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Melkikh AV, Bondar VV. Mechanisms and models of movement of protocells and bacteria in the early stages of evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 175:3-13. [PMID: 35987420 DOI: 10.1016/j.pbiomolbio.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
A review of the physicochemical models of the movement of protocells and bacteria was performed. The mechanisms of gliding and movement based on flagella are considered. Based on the models, the average speed of movement of protocells and bacteria was calculated. A physicochemical model of bacterial gliding was constructed. The efficiency of the process of converting the energy of ATP into the energy of motion is estimated. A review of models of movement with the help of flagella was performed. A model has been constructed for converting ATP energy into proton and sodium motive forces, which, in turn, are converted into energy of rotor rotation. The problem of the accuracy of operation of nanomachines, on the basis of which the directed movement of bacteria occurs, is discussed. The considered models can be applied to create nanomotors for medical purposes.
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Affiliation(s)
- A V Melkikh
- Ural Federal University, Yekaterinburg, Russia.
| | - V V Bondar
- Ural Federal University, Yekaterinburg, Russia
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Melkikh AV, Sutormina MI. From leaves to roots: Biophysical models of transport of substances in plants. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:53-83. [PMID: 35114180 DOI: 10.1016/j.pbiomolbio.2022.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 12/19/2022]
Abstract
The transport processes of substances in various plant tissues are extremely diverse. However, models aimed at elucidating the mechanisms of such processes are almost absent in the literature. A unified view of all these transport processes is necessary, considering the laws of statistical physics and thermodynamics. A model of active ion transport was constructed based on the laws of statistical physics. Using this model, we traced the entire pathway of substances and energy in a plant. The pathway included aspects of the production of energy in the process of photosynthesis, consumption of energy to obtain nutrients from the soil, transport of such substances to the main organelles of all types of plant cells, the rise of water with dissolved substances along the trunk to the leaves, and the evaporation of water, accompanied by a change in the percentage of isotopes caused by different rates of evaporation. Models of ion transport in the chloroplasts and mitochondria of plant cells have been constructed. A generalized model comprising plant cells and their vacuoles was analyzed. A model of the transport of substances in the roots of plants was also developed. Based on this model, the problem of transport of substances in tall trees has been considered. The calculated concentrations of ions in the vacuoles of cells and resting potentials agreed well with the experimental data.
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Affiliation(s)
- A V Melkikh
- Ural Federal University, Yekaterinburg, Russia.
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Melkikh AV, Sutormina M. Intra- and intercellular transport of substances: Models and mechanisms. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:184-202. [PMID: 31678255 DOI: 10.1016/j.pbiomolbio.2019.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/24/2022]
Abstract
Non-equilibrium-statistical models of intracellular transport are built. The most significant features of these models are microscopic reversibility and the explicit considerations of the driving forces of the process - the ATP-ADP chemical potential difference. In this paper, water transport using contractile vacuoles, the transport and assembly of microtubules and microfilaments, the protein distribution within a cell, the transport of neurotransmitters from the synaptic cleft and the transport of substances between cells using plasmodesmata are discussed. Endocytosis and phagocytosis models are considered, and transport tasks and information transfer mechanisms inside the cell are explored. Based on an analysis of chloroplast movement, it was concluded that they have a complicated method of influencing each other in the course of their movements. The role of quantum effects in sorting and control transport mechanisms is also discussed. It is likely that quantum effects play a large role in these processes, otherwise reliable molecular recognition would be impossible, which would lead to very low intracellular transport efficiency.
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Protocells and LUCA: Transport of substances from first physicochemical principles. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:85-104. [PMID: 30612704 DOI: 10.1016/j.pbiomolbio.2018.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 10/25/2018] [Accepted: 12/24/2018] [Indexed: 11/22/2022]
Abstract
Models of the transport of substances in protocells are considered from first physicochemical principles. Functional similarities and differences in the transport systems of archaea, cyanobacteria, E. coli, and diatoms have been analyzed. Based on the selection of the most important transport systems, a model of transport of substances through the membrane of the last universal common ancestor, LUCA, was constructed. Models of isotope separation in protocells were considered. Based on the proposed models, the difference in isotope concentrations in rocks can be predicted, which can serve as an indicator of the presence of life in the early stages of evolution. Mechanisms of energy conversion for the simplest forms of directed motion in protocells are considered. A special stage in the evolution of protocells is proposed - the minimal mobile cell.
