Vol 63, No 6 (2018)

The topography of the potential energy surface (PES) for macromolecules in the configuration space of torsion angles was considered. The effects that interatomic repulsion exerts on the surface topography are discussed. Singularities in interatomic potentials were not found to critically affect the energy landscapes in the space of torsion angles because singularity points are inaccessible at thermal energies. Classically forbidden regions for motions in the vicinity of singularity points lead to an exponential decrease in the coefficients of the Fourier series expansion of the potential energy function as harmonic numbers increase. The minimal frustration principle, which underlies the current ideas that energy funnels exist to ensure the folding of biopolymers into unique 3D structures, was extended to include maxima of the energy landscape, yielding PESs whose topography is characterized not only by a global minimum, but also by a global maximum of the energy landscape (atomic spatial conflicts are excluded in this context). In this case with each of the angular variables, the coordinates of the extreme points differ strongly by π. The resulting surfaces are antisymmetric with respect to the reversal of the directions of the acting interatomic forces (namely, the regions of the global minimum and global maximum interchange when the sign of the interaction energy changes). The topography of such surfaces ideally provides the folding of a macromolecular chain into a unique 3D structure. Entropy effects that arise during the motion of a representative point along the PES form a smooth barrier around the entrance to the energy funnel at lower temperatures and destroy the energy funnel at higher temperatures. The effects agree with data on protein-folding kinetics.

Computer models for the dimers of inulinases from Aspergillus awamori, Aspergillus ficuum and Kluyveromyces marxianus have been developed. The inulinases dimerization mechanisms from various producers and the amino acid composition of binding sites between the monomers in dimer structure have been studied. Exoinulinase dimers are more similar in structure than endoinulinase dimer. Nonpolar amino acids play the key role in the process of inulinase dimerization during the formation of a bond between the monomer forms of the enzyme from both molds and yeast.

This study tested a method designed to correctly identify single nucleotide polymorphisms in DNA sequences that are capable of forming a hairpin. Fragments of the angiotensin (AGT) and cytochrome (CYP2C19) genes with rs699 (T>C) and rs4986893 (G>A), respectively, were chosen as examples. DNA probes complementary to the polymorphic sites formed hairpin structures with a loop of 6 nt in the case of rs699 (AGT) or 4 nt in the case of rs4986893 (CYP2C19). Fluorophore-labeled target DNA was obtained via two-round multiplex PCR with simultaneous incorporation of a fluorescent label in the second round. When target DNA was hybridized to a corresponding pair of probes immobilized in gel pads of a biochip, dramatically low, if any, fluorescent signals were detected from the pads. A replacement of one nucleotide in the DNA probes prevented the formation of intramolecular structures, as was confirmed by melting curves. However, the DNA probes completely lost their complementarity to target DNA as a result of the replacement. To restore the complementary interaction with the DNA probe, corresponding nucleotide replacements were introduced in target DNA via site-directed mutagenesis. The approach significantly increased the specific fluorescent signals from biochip pads, thus allowing correct genotyping of rs699 and rs4986893.

The temperature dependence of the efficiency of energy transfer from polymer coated CdSe/CdS/ZnS quantum dots bearing terminal carboxyl groups to the reaction centers of purple bacteria Rb. sphaeroides was investigated experimentally. It was established that this efficiency remained almost constant with the change of temperature from 100 to approximately 230 K, but decreased 2–3 times when temperature rose to 310 K. A possible mechanism of such a temperature dependence based on the views on the activation caused by the intensification of the molecular motion is proposed. In the framework of these views, the analysis of the temperature dependence of the parameters that influence the efficiency of energy transfer, according to Förster's theory, was performed. It was shown that the main contribution to the observed experimental dependence was made by the change in the fluorescence quantum yield of quantum dots, and an additional contribution could be made by diffusion processes and effects of structural changes.

The least squares method is commonly used to find the parameters and sum of exponentials that form molecular fluorescence decay kinetics. However, the method usually fails to lead to a global minimum of approximation, and more reliable methods are therefore necessary for finding the sum N of exponentials that form the fluorescence decay kinetics. If the sum of the exponentials is not greater than 8 and the signal-to-noise ratio is higher than a critical ratio, which depends on N, then it is possible to calculate the sum of exponentials that form fluorescence decay kinetics. A direct, noniterative method was developed to solve the problem.

