for conformational relaxation were shown to obey the principle of the minimum energy dissipation rate at a given relaxation rate of potential energy (or folding rate).

Determination of the antioxidant activities of various biological objects, for example, food, medicinal preparations, beverages, blood plasma, and other human biological fluids, is an important task for biomedical research. Chemiluminescent methods are widely used for this purpose. These methods are sensitive and rapid and make it possible to directly control the kinetics of inhibition of oxidation by an antioxidant. In the present work, a chemiluminescent model was used of free-radical oxidation of luminol, as initiated by a mixture of hemoglobin–hydrogen peroxide in an aqueous medium. The kinetics of the inhibitory effect of eight water-soluble bioantioxidants with different molecular structures and their binary mixtures was studied; the inhibition parameters of luminol oxidation by these antioxidants and their stoichiometric coefficients were determined. Features of the inhibition kinetics for glutathione are revealed. The synergistic and antagonistic effects of antioxidants in the mixtures were evaluated. The independence of chemiluminescence quenching by individual antioxidants was noted for the majority of the studied binary antioxidant mixtures, with more “active” antioxidants inhibiting oxidation earlier than less “active” ones. Mixtures of some antioxidants that strengthened or weakened each other upon interacting, thus exhibiting synergism or antagonism, were an exception.

It was shown for the first time that myeloperoxidase, a homodimer that consists of two disulfidebonded identical protomers and catalyzes the formation of hypochlorous acid (HOCl), is decomposed by HOCl into monomers (MPO-Cl). Dimeric myeloperoxidase can also be converted into monomers (hemimyeloperoxidase) by reduction of the disulfide bond. In this study, the effects of two monomeric forms of myeloperoxidase, MPO-Cl and hemi-myeloperoxidase, and native dimeric myeloperoxidase on the production of reactive oxygen (^•O₂⁻ and H₂O₂) and halogen (HOCl) species by neutrophils were compared. Neutrophil production of these species was monitored after addition of hemi-myeloperoxidase, MPO-Cl, or dimeric myeloperoxidase and also after the subsequent addition of activators, phorbol-12-myristate-13-acetate or N-formyl-Met-Leu-Phe. HOCl production was assessed by chemiluminescence in the presence of luminol; ^•O₂⁻ production was assessed by chemiluminescence in the presence of lucigenin and by cytochrome c reduction determined spectrophotometrically, and H₂O₂ production was measured using fluorimetry with scopoletin. The results indicate that MPO-Cl and hemi-myeloperoxidase, which can occur in blood under halogenative stress, do not prime neutrophil NADPH oxidase, and do not enhance the production of reactive oxygen (^•O₂⁻ and H₂O₂) and halogen (HOCl) species.

The combined effects of external low static magnetic fields at 0–22 mT and magnesium isotopes on the growth and development of E. coli bacteria has been studied. The magnetic field and ²⁵Mg magnetic isotope effects were obtained in two ranges: 0.8–3.0 and 8–13 mT. The experimental values of the growth rate, the number of CFUs and the ATP pool of bacteria enriched in magnetic magnesium isotope ²⁵Mg (nuclear spin, I = 5/2) in the range of 0.8–3.0 mT are significantly higher compared to bacteria enriched in nonmagnetic isotopes ²⁴Mg, ²⁶Mg, or natural magnesium. The increase in the growth rate, colony-forming ability, and intracellular ATP concentration in bacteria in all groups cultivated under exposure to an external static magnetic field in the range of 0.8 to 3.0 mT confirms the existence of magnetosensitive stages of enzymatic reactions that proceed via the ion-radical mechanism. The combined influence of the magnetic field in the range of 8 to 13 mT and the magnesium magnetic isotope ²⁵Mg on the colony forming ability of E. coli bacteria is associated with processes that are responsible for cell division. The above-mentioned effects of bacterial magnetosensitivity (to magnetic fields and magnetic isotopes) are in good agreement with theoretical predictions of the theory of spin-dependent enzymatic reactions.

Responses of single neurons to tonal signals amplitude-modulated by repeating segments of lowfrequency noise were studied in the dorsal (cochlear) medullary nucleus and midbrain auditory center (torus semicircularis) of the grass frog Rana temporaria. An autocorrelation function of the response to a total presentation and a shuffled autocorrelation function were derived. The latter was obtained by correlating the impulse response to each segment of the modulated signal with responses to all other segments with the exception of the initial one. After the necessary normalization, the function differed from the initial autocorrelation only in lacking postspike changes in excitability. A delay dependence of the ratio of the two functions directly demonstrated the time course of the postspike change in excitability of the studied cell. The majority of second-order neurons, which are in the dorsal nucleus of the medulla oblongata, were characterized only by brief intervals of absolute and relative refractoriness. However, cells with excitability that was markedly facilitated immediately after the refractory period were observed even in this nucleus. Neurons with a complex pattern of postspike changes in excitability were detected in the torus semicircularis. In these cells, a comparatively long postspike decrease in excitability was usually interrupted by intervals in which the neuron sensitivity was significantly higher than normal. The results demonstrate that spike generation has a marked effect on subsequent activity in brainstem auditory units. The effects may play an important role in the formation of the temporal pattern of neuronal responses to auditory signals.