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Melkikh AV, Bokunyaeva AO. A Model of Isotope Separation in Cells at the Early Stages of Evolution. ORIGINS LIFE EVOL B 2016; 46:95-104. [PMID: 26314576 DOI: 10.1007/s11084-015-9463-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 08/11/2015] [Indexed: 10/23/2022]
Abstract
The separation of the isotopes of certain ions can serve as an important criterion for the presence of life in the early stages of its evolution. A model of the separation of isotopes during their transport through the cell membrane is constructed. The dependence of the selection coefficient on various parameters is found. In particular, it is shown that the maximum efficiency of the transport of ions corresponds to the minimum enrichment coefficient. At the maximum enrichment, the efficiency of the transport system approaches ½. Calculated enrichment coefficients are compared with experimentally obtained values for different types of cells, and the comparison shows a qualitative agreement between these quantities.
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Affiliation(s)
- A V Melkikh
- Ural Federal University, Mita str. 19, Yekaterinburg, Russia.
| | - A O Bokunyaeva
- Ural Federal University, Mita str. 19, Yekaterinburg, Russia
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Biological complexity, quantum coherent states and the problem of efficient transmission of information inside a cell. Biosystems 2013; 111:190-8. [DOI: 10.1016/j.biosystems.2013.02.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/31/2013] [Accepted: 02/06/2013] [Indexed: 01/30/2023]
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Melkikh AV, Seleznev VD. Mechanisms and models of the active transport of ions and the transformation of energy in intracellular compartments. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 109:33-57. [DOI: 10.1016/j.pbiomolbio.2012.04.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 04/23/2012] [Accepted: 04/25/2012] [Indexed: 11/26/2022]
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Algorithms for optimization of the transport system in living and artificial cells. SYSTEMS AND SYNTHETIC BIOLOGY 2011; 5:87-96. [PMID: 22654996 DOI: 10.1007/s11693-011-9083-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 02/02/2011] [Accepted: 06/02/2011] [Indexed: 10/18/2022]
Abstract
An optimization of the transport system in a cell has been considered from the viewpoint of the operations research. Algorithms for an optimization of the transport system of a cell in terms of both the efficiency and a weak sensitivity of a cell to environmental changes have been proposed. The switching of various systems of transport is considered as the mechanism of weak sensitivity of a cell to changes in environment. The use of the algorithms for an optimization of a cardiac cell has been considered by way of example. We received theoretically for a cell of a cardiac muscle that at the increase of potassium concentration in the environment switching of transport systems for this ion takes place. This conclusion qualitatively coincides with experiments. The problem of synthesizing an optimal system in an artificial cell has been stated.
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Melkikh AV, Seleznev VD, Chesnokova OI. Analytical model of ion transport and conversion of light energy in chloroplasts. J Theor Biol 2010; 264:702-10. [PMID: 20380840 DOI: 10.1016/j.jtbi.2010.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 03/22/2010] [Accepted: 04/02/2010] [Indexed: 10/19/2022]
Abstract
An analytical model, which describes the stationary transformation of light energy to the energy of pigment electronic excitation, has been constructed. A proton pump of the thylakoid membrane has been considered as a two-level conformon. The difference between the energies of the excited and ground states of both the pigment and the protein complex is assumed to be the energy of an absorbed photon. It has been found how the concentration of ions in a lumen and the potential across the thylakoid membrane depend on the concentration of ions in the stroma and the brightness temperature of absorbed radiation. Conditions for the maximum efficiency of the photosynthesis process have been analyzed. This model has been used to determine the electric potential (phi approximately 6.7mV) at the chloroplast thylakoid membrane. The calculated value of the electric potential is in good agreement with the experimental data. A limitation on the stoichiometric coefficient of the proton transport through ATP-synthase, m>3, has been found theoretically.
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Affiliation(s)
- Alexey V Melkikh
- Ural State Technical University, 19 Mira St, 620002 Ekaterinburg, Russia.
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Melkikh AV, Bessarab DS. Model of active transport of ions through diatom cell biomembrane. Bull Math Biol 2010; 72:1912-24. [PMID: 20180033 DOI: 10.1007/s11538-010-9520-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 02/08/2010] [Indexed: 10/19/2022]
Abstract
A model of the active transport of ions in the Cascinodiscus wailesii diatom cell is constructed taking into account the transport of H(+), Na(+), K(+), Ca(+2), NO(3)(-), Cl(-), and NH(4)(+) ions. This model allows calculating intracellular concentrations of basic ions and the biomembrane resting potential. A hierarchical algorithm "one ion--one transport system" is used in the model. The dependence of the resting potential on the extracellular concentration of potassium is plotted in terms of the model. The calculated values are in good agreement with the corresponding experimental data.