Using the sensory neuron membrane model we have demonstrated that the ectopic burst activity that arises in response to the pronociceptive stimulus is determined by the dynamics of the system with one slow variable describing inactivation of slow sodium Na_V1.8 channels. This activity can be suppressed exclusively by modification of the activation gating system of these channels under the influence of comenic acid, which is the active substance of the novel non-opioid analgesic anoceptin. It has been shown that when the potassium channels are blocked, the burst activity of the first type is suppressed after modification of Na_V1.8 channels caused by comenic acid at positive and negative conductance, while the burst activity of the second type is kept at the same level, but the range of stimuli within which this activity may occur significantly decreases.

Extracellular heat shock protein 90 (eHsp90) plays an important role in cell motility, invasion, and metastasis of tumor cells. eHsp90 stimulates migration and invasion of cells via interaction with surface receptors, which is accompanied by the activation of multiple cell motility-related signaling pathways. In addition, еHsp90 promotes cell invasion by the activation of extracellular matrix metalloproteinases. The role of different receptors, intracellular signaling pathways, and matrix metalloproteinases in the еHsp90-dependent migration and invasion of different types of cells has been investigated insufficiently. In this study, we demonstrated that HER2 is involved in the еHsp90-mediated stimulation of migration and invasion of human glioblastoma A-172 and fibrosarcoma HT1080 cells in vitro. eHsp90-induced migration and invasion of cells are accompanied by the activation of ERK1/2-, IKK/NF-κB-, FAK-, ROCK1- and Src-mediated signaling pathways and by the limited activation of JNK, while the p38-mediated signaling cascade is not activated. eHsp90 also stimulates PI3K-Akt signaling pathway in А-172 cells, while in НТ1080 cells Akt is activated regardless of PI3K. It has been established that matrix metalloproteinases are involved in the eHsp90-dependent stimulation of invasion of А-172 and НТ1080 cells in vitro.

This review analyzes the general patterns of synergism, whose manifestation under the simultaneous actions of various agents does not depend on the biological objects and the effect being analyzed. The existence of an optimum temperature that provides the maximum synergy for simultaneous application of hyperthermia with various physical or chemical agents is demonstrated. Examples of the dependence of synergism on the intensity of electromagnetic radiation applied simultaneously with a fixed elevated temperature are given. It is shown that the synergistic effect of interaction of these factors with hyperthermia increases as the intensity of applied agents increases, reaches a maximum, and then decreases. A biophysical interpretation of this original dependence of synergism on the intensity of the used agents is suggested. This interpretation is based on the idea that the formation of additional lethal changes as a result of the interaction of sub-lesions underlies the mechanism of synergistic interaction.

Cerebral concentrations of N-acetylaspartate, aspartate, and glutamate were determined for the first time simultaneously in patients with severe traumatic brain injury in the remote period using J-modulated editing of ¹H magnetic resonance spectra in vivo. It has been shown that the N-acetylaspartate and aspartate concentrations in the frontal lobes of the brain were significantly reduced (by 65 and 61%, respectively) with a constant concentration of glutamate in the remote period after severe brain injury. Our findings indicate that a decrease in the N-acetylaspartate concentration in the delayed period after brain injury is caused by a decrease in the concentration of aspartate, a precursor of the synthesis of N-acetylaspartate. The decrease in the aspartate level with a constant level of glutamate is a consequence of the dysfunction of one of the most important metabolism regulation systems, namely, the malate–aspartate shuttle.

The results of calorimetric studies of a histological preparation of a surgically excised Baker’s cyst are presented. The measurements were performed on a DSC 204 F1 Phoenix differential scanning calorimeter (Netzsch, Germany). The measurement error of the temperature dependences of the specific heat capacity of the samples analyzed did not exceed 2%. The denaturation temperature, which corresponded to the peak of the thermal signal, was 68.1°C for Baker’s cyst tissues and the denaturation enthalpy was 4.352 J/g. No thermal effects were observed on the thermograms when the samples were re-scanned; this is indicative of irreversible changes related to complete denaturation of collagen in the samples.

The experimental data that describe and confirm the validity of the physical event referred to as “the magnetism of living matter,” which was discovered by L.A. Blumenfeld and his team at the end of the 1950s, are discussed and analyzed, as well as the corresponding theoretical debate of the 1960s. This debate did not propose any explanations for the observed effects but rather questioned them; as a result, the discovery was not only forgotten, but even scientifically discredited. A new theoretical explanation (a physical hypothesis) for the experimental dataset was proposed by Blumenfeld et al. in a series of publications in the 1960s to the 1990s. The physical hypothesis on the magnetism of living matter relies on the analysis of the experimental results by Blumenfeld, the theoretical view of the authors on the physical principles underlying the functioning of living matter, and the known and earlier described data on the mitotic stages in eukaryotic cell division, which was the object of Blumenfeld’s experimental studies.