The evolution rate v(t) varies among diverse biosystems, but a general theory can be formulated when the dynamics of the biosystem stater x = x(t) = (x₁, x₂, x_m)^T is considered in the m-dimensional space of states. A mathematical approach is proposed for evaluating such processes and describes the processes in terms of particular chaos of the statistical distribution functions f(x). In the case of complex multicomponent systems with a high dimension number m (m ≫1) of the phase space of states, we propose using pairwise comparison matrices of samples x(t) when homeostasis is constant and calculating the parameters of quasiattractors. The Glensdorff–Prigogine thermodynamic approach to estimating evolution is inefficient in assessing the third-type systems, while it is applicable and the Prigogine theorem works at the level of molecular systems. Alterations in the state of the human neuromuscular system were found to lead to chaotic changes in the statistical functions f(x) in tremor recording samples, while quasiattractor parameters demonstrate a certain regularity.

Relative measurements of the concentration of CO₂ released through the skin in rats in response to thermal stimulation were performed using a mass spectrometer with a membrane interface. It is demonstrated that the antinociceptive response to a pain stimulus during intraperitoneal propofol–lidocaine and propofol–ketamine anesthesia can be monitored using a mass spectrometer with a membrane interface. Lidocaine exerts direct action on the central nervous system and induces an antinociceptive effect in response to thermal stimulation.

A two-component model of the eyeball that represents the cornea as a momentless, linearly elastic deformable surface and the scleral region, as an elastic element that responds to intraocular pressure changes by volume changes, has been used to analyze the effect of spatial inhomogeneity in the distribution of effective corneal stiffness on the mechanical properties of the eye. The effective stiffness of the cornea characterized both the elastic properties and the thickness of the cornea within the framework of the model. Various axisymmetric forms of the effective stiffness distribution characterized by monotonic increase along the arc between a point on the corneal surface and the apex of the cornea were studied. The considered distributions simulated both natural inhomogeneity and apical region weakening due to surgical interventions. Numerical simulation yielded the dependences of deformation parameters on intraocular pressure changes. These parameters characterized the deformation properties of both the cornea (apex displacement) and the eyeball as a whole (intraocular volume change). In the case of moderate inhomogeneity, the dependences were only slightly different from those for a homogeneous cornea with an effective stiffness equal to the mean value for the corresponding inhomogeneous distribution. A noticeable increase in the integral response of the cornea and the eyeball as a whole to changes in pressure was observed if the effective stiffness amplitude was very high (two or more times higher than the mean value). The effect of inhomogeneity on the results of tonometric measurements with a Maklakoff tonometer (flat stamp) was studied. The tonometric difference, that is, the difference between the tonometric pressure (in the loaded eye) and the true pressure (before loading), mainly depended on the average stiffness of the cornea in this case as well, with a substantial increase observed at very high stiffness amplitudes only. Apical weakening of the cornea led to an increase (although not very pronounced) of the tonometric difference.

Oxidative stress is the main component of pathogenesis in ischemia–reperfusion injury. The administration of exogenous antioxidants suppresses oxidative stress and may decrease the severity of ischemia–reperfusion injury. The intestine is one of the most sensitive organs to the effect of ischemia–reperfusion. A rat model of a small intestine ischemia–reperfusion injury, based on occlusion of the superior mesenteric artery, was used in this work. Recombinant peroxiredoxin 6, a representative of an ancient family of peroxidases that are able to neutralize a broad range of both organic and inorganic peroxides, was used as an exogenous antioxidant. The intravenous administration of the exogenous peroxiredoxin 6 prior to ischemia–reperfusion minimizes tissue injury and reduces apoptotic cell death in the intestine and the mesenteric vessels. The impact of the exogenous peroxiredoxin 6 upon the NO level elevation in animal blood has been shown to be correlated with the enhanced inducible NO synthase expression. Thus, the use of exogenous peroxiredoxin 6 in ischemia–reperfusion injury of the intestine and the mesenteric vessels promotes normalization of the tissue redox homeostasis, structure protection, and restoration of the microvasculature.

The most common myths about mitochondria are summarized and the author’s alternative interpretation is given.

An improved Fourier analysis and wavelet transform revealed a large-scale periodicity in the locations of sites with a characteristic local AT–GC composition in the nucleotide sequences of Drosophila early developmental genes. A localization of periodic locus sections indicated that they predominantly occur in transcription regulation modules (enhancers). The period lengths observed in ranges of 80–85, 165–180, and 330–400 nt agree well with the lengths typical of the nucleosomal level of chromatin organization. The harmonic periods in a range of 600–750 nt are approximately four nucleosomal repeats and are close to the minimum enhancer length typical of the Drosophila genome.