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  1. Article ; Online: The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems.

    Aristov, Vladimir V / Buchelnikov, Anatoly S / Nechipurenko, Yury D

    Entropy (Basel, Switzerland)

    2022  Volume 24, Issue 2

    Abstract: Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of ... ...

    Abstract Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger's concept of the maintenance biosystems by "negentropy feeding", is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.
    Language English
    Publishing date 2022-01-24
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e24020172
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  2. Article ; Online: The Degradation and Aging of Biological Systems as a Process of Information Loss and Entropy Increase.

    Aristov, Vladimir V / Karnaukhov, Alexey V / Buchelnikov, Anatoly S / Levchenko, Vladimir F / Nechipurenko, Yury D

    Entropy (Basel, Switzerland)

    2023  Volume 25, Issue 7

    Abstract: The problem of the degradation and aging of bioorganisms is herein considered from the viewpoint of statistical physics. Two typical timescales in biological systems-the time of metabolic processes and the time of the life cycle-are used. A kinetic ... ...

    Abstract The problem of the degradation and aging of bioorganisms is herein considered from the viewpoint of statistical physics. Two typical timescales in biological systems-the time of metabolic processes and the time of the life cycle-are used. A kinetic equation describing the small timescales of the systems' characteristic processes in is proposed. Maintaining a biosystem in a time-stable state requires a constant inflow of negative entropy (negentropy). Ratios are proposed to evaluate the aging and degradation of systems in terms of entropy. As an example, the aging of the epithelium is studied. The connection of our approach to the information theory of aging is discussed, as well as theoretical constructions related to the concept of cooperon and its changing with time.
    Language English
    Publishing date 2023-07-15
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e25071067
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  3. Article: Mathematical models describing oxygen binding by hemoglobin.

    Lavrinenko, Igor A / Vashanov, Gennady A / Hernández Cáceres, José L / Nechipurenko, Yury D

    Biophysical reviews

    2023  Volume 15, Issue 5, Page(s) 1269–1278

    Abstract: Despite the fact that the investigation of the structural and functional properties of hemoglobin dates back more than 150 years, the topic has not lost its relevance today. The most important component of these studies is the development of mathematical ...

    Abstract Despite the fact that the investigation of the structural and functional properties of hemoglobin dates back more than 150 years, the topic has not lost its relevance today. The most important component of these studies is the development of mathematical models that formalize and generalize the mechanisms determining the cooperative binding of ligands based on data on the structural and functional state of the protein. In this work, we review the mathematical relationships describing oxygen binding by hemoglobin, ranging from the classical Hüfner, Hill, and Adair equations to the Szabo-Karplus and tertiary two-state mathematical models based on the Monod-Wyman-Changeux and Koshland-Némethy-Filmer concepts. The generality of the considered equations as mathematical functions, bearing in their basis a power dependence, is demonstrated. The problems and possible solutions related to approximation of experimental data by the oxygenation equations with correlated fitting parameters are noted. Attention is paid to empirical equations, extended versions of the Hill equation, where the coefficient of cooperation is modulated by Gauss and Lorentz distributions as functions of partial oxygen pressure.
    Language English
    Publishing date 2023-08-16
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2486483-3
    ISSN 1867-2469 ; 1867-2450
    ISSN (online) 1867-2469
    ISSN 1867-2450
    DOI 10.1007/s12551-023-01110-4
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  4. Article ; Online: Theoretical Explanation for the Rarity of Antibody-Dependent Enhancement of Infection (ADE) in COVID-19.

    Boldova, Anna E / Korobkin, Julia D / Nechipurenko, Yury D / Sveshnikova, Anastasia N

    International journal of molecular sciences

    2022  Volume 23, Issue 19

    Abstract: Global vaccination against the SARS-CoV-2 virus has proved to be highly effective. However, the possibility of antibody-dependent enhancement of infection (ADE) upon vaccination remains underinvestigated. Here, we aimed to theoretically determine ... ...

    Abstract Global vaccination against the SARS-CoV-2 virus has proved to be highly effective. However, the possibility of antibody-dependent enhancement of infection (ADE) upon vaccination remains underinvestigated. Here, we aimed to theoretically determine conditions for the occurrence of ADE in COVID-19. We developed a series of mathematical models of antibody response: model Ab-a model of antibody formation; model Cv-a model of infection spread in the body; and a complete model, which combines the two others. The models describe experimental data on SARS-CoV and SARS-CoV-2 infections in humans and cell cultures, including viral load dynamics, seroconversion times and antibody concentration kinetics. The modelling revealed that a significant proportion of macrophages can become infected only if they bind antibodies with high probability. Thus, a high probability of macrophage infection and a sufficient amount of pre-existing antibodies are necessary for the development of ADE in SARS-CoV-2 infection. However, from the point of view of the dynamics of pneumocyte infection, the two cases where the body has a high concentration of preexisting antibodies and a high probability of macrophage infection and where there is a low concentration of antibodies in the body and no macrophage infection are indistinguishable. This conclusion could explain the lack of confirmed ADE cases for COVID-19.
    MeSH term(s) Antibodies, Viral ; Antibody-Dependent Enhancement ; COVID-19 ; Humans ; SARS Virus ; SARS-CoV-2
    Chemical Substances Antibodies, Viral
    Language English
    Publishing date 2022-09-26
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms231911364
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  5. Article ; Online: Fitting Parameters of a Modified Hill’s Equation and Their Influence on the Shape of the Model Hemoglobin Oxygenation Curve

