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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 18085

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Special Issue Editors

Dr. Stepan Dzhimak

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Guest Editor

1. Laboratory of Problems of Stable Isotope Spreading in Living Systems, Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don, Russia
2. Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
Interests: biophysics of stable isotopes; DNA mechanics

Dr. Anastasia Anashkina

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Guest Editor

Laboratory of DNA-Protein Interactions, Engelhardt Institute of Molecular Biology of RAS, 119991 Moscow, Russia
Interests: DNA; protein; recognition; affinity; specificity; selectivity; local structure; pattern; motif; interaction energy

Special Issue Information

Dear Colleagues,

The Special Issue is devoted to the publication of materials presented at the VII Congress of Russian Biophysicists, which will be held on April 17–23, 2023, in Krasnodar, Russia.

Biophysics, located at the intersection of biology, physics, molecular biology, mathematics and computer science, receives a new impetus in development with each new achievement in these sciences. New results and discoveries in biophysics are continued in the development of new methods of research and treatment in medicine, in the formation of new ecological approaches. The main goal of the Congress, first of all, is to understand the current state of modern biophysics in Russia, assess its resources, opportunities and identify new breakthrough areas.

At the Congress, it is planned to discuss reports on topical areas of biophysics: biophysics of complex systems, cell biophysics, membrane processes, molecular motors, bioenergetics, nanobiotechnologies, structure and dynamics of proteins, structure and dynamics of nucleic acids, neurobiology, bioinformatics, biophotonics, ecological biophysics, etc. The Congress provides for plenary speeches, invited reports in areas (sections), poster messages, discussion forums, round tables, and an exhibition of new scientific developments (methods and devices). Thus, the platform of the VII Congress of Biophysicists of Russia will provide participants with ample opportunities to discuss the current state and prospects for the development of the main sections of biophysics and related areas of science.

Dr. Stepan Dzhimak
Dr. Anastasia Anashkina
Guest Editors

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Keywords

biophysics of complex systems
cell biophysics
membrane processes
molecular motors
bioenergetics
nanobiotechnologies
structure and dynamics of proteins
structure and dynamics of nucleic acids
neurobiology
bioinformatics
biophotonics
biomechanics
ecological biophysics

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Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 151 KiB

Open AccessEditorial

The Best Material from the VII Congress of Russian Biophysicists

by Anastasia A. Anashkina and Stepan S. Dzhimak

Int. J. Mol. Sci. 2024, 25(7), 4016; https://doi.org/10.3390/ijms25074016 - 4 Apr 2024

Viewed by 784

Abstract

The purpose of this Special Issue is to demonstrate the current state of research in the field of biophysics in the Russian Federation [...] Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

Research

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14 pages, 2345 KiB

Open AccessArticle

Structure and Neuroprotector Properties of a Complex Compound of Lithium with Comenic Acid

by Stanislav Kozin, Alexandr Kravtsov, Lev Ivashchenko, Victor Dotsenko, Stepan Dzhimak, Nicolai Aksenov, Arthur Vashurin, Vasily Ivlev, Mikhail Baryshev, Alexandr Bespalov, Lilia Fedulova, Anna Dorohova and Anastasia Anashkina

Int. J. Mol. Sci. 2024, 25(1), 286; https://doi.org/10.3390/ijms25010286 - 24 Dec 2023

Cited by 1 | Viewed by 1550

Abstract

The structure, antioxidant and neuroprotective properties of lithium comenate (lithium 5-hydroxy-4-oxo-4H-pyran-2-carboxylate) were studied. Lithium comenate was obtained by reacting comenic acid (H₂Com) with lithium hydroxide in an aqueous solution. The structure of lithium comenate was confirmed via thermal analysis, mass spectrometry, IR, NMR and UV spectroscopy. The crystal structure was studied in detail via X-ray diffraction. The compound crystallized in a non-centrosymmetric space group of symmetry of the orthorhombic system Pna2₁ in the form of a hydrate, with three water molecules entering the first coordination sphere of the cation Li⁺ and one molecule forming a second environment through non-valent contacts. The gross formula of the complex compound was established [Li(HCom)(H₂O)₃]·H₂O. It has been established that lithium comenate has a pronounced neuroprotective activity under the excitotoxic effect of glutamate, increasing the survival rate of cultured rat cerebellar neurons more than two-fold. It has also been found that the pre-stress use of lithium comenate at doses of 1 and 2 mg/kg has an antioxidant effect, which is manifested in a decrease in oxidative damage to the brain tissues of mice subjected to immobilization stress. Based on the data available in the literature, we believe that the high neuroprotective and antioxidant efficacy of lithium comenate is a consequence of the mutual potentiation of the pharmacological effects of lithium and comenic acid. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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20 pages, 1447 KiB

