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Chakraborty J, Mahali K, Henaish AMA, Ahmed J, Alshehri SM, Hossain A, Roy S. Exploring the solubility and intermolecular interactions of biologically significant amino acids l-serine and L-cysteine in binary mixtures of H 2O + DMF, H 2O + DMSO and H 2O + ACN in temperature range from T = 288.15 K to 308.15 K. Biophys Chem 2024; 311:107272. [PMID: 38824845 DOI: 10.1016/j.bpc.2024.107272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/14/2024] [Accepted: 05/26/2024] [Indexed: 06/04/2024]
Abstract
In the presented work, a study on the solubility and intermolecular interactions of l-serine and L-cysteine was carried out in binary mixtures of H2O + dimethylformamide (DMF), H2O + dimethylsulfoxide (DMSO), and H2O + acetonitrile (ACN) in the temperature range of T = 288.15 K to 308.15 K. l-serine exhibited the highest solubility in water, while L-cysteine was more soluble in water-DMF. The solvation process was assessed through standard Gibbs energy calculations, indicating the solvation stability order: water-ACN > water-DMSO > water-DMF for l-serine, and water-DMF > water-DMSO > water-ACN for L-cysteine. This study also explored the influence of these amino acids on solvent-solvent interactions, revealing changes in chemical entropies and self-association patterns within the binary solvent mixtures.
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Affiliation(s)
- Jit Chakraborty
- Department of Chemistry, University of Kalyani, Kalyani 741235, Nadia, India; Department of Chemistry, JIS College of Engineering, Kalyani 741235, Nadia, India
| | - Kalachand Mahali
- Department of Chemistry, University of Kalyani, Kalyani 741235, Nadia, India.
| | - A M A Henaish
- Physics Department, Faculty of Science, Tanta University, Tanta 31527, Egypt; NANOTECH Center, Ural Federal University, Ekaterinburg 620002, Russia
| | - Jahangeer Ahmed
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Saad M Alshehri
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Aslam Hossain
- Smart Materials Research Institute, Southern Federal University, Sladkova 178/24, 344090 Rostov-on-Don, Russian Federation
| | - Sanjay Roy
- Department of Chemistry, School of Sciences, Netaji Subhas Open University, Kolkata, West Bengal, India.
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Drobotenko MI, Svidlov AA, Dorohova АA, Baryshev MG, Dzhimak SS. Medium viscosity influence on the open states genesis in a DNA molecule. J Biomol Struct Dyn 2023:1-9. [PMID: 38102872 DOI: 10.1080/07391102.2023.2294178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/01/2023] [Indexed: 12/17/2023]
Abstract
The studies were carried out by the mathematical modeling of DNA mechanical deformations. Numerical calculations done for the interferon alpha 17 gene, which consists of 980 base pairs. It has been established that the genesis and dynamics of open states in the DNA molecule depends on the magnitude of the external influence (torque) and on the viscosity of the environment. In addition, it is shown that the dynamics of open states zones can have a jump-like character with a small change in the magnitude of the torque. When torque is applied to all 980 base pairs of the gene, the following effect is observed: an increase in the viscosity of the medium leads to an increase in the value of the torque necessary for the occurrence of OS and DNA unwinding, i.e. viscosity plays an important stabilizing role in DNA dynamics. Under the influence of a localized torque on different (by the content of A-T and G-C pairs and location) regions of the interferon alpha 17 gene, it was found that the magnitude of the external torque necessary for the occurrence of open states at all calculated values of viscosity depends on the nucleotide composition. The dependence of the torque magnitude required for the open states occurrence on viscosity is observed when the torque is applied to areas close to the gene boundaries. At the same time, the significance of the end effect, which weakens DNA, decreased with increasing viscosity of the medium.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mikhail I Drobotenko
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
| | - Alexandr A Svidlov
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- 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
| | - Аnna A Dorohova
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- 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
| | - Mikhail G Baryshev
- Department of Safety and Productivity of agroecosystems, All-Russian Research Institute of Phytopathology, Russia
| | - Stepan S Dzhimak
- Department of Radiophysics and Nanothechnology, Physics Faculty, Kuban State University, Krasnodar, Russia
- 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
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Svidlov A, Drobotenko M, Basov A, Gerasimenko E, Elkina A, Baryshev M, Nechipurenko Y, Dzhimak S. Influence of Environmental Parameters on the Stability of the DNA Molecule. ENTROPY (BASEL, SWITZERLAND) 2021; 23:1446. [PMID: 34828144 PMCID: PMC8622188 DOI: 10.3390/e23111446] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022]
Abstract
Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.
