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Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex. Molecules 2022; 27:molecules27030799. [PMID: 35164065 PMCID: PMC8839245 DOI: 10.3390/molecules27030799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/02/2022] Open
Abstract
The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.
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Kruchinin SE, Fedotova MV. Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions. J Phys Chem B 2021; 125:11219-11231. [PMID: 34597044 DOI: 10.1021/acs.jpcb.1c05117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu--Glu- pairing. Namely, the RISM data indicate Glu--Glu- binding by NH3+-COO- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.
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Affiliation(s)
- Sergey E Kruchinin
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
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3
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Chuev GN, Fedotova MV, Valiev M. Renormalized site density functional theory for models of ion hydration. J Chem Phys 2021; 155:064501. [PMID: 34391371 DOI: 10.1063/5.0060249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The development of accurate statistical mechanics models of molecular liquid systems is a problem of great practical and fundamental importance. Site-density functional theory (SDFT) is one of the promising directions in this area, but its success hinges upon the ability to efficiently reconcile the co-existence of two distinct intra- and inter-molecular interaction regimes in a molecular liquid. The renormalized formulation of SDFT (RSDFT), which we have recently developed, resolves this problem by introducing an additional potential field variable that decouples two interaction scales and maps the molecular liquid problem onto the effective simple liquid mixture. This work provides a critical assessment of RSDFT for the hydrated ion system-a problem that historically has always been one of the most difficult cases for SDFT applications. Using a two-site model of water, we perform a comprehensive analysis of hydrated alkali metal and halogen ions, including both structural and free energy based characteristics. The results indicate that RSDFT provides a significant improvement over conventional three-dimensional reference interaction site model implementations and may prove useful in coarse grained simulations based on two-site solvent models.
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Affiliation(s)
- Gennady N Chuev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science, Pushchino, Moscow Region 142290, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Akademicheskaya St., 1, 153045 Ivanovo, Russia
| | - Marat Valiev
- Molecular Sciences Software Group, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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Abstract
Schematic representation of the multipolar molecule surrounded by salt ions in a dielectric solvent medium.
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Affiliation(s)
- Yury A. Budkov
- School of Applied Mathematics
- National Research University Higher School of Economics
- 123458 Moscow
- Russia
- G. A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences
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Fedotova MV. Compatible osmolytes - bioprotectants: Is there a common link between their hydration and their protective action under abiotic stresses? J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111339] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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Cao S, Konovalov KA, Unarta IC, Huang X. Recent Developments in Integral Equation Theory for Solvation to Treat Density Inhomogeneity at Solute–Solvent Interface. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201900049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Siqin Cao
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Kirill A. Konovalov
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
| | - Ilona Christy Unarta
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
| | - Xuhui Huang
- Department of Chemistrythe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- Center of System Biology and Human HealthState Key Laboratory of Molecular Neuroscience, Hong Kong Branch Clear Water Bay Kowloon Hong Kong
- Bioengineering Graduate Programthe Hong Kong University of Science and TechnologyHong Kong of Chinese National EngineeringResearch Center for Tissue Restoration and Reconstructionthe Hong Kong University of Science and Technology Clear Water Bay Kowloon Hong Kong
- HKUST‐Shenzhen Research Institute Hi‐Tech Park, Nanshan Shenzhen 518057 China
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Shaukat S, Fedotova MV, Kruchinin SE, Bešter-Rogač M, Podlipnik Č, Buchner R. Hydration and ion association of aqueous choline chloride and chlorocholine chloride. Phys Chem Chem Phys 2019; 21:10970-10980. [DOI: 10.1039/c9cp01016e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Choline hydration occurs predominantly via its hydroxyl group, and weak contact ion pair formation with Cl− is via the onium moiety.
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Affiliation(s)
- Saadia Shaukat
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marija Bešter-Rogač
- Faculty of Chemistry and Chemical Technology
- Večna pot 113
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology
- Večna pot 113
- University of Ljubljana
- SI-1000 Ljubljana
- Slovenia
| | - Richard Buchner
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
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Levina E, Penkov NV, Rodionova NN, Tarasov SA, Barykina DV, Vener MV. Hydration of the Carboxylate Group in Anti-Inflammatory Drugs: ATR-IR and Computational Studies of Aqueous Solution of Sodium Diclofenac. ACS OMEGA 2018; 3:302-313. [PMID: 30023777 PMCID: PMC6044930 DOI: 10.1021/acsomega.7b01034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 12/27/2017] [Indexed: 05/12/2023]
Abstract
Diclofenac (active ingredient of Voltaren) has a significant, multifaceted role in medicine, pharmacy, and biochemistry. Its physical properties and impact on biomolecular structures still attract essential scientific interest. However, its interaction with water has not been described yet at the molecular level. In the present study, we shed light on the interaction between the steric hindrance (the intramolecular N-H···O bond, etc.) carboxylate group (-CO2-) with water. Aqueous solution of sodium declofenac is investigated using attenuated total reflection-infrared (ATR-IR) and computational approaches, i.e., classical molecular dynamics (MD) simulations and density functional theory (DFT). Our coupled classical MD simulations, DFT calculations, and ATR-IR spectroscopy results indicated that the -CO2- group of the diclofenac anion undergoes strong specific interactions with the water molecules. The combined experimental and theoretical techniques provide significant insights into the spectroscopic manifestation of these interactions and the structure of the hydration shell of the -CO2- group. Moreover, the developed methodology for the theoretical analysis of the ATR-IR spectrum could serve as a template for the future IR/Raman studies of the strong interaction between the steric hindrance -CO2- group of bioactive molecules with the water molecules in dilute aqueous solutions.