Open AccessCommunication

Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software

by Alexander A. Seregin, Liudmila P. Smirnova, Elena M. Dmitrieva, Maria G. Zavialova, German G. Simutkin and Svetlana A. Ivanova

Int. J. Mol. Sci. 2023, 24(20), 15250; https://doi.org/10.3390/ijms242015250 - 17 Oct 2023

Viewed by 2008

Abstract

The prevalence of bipolar disorder (BD) in modern society is growing rapidly, but due to the lack of paraclinical criteria, its differential diagnosis with other mental disorders is somewhat challenging. In this regard, the relevance of proteomic studies is increasing due to the development of methods for processing large data arrays; this contributes to the discovery of protein patterns of pathological processes and the creation of new methods of diagnosis and treatment. It seems promising to search for proteins involved in the pathogenesis of BD in an easily accessible material—blood serum. Sera from BD patients and healthy individuals were purified via affinity chromatography to isolate 14 major proteins and separated using 1D SDS-PAGE. After trypsinolysis, the proteins in the samples were identified via HPLC/mass spectrometry. Mass spectrometric data were processed using the OMSSA and X!Tandem search algorithms using the UniProtKB database, and the results were analyzed using PeptideShaker. Differences in proteomes were assessed via an unlabeled NSAF-based analysis using a two-tailed Bonferroni-adjusted t-test. When comparing the blood serum proteomes of BD patients and healthy individuals, 10 proteins showed significant differences in NSAF values. Of these, four proteins were predominantly present in BD patients with the maximum NSAF value: 14-3-3 protein zeta/delta; ectonucleoside triphosphate diphosphohydrolase 7; transforming growth factor-beta-induced protein ig-h3; and B-cell CLL/lymphoma 9 protein. Further exploration of the role of these proteins in BD is warranted; conducting such studies will help develop new paraclinical criteria and discover new targets for BD drug therapy. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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18 pages, 4087 KiB

Open AccessArticle

Changes in Hemoglobin Properties in Complex with Glutathione and after Glutathionylation

by Iuliia D. Kuleshova, Pavel I. Zaripov, Yuri M. Poluektov, Anastasia A. Anashkina, Dmitry N. Kaluzhny, Evgeniia Yu. Parshina, Georgy V. Maksimov, Vladimir A. Mitkevich, Alexander A. Makarov and Irina Yu. Petrushanko

Int. J. Mol. Sci. 2023, 24(17), 13557; https://doi.org/10.3390/ijms241713557 - 31 Aug 2023

Cited by 5 | Viewed by 2131

Abstract

Hemoglobin is the main protein of red blood cells that provides oxygen transport to all cells of the human body. The ability of hemoglobin to bind the main low-molecular-weight thiol of the cell glutathione, both covalently and noncovalently, is not only an important part of the antioxidant protection of red blood cells, but also affects its affinity for oxygen in both cases. In this study, the properties of oxyhemoglobin in complex with reduced glutathione (GSH) and properties of glutathionylated hemoglobin bound to glutathione via an SS bond were characterized. For this purpose, the methods of circular dichroism, Raman spectroscopy, infrared spectroscopy, tryptophan fluorescence, differential scanning fluorimetry, and molecular modeling were used. It was found that the glutathionylation of oxyhemoglobin caused changes in the secondary structure of the protein, reducing the alpha helicity, but did not affect the heme environment, tryptophan fluorescence, and the thermostability of the protein. In the noncovalent complex of oxyhemoglobin with reduced glutathione, the secondary structure of hemoglobin remained almost unchanged; however, changes in the heme environment and the microenvironment of tryptophans, as well as a decrease in the protein’s thermal stability, were observed. Thus, the formation of a noncovalent complex of hemoglobin with glutathione makes a more significant effect on the tertiary and quaternary structure of hemoglobin than glutathionylation, which mainly affects the secondary structure of the protein. The obtained data are important for understanding the functioning of glutathionylated hemoglobin, which is a marker of oxidative stress, and hemoglobin in complex with GSH, which appears to deposit GSH and release it during deoxygenation to increase the antioxidant protection of cells. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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22 pages, 3147 KiB