    Igor A. Lavrinenko / Gennady A. Vashanov / José L. Hernández Cáceres / Yury D. Nechipurenko

    Oxygen, Vol 3, Iss 7, Pp 90-

    2023  Volume 101

    Abstract: Oxygen binds to hemoglobin cooperatively, and a correct description of this binding is relevant not only for understanding the mechanisms of involved molecular processes but also for clinical purposes. Hill’s equation, derived over a hundred years ago, ... ...

    Abstract Oxygen binds to hemoglobin cooperatively, and a correct description of this binding is relevant not only for understanding the mechanisms of involved molecular processes but also for clinical purposes. Hill’s equation, derived over a hundred years ago, is still the simplest and most efficient way to perform this description. However, in terms of accuracy, it is inferior to Adair´s equation, which contains more parameters. We proposed to use a modified Hill equation and showed that it allows a more accurate description of the binding of oxygen to hemoglobin than Adair’s equation. At the same time, unlike Adair’s equation, our model retains the physical meaning given to the original Hill equation. We considered and analyzed the influence of the equation parameters on the course of the oxygenation curve and presented the relationship between the fitting parameters and other parameters derived from them in the form of a diagram-graph, which, in our opinion, simplifies the perception of these estimates and can be useful in solving a number of problems for which the traditional way of analyzing the degree of cooperative interaction was via the Hill equation. We suggest that the newly proposed parameter h max introduced in our model should be regarded as crucial for a better description of the oxygenation curve.
    Keywords cooperativity ; oxygenation ; oxygenation curve ; oxyhemoglobin dissociation curve ; Hill equation ; Hill coefficient ; Analytical chemistry ; QD71-142 ; Inorganic chemistry ; QD146-197
    Subject code 612
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
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  6. Article ; Online: The Use of the Statistical Entropy in Some New Approaches for the Description of Biosystems

    Vladimir V. Aristov / Anatoly S. Buchelnikov / Yury D. Nechipurenko

    Entropy, Vol 24, Iss 172, p

    2022  Volume 172

    Abstract: Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of ... ...

    Abstract Some problems of describing biological systems with the use of entropy as a measure of the complexity of these systems are considered. Entropy is studied both for the organism as a whole and for its parts down to the molecular level. Correlation of actions of various parts of the whole organism, intercellular interactions and control, as well as cooperativity on the microlevel lead to a more complex structure and lower statistical entropy. For a multicellular organism, entropy is much lower than entropy for the same mass of a colony of unicellular organisms. Cooperativity always reduces the entropy of the system; a simple example of ligand binding to a macromolecule carrying two reaction centers shows how entropy is consistent with the ambiguity of the result in the Bernoulli test scheme. Particular attention is paid to the qualitative and quantitative relationship between the entropy of the system and the cooperativity of ligand binding to macromolecules. A kinetic model of metabolism. corresponding to Schrödinger’s concept of the maintenance biosystems by “negentropy feeding”, is proposed. This model allows calculating the nonequilibrium local entropy and comparing it with the local equilibrium entropy inherent in non-living matter.
    Keywords biological systems ; statistical entropy ; cooperative interactions ; macromolecule-ligand binding ; adsorption model ; kinetic model of metabolism ; Science ; Q ; Astrophysics ; QB460-466 ; Physics ; QC1-999
    Subject code 612
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: A New Model of Hemoglobin Oxygenation.

    Lavrinenko, Igor A / Vashanov, Gennady A / Hernández Cáceres, José L / Buchelnikov, Anatoly S / Nechipurenko, Yury D

    Entropy (Basel, Switzerland)

    2022  Volume 24, Issue 9

    Abstract: The study of hemoglobin oxygenation, starting from the classical works of Hill, has laid the foundation for molecular biophysics. The cooperative nature of oxygen binding to hemoglobin has been variously described in different models. In the Adair model, ...