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Affiliation(s)
- Alexander Svidlov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
| | - Mikhail Drobotenko
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
| | - Alexander Basov
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, 350063 Krasnodar, Russia
| | - Eugeny Gerasimenko
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Anna Elkina
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Mikhail Baryshev
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
| | - Yury Nechipurenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Stepan Dzhimak
- Department of Radiophysics and Nanothechnology, Kuban State University, 350040 Krasnodar, Russia; (A.S.); (M.D.); (A.B.); (A.E.); (M.B.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia
- Department of Technology of Fats, Cosmetics, Commodity Science, Processes and Devices Kuban State Technological University, 350072 Krasnodar, Russia;
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Najamuddin U, Gorji SG, Fitzgerald M. Genotypic variability in the composition of soluble protein from rice bran – Opportunities for nutrition. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.104077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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da Silva N, Ferreira LA, Belgovskiy AI, Madeira PP, Teixeira JA, Mann EK, Adin Mann J, Meyer WV, Smart AE, Chernyak VY, Uversky VN, Zaslavsky BY. Effects of different solutes on the physical chemical properties of aqueous solutions via rearrangement of hydrogen bonds in water. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Nomoto A, Nishinami S, Shiraki K. Solubility Parameters of Amino Acids on Liquid-Liquid Phase Separation and Aggregation of Proteins. Front Cell Dev Biol 2021; 9:691052. [PMID: 34222258 PMCID: PMC8242209 DOI: 10.3389/fcell.2021.691052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
The solution properties of amino acids determine the folding, aggregation, and liquid–liquid phase separation (LLPS) behaviors of proteins. Various indices of amino acids, such as solubility, hydropathy, and conformational parameter, describe the behaviors of protein folding and solubility both in vitro and in vivo. However, understanding the propensity of LLPS and aggregation is difficult due to the multiple interactions among different amino acids. Here, the solubilities of aromatic amino acids (SAs) were investigated in solution containing 20 types of amino acids as amino acid solvents. The parameters of SAs in amino acid solvents (PSASs) were varied and dependent on the type of the solvent. Specifically, Tyr and Trp had the highest positive values while Glu and Asp had the lowest. The PSAS values represent soluble and insoluble interactions, which collectively are the driving force underlying the formation of droplets and aggregates. Interestingly, the PSAS of a soluble solvent reflected the affinity between amino acids and aromatic rings, while that of an insoluble solvent reflected the affinity between amino acids and water. These findings suggest that the PSAS can distinguish amino acids that contribute to droplet and aggregate formation, and provide a deeper understanding of LLPS and aggregation of proteins.
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Affiliation(s)
- Akira Nomoto
- Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Suguru Nishinami
- Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kentaro Shiraki
- Pure and Applied Sciences, University of Tsukuba, Tsukuba, Japan
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Santra S, Dhurua S, Jana M. Analyzing the driving forces of insulin stability in the basic amino acid solutions: A perspective from hydration dynamics. J Chem Phys 2021; 154:084901. [PMID: 33639734 DOI: 10.1063/5.0038305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amino acids having basic side chains, as additives, are known to increase the stability of native-folded state of proteins, but their relative efficiency and the molecular mechanism are still controversial and obscure as well. In the present work, extensive atomistic molecular dynamics simulations were performed to investigate the hydration properties of aqueous solutions of concentrated arginine, histidine, and lysine and their comparative efficiency on regulating the conformational stability of the insulin monomer. We identified that in the aqueous solutions of the free amino acids, the nonuniform relaxation of amino acid-water hydrogen bonds was due to the entrapment of water molecules within the amino acid clusters formed in solutions. Insulin, when tested with these solutions, was found to show rigid conformations, relative to that in pure water. We observed that while the salt bridges formed by the lysine as an additive contributed more toward the direct interactions with insulin, the cation-π was more prominent for the insulin-arginine interactions. Importantly, it was observed that the preferentially more excluded arginine, compared to histidine and lysine from the insulin surface, enriches the hydration layer of the protein. Our study reveals that the loss of configurational entropy of insulin in arginine solution, as compared to that in pure water, is more as compared to the entropy loss in the other two amino acid solutions, which, moreover, was found to be due to the presence of motionally bound less entropic hydration water of insulin in arginine solution than in histidine or lysine solution.
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Affiliation(s)
- Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Shakuntala Dhurua
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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Mehrabi K, Javanmardi J, Rasoolzadeh A, Mohammadi AH. Thermodynamic modeling of clathrate hydrate stability conditions in the presence of amino acid aqueous solution. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113488] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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