Open AccessArticle

Influence of a Single Deuterium Substitution for Protium on the Frequency Generation of Different-Size Bubbles in IFNA17

by Alexandr Basov, Anna Dorohova, Vadim Malyshko, Arkadii Moiseev, Alexandr Svidlov, Maria Bezhenar, Yury Nechipurenko and Stepan Dzhimak

Int. J. Mol. Sci. 2023, 24(15), 12137; https://doi.org/10.3390/ijms241512137 - 28 Jul 2023

Cited by 1 | Viewed by 1284

Abstract

The influence of a single ²H/¹H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an ²H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11–30 base pair (bp) bubbles (higher by 319%), 2–4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11–30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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19 pages, 4304 KiB

Open AccessArticle

Study of the Magnesium Comenate Structure, Its Neuroprotective and Stress-Protective Activity

by Stanislav Kozin, Alexandr Kravtsov, Lev Ivashchenko, Victor Dotsenko, Lada Vasilyeva, Alexander Vasilyev, Elena Tekutskaya, Nicolai Aksenov, Mikhail Baryshev, Anna Dorohova, Lilia Fedulova and Stepan Dzhimak

Int. J. Mol. Sci. 2023, 24(9), 8046; https://doi.org/10.3390/ijms24098046 - 28 Apr 2023

Cited by 4 | Viewed by 1694

Abstract

The crystal structure and the biological activity of a new coordination compound of magnesium ions with comenic acid, magnesium comenate, was characterized and studied. Quantitative and qualitative analysis of the compound was investigated in detail using elemental X-ray fluorescent analysis, thermal analysis, IR-Fourier spectrometry, UV spectroscopy, NMR spectroscopy, and X-ray diffraction analysis. Based on experimental analytical data, the empirical formula of magnesium comenate [Mg(HCom)₂(H₂O)₆]·2H₂O was established. This complex compound crystallizes with eight water molecules, six of which are the hydration shell of the Mg²⁺ cation, and two more molecules bind the [Mg(H₂O)₆]²⁺ aquacation with ionized ligand molecules by intermolecular hydrogen bonds. The packing of molecules in the crystal lattice is stabilized by a branched system of hydrogen bonds with the participation of solvate water molecules and oxygen atoms of various functional groups of ionized ligand molecules. With regard to the biological activity of magnesium comenate, a neuroprotective, stress-protective, and antioxidant effect was established in in vitro and in vivo models. In in vitro experiments, magnesium comenate protected cerebellar neurons from the toxic effects of glutamate and contributed to the preservation of neurite growth parameters under oxidative stress caused by hydrogen peroxide. In animal studies, magnesium comenate had a stress-protective and antioxidant effect in models of immobilization–cold stress. Oral administration of magnesium comenate at a dose of 2 mg/kg of animal body weight for 3 days before stress exposure and for 3 days during the stress period led to a decrease in oxidative damage and normalization of the antioxidant system of brain tissues against the background of induced stress. The obtained results indicate the advisability of further studies of magnesium comenate as a compound potentially applicable in medicine for the pharmacological correction of conditions associated with oxidative and excitotoxic damage to nerve cells. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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12 pages, 1456 KiB

Open AccessArticle

Bilateral Shifts in Deuterium Supply Similarly Change Physiology of the Pituitary–Thyroid Axis, but Differentially Influence Na⁺/I⁻ Symporter Production

by Nataliya V. Yaglova, Sergey S. Obernikhin, Ekaterina P. Timokhina, Valentin V. Yaglov, Dibakhan A. Tsomartova, Svetlana V. Nazimova, Elina S. Tsomartova, Marina Y. Ivanova, Elizaveta V. Chereshneva and Tatiana A. Lomanovskaya