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Affiliation(s)
- A V Melkikh
- Ural State Technical University, 19 Mira St, Ekaterinburg, Russia.
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Melkikh AV, Sutormina MI. A model of active transport of ions in hepatocytes. Biophysics (Nagoya-shi) 2010. [DOI: 10.1134/s0006350910010124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Model of Active Transport of Ions in Archaea Cells. Bull Math Biol 2008; 71:383-98. [DOI: 10.1007/s11538-008-9366-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 10/14/2008] [Indexed: 10/21/2022]
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Melkikh AV, Seleznev VD. Early stages of the evolution of life: a cybernetic approach. ORIGINS LIFE EVOL B 2008; 38:343-53. [PMID: 18521718 DOI: 10.1007/s11084-008-9139-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Accepted: 05/02/2008] [Indexed: 10/22/2022]
Abstract
Early stages of the evolution of life are considered in terms of control theory. A model is proposed for the transport of substances in a protocell possessing the property of robustness with regard to changes in the environmental concentration of a substance.
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Affiliation(s)
- Alexey V Melkikh
- Ural State Technical University, Mira str. 19, Yekaterinburg, Russia.
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Melkikh AV, Sutormina MI. Model of active transport of ions in cardiac cell. J Theor Biol 2008; 252:247-54. [PMID: 18353373 DOI: 10.1016/j.jtbi.2008.02.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 02/04/2008] [Accepted: 02/05/2008] [Indexed: 10/22/2022]
Abstract
A model of the active transport of ions in a cardiac muscle cell, which takes into account the active transport of Na(+), K(+), Ca(2+), Mg(2+), HCO(3)(-) and Cl(-) ions, has been constructed. The model allows independent calculations of the resting potential at the biomembrane and concentrations of basic ions (sodium, potassium, chlorine, magnesium and calcium) in a cell. For the analysis of transport processes in cardiac cell hierarchical algorithm "one ion-one transport system" was offered. The dependence of the resting potential on concentrations of the ions outside a cell has been established. It was shown, that ions of calcium and magnesium, despite their rather small concentration, play an essential role in maintenance of resting potential in cardiac cell. The calculated internal concentrations of ions are in good agreement with the corresponding experimental values.
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Affiliation(s)
- A V Melkikh
- Molecular Physics Chair, Ural State Technical University, 19 Mira Street, Yekaterinburg, Russia.
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Melkikh AV, Seleznev VD. Nonequilibrium statistical model of active transport of ions and ATP production in mitochondria. J Biol Phys 2008; 33:161-70. [PMID: 19669548 DOI: 10.1007/s10867-007-9053-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Accepted: 12/24/2007] [Indexed: 11/28/2022] Open
Abstract
A model of the active transport of ions through internal membranes of mitochondria is proposed. If concentrations of ions in a cell are known, this model allows calculating concentrations of all main ions (H(+), Ca(+2), K(+), Mg(2+), Na(+), Cl(-)) in the mitochondrion matrix and the resting potential across the membrane. The theoretical values satisfactorily agree with available experimental data on the concentrations and the potentials, including different operating regimes of the adenosine triphosphate (ATP) synthetase (the main regime, short circuiting or ATP synthetase blocking). The active transport of Mg(2+) ions in exchange for protons was assumed. In accordance with the model, the ATP synthetase operation is possible only if the stoichiometric coefficient of protons is 3.
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Melkikh AV, Seleznev VD. Models of active transport of neurotransmitters in synaptic vesicles. J Theor Biol 2007; 248:350-3. [PMID: 17583751 DOI: 10.1016/j.jtbi.2007.05.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Revised: 05/10/2007] [Accepted: 05/17/2007] [Indexed: 10/23/2022]
Abstract
Models of the active transport of neurotransmitters in synaptic vesicles were constructed. The models were used to determine the resting potential at membranes of synaptic vesicles: 40mV (monoamines and acetylcholine) and -40mV (glutamate). The potential at the membrane of a synaptic vesicle was almost absent for the transport of GABA and glycine. The neurotransmitter concentration of a cell was 0.1-18mM at the concentration of neurotransmitters in a vesicle equal to 0.5M. This result is in qualitative agreement with the relevant experimental data.
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Affiliation(s)
- Alexey V Melkikh
- Molecular Physics Chair, Ural State Technical University, 19 Mira Street, 620002 Yekaterinburg, Russia.
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