Vol 68, No 2 (2023)

Data from the experiments provides a possibility to talk about anomalously large contribution of alanine to the stability of an alpha-helix and other protein conformations. Independent data (and also experimental ones) suggest that alanine plays an especially big role in stabilization of the alpha-helix. This can be seen through the positive contribution of alanine both to the entropy of the system and to the enthalpy. The high contribution of alanine to the enthalpy of formation of the alpha helix contradicts the generally accepted view that the entropy should decrease during the formation of regular structures in proteins. Among three types of helices in proteins, alanine stabilizes two secondary structures: the alpha helix and the left helix of polyproline II, and in the case of fibrillar proteins, alanine also stabilizes the beta sheet. The stabilizing effect of alanine on the alpha helix structure extends to both natively unfolded proteins and alpha helix-support conjugates. Thus, it is no exaggeration to say that formation of secondary structure relies on alanine. The revealed contradictions are of paradoxical nature and yet there is no interpretation of the above-mentioned findings (first of all, substantiation of the contribution of alanine to the enthalpy of fusion in terms of fundamental physics) so far to resolve them. Meanwhile, the data and comments presented in this work hold out the promise of progress in resolving the revealed contradictions.

The effects of different ultra-high dilutions of luciferin ranged from 10¹⁰ to 10¹⁰² on luciferin-luciferase reaction of fireflies were investigated. Luciferin substrate concentration varied from 0.0025 nM to 2.5 nM and ATP concentration remained unchanged. This study evaluated the bioluminescence intensity after addition of ultra-high dilutions of luciferin or ultra-high dilutions of water to the bioluminescent system and some multidirectional and significant differences were found. The number of ultra-high dilutions from studied starting materials, for which significant differences were found, increased sharply with decreasing substrate concentration to 0.0025 nM. No differences were found when the effects of ultra-high dilutions of a non-specific control imidazole and ultra-high dilutions of water on the signal intensity were compared. Our results suggest that ultra-high dilutions of luciferin can specifically inhibit the luciferin-luciferase reaction.

Flexible molecular docking, Fourier-transform infrared spectroscopy (FTIR) and Raman spectroscopy were used to investigate the interaction mechanism between ficin and a graft copolymer of carboxymethyl cellulose sodium salt and N-vinylimidazole. Functional groups and fragments of the graft copolymer as well as amino acid residues that form primary structure of enzyme and participate in interactions between ficin and a graft copolymer are identified. It is shown that Raman spectroscopy yields more complete information about graft copolymer fragments interacting with the protein than that FTIR can provide. It is found that the amino acid residues that form the active site of ficin are involved in the formation of hydrogen bonds and hydrophobic interactions with the graft copolymer leading to an increase in the proteolytic activity of the conjugated enzyme.

Whole genome sequencing data allow access not only to information about genetic variation, but also provide an opportunity to evaluate the overall genome stability. Sequencing coverage signal considered as the number of fragments alligned to a given region within the genome can be used as a trustworthy source of data both on discovery of genomic rearrangements and the current state of whole genome sequencing as well as on precision of structural variant predictions by computational algorithms. The latter is of utmost importance as conflicting data on gene rearrangement events obtained by tools for finding gene rearrangements often appear. However, until recently, validation of predicted variants may present a significant challenge mainly due to the lack of information sources that may assist researchers with direct work with coverage signals and signal visualization with high precision. The present study proposes Sequence COverage ProfilEs (SCOPE), a prototype toolset that includes databases, web-interface and a series of programs for the processing of sequencing data, visualizing and storing of signal coverage profiles. The computer platform and interface is equipped with open-source software, supports local host deployment and allows users to process and analyze their own sequencing data.

Small-angle scattering makes it possible to solve structural biology problems without specific sample preparation, which is typical for methods such as X-ray diffraction of protein crystals or cryo-electron microscopy of proteins. In our review, it is shown how to use small-angle scattering to address biological problems. The use of small-angle scattering is suggested for applications as a tool to control the quality of the assembly of proteins and protein complexes and to test the identity of the structural organization of biological objects in the native state and in prepared samples before measurements by X-ray diffraction or cryo-electron microscopy. This work demonstrates the possibilities of the small-angle neutron scattering spectrometer YuMO based on the IBR-2 pulsed reactor (Laboratory of neutron physics, Joint Institute for Nuclear Research, Dubna, Russia) to solve a whole array of problems, with an eye toward applying these in biophysics, structural biology, and biotechnology. This review presents and discusses the main findings of the studies of various biological systems obtained by using the setup small-angle scattering of neutrons YuMO. The possibilities of development of structural biology methods with the help of small-angle scattering, including protein crystallization, are shown.

The paper proposes a method for determination of the dynamic properties of conduction within voltage-gated ion channels with several sequentially located energy barriers named gate particles using a theory of Markov random processes in continuous time and with a discrete state space. The number of states was taken equal to the number of energy barriers in the channel plus one. If the hypothesis that random flows switching gate particles between an open and a closed are Poisson process, is true, then mathematical description of the system’s state of similar channels can be a system of Kolmogorov linear differential equations for state probabilities. Using this model and based on Volt-Clamp test results, published in open access journals, it is possible to find out how fixed values of membrane potential depend on the intensities of Poisson process for different types of potassium channels. Function parameters, that describe the intensity of ion transition across the channel, in the Kolmogorov equation can be restored using the generalized least squares method. This paper contains the examples of determining the intensities of transitions for two types of voltage-dependent potassium channels known as «delayed rectifiier potassium channels» (IKdr, two identical activation gate particles) and channels with fast activation and inactivation processes (IKa, three identical activation and one inactivation gate particles). It is shown that channel activation and deactivation is described by solving the general Kolmogorov equation.