Int. J. Mol. Sci. 2023, 24(7), 6803; https://doi.org/10.3390/ijms24076803 - 6 Apr 2023

Cited by 4 | Viewed by 1794

Abstract

Deuterium, a stable isotope of hydrogen, is abundant in organisms. It is known to produce various biological effects. However, its impact in thyroid hormone synthesis and secretion is poorly studied. The aim of this investigation was to evaluate the dynamics of thyroid hormones and pituitary thyroid-stimulating hormone secretion during bilateral shifts in deuterium supply and assess a possible role of the Na⁺/I⁻ symporter (NIS), the main iodide transporter, in altered thyroid function. The experiment was performed on adult male Wistar rats, which consumed deuterium-depleted ([D] = 10 ppm) and deuterium-enriched ([D] = 500,000 ppm) water for 21 days. The assessment of total thyroxine and triiodothyronine and their free fractions, as well as thyroid-stimulating hormone in blood serum, revealed the rapid response of the thyroid gland to shifts in the deuterium/protium balance. The present investigation shows that the bilateral changes in the deuterium body content similarly modulate thyroid hormone production and functional activity of the pituitary gland, but the responses of the thyroid and pituitary glands differ. The response of the thyroid cells was to increase the synthesis of the hormones and the pituitary thyrotropes, in order to reduce the production of the thyroid-stimulating hormone. The evaluation of NIS serum levels found a gradual increase in the rats that consumed deuterium-enriched water and no differences in the group exposed to deuterium depletion. NIS levels in both groups did not correlate with thyroid hormones and pituitary thyroid-stimulating hormone production. The data obtained show that thyroid gland has a higher sensitivity to shifts in the deuterium body content than the hypothalamic–pituitary complex, which responded later but similarly in the case of deuteration or deuterium depletion. It indicates a different sensitivity of the endocrine glands to alterations in deuterium content. It suggests that thyroid hormone production rate may depend on deuterium blood/tissue and cytosol/organelle gradients, which possibly disturb the secretory process independently of the NIS. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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18 pages, 3785 KiB

Open AccessArticle

Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range

by Alexander Basov, Mikhail Drobotenko, Alexander Svidlov, Maria Bezhenar, Eugeny Gerasimenko, Arkadii Moiseev, Vadim Malyshko, Anna Dorohova, Andrey Drozdov, Mikhail Baryshev and Stepan Dzhimak

Int. J. Mol. Sci. 2022, 23(24), 15487; https://doi.org/10.3390/ijms232415487 - 7 Dec 2022

Cited by 2 | Viewed by 1539

Abstract

The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single ²H/¹H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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Review

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13 pages, 933 KiB

Open AccessReview

Emerging Role of Deuterium/Protium Disbalance in Cell Cycle and Apoptosis

by Nataliya V. Yaglova, Ekaterina P. Timokhina, Sergey S. Obernikhin and Valentin V. Yaglov

Int. J. Mol. Sci. 2023, 24(4), 3107; https://doi.org/10.3390/ijms24043107 - 4 Feb 2023

Cited by 6 | Viewed by 4313

Abstract

Deuterium, a stable isotope of hydrogen, is a component of water and organic compounds. It is the second most abundant element in the human body after sodium. Although the concentration of deuterium in an organism is much lower than that of protium, a wide variety of morphological, biochemical, and physiological changes are known to occur in deuterium-treated cells, including changes in fundamental processes such as cell division or energy metabolism. The mode and degree of changes in cells and tissues, both with an increase and a decrease in the concentration of deuterium, depends primarily on the time of exposure, as well as on the concentration. The reviewed data show that plant and animal cells are sensitive to deuterium content. Any shifts in the D/H balance outside or inside cells promote immediate responses. The review summarizes reported data on the proliferation and apoptosis of normal and neoplastic cells in different modes of deuteration and deuterium depletion in vivo and in vitro. The authors propose their own concept of the effects of changes in deuterium content in the body on cell proliferation and death. The altered rate of proliferation and apoptosis indicate a pivotal role of the hydrogen isotope content in living organisms and suggest the presence of a D/H sensor, which is yet to be detected. Full article

(This article belongs to the Special Issue Best Materials of the VII Congress of Russian Biophysicists)

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