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Affiliation(s)
- Elena
O. Levina
- Department
of Molecular and Chemical Physics, Moscow
Institute of Physics and Technology, 7 Institutskiy per., 141700 Dolgoprudny, Russia
| | - Nikita V. Penkov
- Department
of Methods of Optical and Spectral Analysis, Institute of Cell Biophysics, Russian Academy of Sciences, 3 Institutskaya Street, 142292 Pushchino, Russia
| | - Natalia N. Rodionova
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Sergey A. Tarasov
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Daria V. Barykina
- OOO
“NPF” Materia Medica Holding, 47-1 Trifonovskaya Street, 129272 Moscow, Russia
| | - Mikhail V. Vener
- Department
of Quantum Chemistry, Mendeleev University
of Chemical Technology, 9 Miusskaya Square, 125047 Moscow, Russia
- E-mail:
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Fedotova MV, Kruchinin SE, Chuev GN. Local ion hydration structure in aqueous imidazolium-based ionic liquids: The effects of concentration and anion nature. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.09.087] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Hydration and ion-binding of glycine betaine: How they may be involved into protection of proteins under abiotic stresses. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.08.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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Fedotova MV, Kruchinin SE, Chuev GN. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. NEW J CHEM 2017. [DOI: 10.1039/c6nj03296f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics
- The Russian Academy of Sciences
- Pushchino
- Russia
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Dmitrieva OA, Fedotova MV, Buchner R. Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline. Phys Chem Chem Phys 2017; 19:20474-20483. [DOI: 10.1039/c7cp04335j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Strongly hydrated l-proline cooperatively binds Na+ and Cl− ions in aqueous solution.
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Affiliation(s)
- Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
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16
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Proline hydration at low temperatures: its role in the protection of cell from freeze-induced stress. Amino Acids 2016; 48:1685-94. [DOI: 10.1007/s00726-016-2232-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
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Bešter-Rogač M, Fedotova MV, Kruchinin SE, Klähn M. Mobility and association of ions in aqueous solutions: the case of imidazolium based ionic liquids. Phys Chem Chem Phys 2016; 18:28594-28605. [DOI: 10.1039/c6cp05010g] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining MD simulations and RISM calculations with experiments, we demonstrated that the interionic interactions of investigated ILs as model 1,1 electrolytes in water solutions are weak but evidently dependent on the molecular structure.
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Affiliation(s)
| | | | | | - Marco Klähn
- Institute of Chemical and Engineering Sciences
- Agency for Science
- Technology and Research
- Singapore
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Eiberweiser A, Nazet A, Kruchinin SE, Fedotova MV, Buchner R. Hydration and Ion Binding of the Osmolyte Ectoine. J Phys Chem B 2015; 119:15203-11. [PMID: 26565946 DOI: 10.1021/acs.jpcb.5b09276] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ectoine is a widespread osmolyte enabling halophilic bacteria to withstand high osmotic stress that has many potential applications ranging from cosmetics to its use as a therapeutic agent. In this contribution, combining experiment and theory, the hydration and ion-binding of this zwitterionic compound was studied to gain information on the functioning of ectoine in particular and of osmolytes in general. Dielectric relaxation spectroscopy was used to determine the effective hydration number of ectoine and its effective dipole moment in aqueous solutions with and without added NaCl. The obtained experimental data were compared with structural results from 1D-RISM and 3D-RISM calculations. It was found that ectoine is strongly hydrated, even in the presence of high salt concentrations. Upon addition of NaCl, ions are bound to ectoine but the formed complexes are not very stable. Interestingly, this osmolyte strongly rises the static relative permittivity of its solutions, shielding thus effectively long-range Coulomb interactions among ions in ectoine-containing solutions. We believe that via this effect, which should be common to all zwitterionic osmolytes, ectoine protects against excessive ions within the cell in addition to its strong osmotic activity protecting against ions outside.
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Affiliation(s)
- Andreas Eiberweiser
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Andreas Nazet
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences , Akademicheskaya st. 1, Ivanovo, Russia
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg , D-93040 Regensburg, Germany
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Fedotova MV, Dmitrieva OA. Characterization of selective binding of biologically relevant inorganic ions with the proline zwitterion by 3D-RISM theory. NEW J CHEM 2015. [DOI: 10.1039/c5nj01559f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The features of selective binding of several biologically relevant mono- and divalent inorganic ions with the proline zwitterion were studied over a wide range of electrolyte concentrations.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- Ivanovo 153045
- Russia
| | - Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- Ivanovo 153045
- Russia
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