The quantity of neurotrophic factors and the protein composition of somatic nerve membranes in rats during injury and survival of nerves under the action of clobetasol have been explored. It has been shown that the drug administered intramuscularly produces more pronounced effect on the increase in the level of neurotrophic growth factors and structural proteins responsible for recovery processes than the drug released from hydrogel derived from microbial polysaccharides as well as stabilizes the content of the total protein fraction of damaged somatic nerves. Proteins of the injured neural conductor are less degraded during intramuscular injection of clobetasol probably because of better availability of the drug administered by injection than availability of the drug administered (slow drug release) from hydrogel composite. In addition, an increase in the amount of DNA and some protein fractions indicates that clobetasol is able to participate in an activation of genes associated with remyelination. We suppose that clobetasol can stimulate synthesis of neurotrophic growth factors, thereby triggering phosphatidylinositol-3-kinase and mitogen-activated protein kinase signaling pathways that regulate the processes of cytoskeletal reorganization and axonal growth, as well as enhance the rate of synthesis of structural and axonal proteins necessary to restore the functional activity of injured nerve conductors.

Our previous studies have shown that function of ionotropic glutamate receptors such as AMPA (a-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid) and NMDA (N-methyl-D-aspartate) was impaired after long-term cryopreservation of brain slices at -10°C within 30-50 days. To elucidate the reasons for cryodamage to AMPA- and NMDA-dependent mechanisms, artificial cerebrospinal fluid (aCSF) solutions that contain agar at different concentrations (33, 44, and 50%) were used for cryopreservation of the rat olfactory cortex slices. After cryopreservation, the slices were warmed to 37°C and the amplitudes changes of AMPA and NMDA potentials, which reflected the activities of the AMPA and NMDA mechanisms, were evaluated; the results were compared with those obtained before cryopreservation. It was found that AMPA and NMDA potentials changed differently depending on the concentration of agar in artificial cerebrospinal fluid. In solutions with 33% agar, the amplitude of AMPA potentials increased by 60%, whereas, in contrast, the amplitude of NMDA potentials was equal to the values before cryopreservation. At agar concentration of 44% in the solution, the AMPA and NMDA amplitudes were increased by 70% and 80%, respectively. A complete recovery of the activities of AMPA and NMDA mechanisms was obtained after cryopreservation in a freezing solution with an agar concentration of 50%. Under these conditions, the amplitudes of the AMPA and NMDA potentials corresponded to those seen before cryopreservation. Thus, the results obtained indicate that agar added to the artificial cerebrospinal fluid solution is a cryoprotectant that protects AMPA- and NMDA-dependent mechanisms from cryoinjury. The freezing solution (artificial cerebrospinal fluid and agar) developed by us for cryopreservation of brain explants of non-hibernating animals will be used to create a cryobank of nervous tissue.

Alginates with various modifying additives (for example, chitosan) and various methods of physical treatment are used in the design of prototypes of innovative wound dressing. The aim of this study was to create and explore the properties of a prototype of textile-based sodium alginate wound dressing containing silver nanoparticles subjected to10 freeze cycles, and to evaluate its efficacy on the course of the purulent wound process in rats. The study showed that the developed technology of 10-fold cyclic freezing makes it possible to significantly increase the amount of silver nanoparticles in the composition of textile-based sodium alginate wound dressing, primarily due to silver nanoparticles that have a diameter not larger than 15 nm, and are characterized by the highest antibacterial activity. The use of the developed wound dressing with silver nanoparticles reduces metabolic disturbances when the nonspecific defense system response occurs in the wound tissue; on the 3rd and 5th day after wounding less pronounced changes in free radical oxidation indices were found, the levels of antioxidant defence enzymes (catalase and superoxide dismutase) in wound tissue were lower than those observed after the use of wound dressing with silver nanoparticles, but not containing alginate, or after wound debridement without alginate or nanoparticles done every day.

An intelligent optical system for medical express diagnostics has been developed and tested. A method for visualizing the oxygen status of biological tissues in the form of "digital images" describing the general functional state of the human body is demonstrated. It has been shown that the method of principal components and hierarchical clustering can be used in combination with optical methods for detecting hemoglobin forms in biological tissues to perform non-invasive monitoring and express diagnostics of the oxygen status of the human body. The results obtained show that it is possible to stratify the subjects into risk groups based on optical sensor readings. In comparison with pulse oximetry, the use of which is common for determining the oxygen saturation level of blood, the described method can be employed to estimate peripheral oxygen saturation, and thus thrombosis and ischemia of the extremities can be detected in time.

This article proposes a theoretical model of mechanical feedback in pattern formation on deforming a membrane when coronavirus enters a cell. Coronavirus stiff and flexible spike proteins attach to ACE2 receptors on the cell membrane of the target cell. TMPRSS2 triggers the fusion of the viral and cell membranes with the formation of a fusion pore leading to opening of a capsid surrounded by the coronavirus envelope and viral RNA release into the cell. Based on mechanical feedback analysis of contact interaction and elastic shell theory, a critical value of cell radius, at which a fusion pore is formed and membrane damage occurs locally, is determined. The results revealed that the smaller the cell size, the less likely that the cell will be damaged mechanically when exposed to the virus. One of the ways to reduce the cell size is to decrease intracellular fluid volume through the use of medicines - diuretics. The critical value of cell radius is inversely proportional to the value of binding energy at the time of attachment of the coronavirus to the cell membrane. Further research is required to improve our knowledge of the dependency of binding energy on the shape and sizes of spikelike bumps for various types of coronavirus strains. It may be predicted that when a new coronavirus strain will emerge, it may produce lower binding energy to cell surface and the severity of the disease may decrease. It is necessary to verify the conclusions of the theoretical study by experimental methods.