    Abstract The study of hemoglobin oxygenation, starting from the classical works of Hill, has laid the foundation for molecular biophysics. The cooperative nature of oxygen binding to hemoglobin has been variously described in different models. In the Adair model, which better fits the experimental data, the constants of oxygen binding at various stages differ. However, the physical meaning of the parameters in this model remains unclear. In this work, we applied Hill's approach, extending its interpretation; we obtained a good agreement between the theory and the experiment. The equation in which the Hill coefficient is modulated by the Lorentz distribution for oxygen partial pressure approximates the experimental data better than not only the classical Hill equation, but also the Adair equation.
    Language English
    Publishing date 2022-08-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2014734-X
    ISSN 1099-4300 ; 1099-4300
    ISSN (online) 1099-4300
    ISSN 1099-4300
    DOI 10.3390/e24091214
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  8. Article ; Online: A New Bias Site for Epigenetic Modifications: How Non-Canonical GC Base Pairs Favor Mechanochemical Cleavage of DNA.

    Semyonov, Denis A / Eltsov, Ilia V / Nechipurenko, Yury D

    BioEssays : news and reviews in molecular, cellular and developmental biology

    2020  Volume 42, Issue 11, Page(s) e2000051

    Abstract: Properties of non-canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and ... ...

    Abstract Properties of non-canonical GC base pairs and their relations with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the transient GC wobble base pairs both in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms involving of 5-methylcytosine, is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar-phosphate backbone of DNA after cytosines, the asymmetric character of these breaks, and an increase in break frequency in CpG after cytosine methylation. As an alternative hypothesis, probable implication of GC
    MeSH term(s) 5-Methylcytosine ; Base Pairing/genetics ; Cytosine ; DNA/genetics ; Epigenesis, Genetic ; Nucleic Acid Conformation
    Chemical Substances 5-Methylcytosine (6R795CQT4H) ; Cytosine (8J337D1HZY) ; DNA (9007-49-2)
    Language English
    Publishing date 2020-08-23
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 50140-2
    ISSN 1521-1878 ; 0265-9247
    ISSN (online) 1521-1878
    ISSN 0265-9247
    DOI 10.1002/bies.202000051
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  9. Book ; Online: Non-Canonical GC Base Pairs and Mechanochemical Cleavage of DNA

    Semyonov, Denis A. / Nechipurenko, Yury D.

    2019  

    Abstract: Properties of non-canonical GC Base Pairs and their relation with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the Transient GC Wobble Base Pairs in the mechanisms of the mechanochemical cleavage of DNA and epigenetic ... ...

    Abstract Properties of non-canonical GC Base Pairs and their relation with mechanochemical cleavage of DNA are analyzed. A hypothesis of the involvement of the Transient GC Wobble Base Pairs in the mechanisms of the mechanochemical cleavage of DNA and epigenetic mechanisms with participation of 5-methylcytosine is proposed. The hypothesis explains the increase in the frequency of the breaks of the sugar-phosphate backbone of DNA after cytosines, asymmetric character of these breaks, and an increase in the frequency of breaks in CpG after cytosine methylation.

    Comment: 10 pages, 4 figures
    Keywords Quantitative Biology - Biomolecules ; Physics - Biological Physics
    Publishing date 2019-12-30
    Publishing country us
    Document type Book ; Online
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  10. Article: The Role of Acidosis in the Pathogenesis of Severe Forms of COVID-19.

    Nechipurenko, Yury D / Semyonov, Denis A / Lavrinenko, Igor A / Lagutkin, Denis A / Generalov, Evgenii A / Zaitceva, Anna Y / Matveeva, Olga V / Yegorov, Yegor E

    Biology

    2021  Volume 10, Issue 9

    Abstract: COVID-19 has specific characteristics that distinguish this disease from many other infections. We suggest that the pathogenesis of severe forms of COVID-19 can be associated with acidosis. This review article discusses several mechanisms potentially ... ...

    Abstract COVID-19 has specific characteristics that distinguish this disease from many other infections. We suggest that the pathogenesis of severe forms of COVID-19 can be associated with acidosis. This review article discusses several mechanisms potentially linking the damaging effects of COVID-19 with acidosis and shows the existence of a vicious cycle between the development of hypoxia and acidosis in COVID-19 patients. At the early stages of the disease, inflammation, difficulty in gas exchange in the lungs and thrombosis collectively contribute to the onset of acidosis. In accordance with the Verigo-Bohr effect, a decrease in blood pH leads to a decrease in oxygen saturation, which contributes to the exacerbation of acidosis and results in a deterioration of the patient's condition. A decrease in pH can also cause conformational changes in the S-protein of the virus and thus lead to a decrease in the affinity and avidity of protective antibodies. Hypoxia and acidosis lead to dysregulation of the immune system and multidirectional pro- and anti-inflammatory reactions, resulting in the development of a "cytokine storm". In this review, we highlight the potential importance of supporting normal blood pH as an approach to COVID-19 therapy.
    Language English
    Publishing date 2021-08-31
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2661517-4
    ISSN 2079-7737
    ISSN 2079-7737
    DOI 10.3390/biology10090852
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