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Irie K, Oda Y, Sumikama T, Oshima A, Fujiyoshi Y. The structural basis of divalent cation block in a tetrameric prokaryotic sodium channel. Nat Commun 2023; 14:4236. [PMID: 37454189 PMCID: PMC10349818 DOI: 10.1038/s41467-023-39987-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Divalent cation block is observed in various tetrameric ion channels. For blocking, a divalent cation is thought to bind in the ion pathway of the channel, but such block has not yet been directly observed. So, the behaviour of these blocking divalent cations remains still uncertain. Here, we elucidated the mechanism of the divalent cation block by reproducing the blocking effect into NavAb, a well-studied tetrameric sodium channel. Our crystal structures of NavAb mutants show that the mutations increasing the hydrophilicity of the inner vestibule of the pore domain enable a divalent cation to stack on the ion pathway. Furthermore, non-equilibrium molecular dynamics simulation showed that the stacking calcium ion repel sodium ion at the bottom of the selectivity filter. These results suggest the primary process of the divalent cation block mechanism in tetrameric cation channels.
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Affiliation(s)
- Katsumasa Irie
- Department of Biophysical Chemistry, School of Pharmaceutical Sciences, Wakayama Medical University, 25-1, Shichibancho, Wakayama, 640-8156, Japan.
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan.
| | - Yoshinori Oda
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
| | - Takashi Sumikama
- PRESTO, JST, Kawaguchi, 332-0012, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, 920-1192, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu, 501-11193, Japan
| | - Yoshinori Fujiyoshi
- Cellular and Structural Physiology Laboratory (CeSPL), Advanced Research Institute, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo, 113-8510, Japan
- CeSPIA Inc., 2-1-1, Otemachi, Chiyoda, Tokyo, 100-0004, Japan
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Panagiotopoulos AZ, Yue S. Dynamics of Aqueous Electrolyte Solutions: Challenges for Simulations. J Phys Chem B 2023; 127:430-437. [PMID: 36607836 DOI: 10.1021/acs.jpcb.2c07477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This Perspective article focuses on recent simulation work on the dynamics of aqueous electrolytes. It is well-established that full-charge, nonpolarizable models for water and ions generally predict solution dynamics that are too slow in comparison to experiments. Models with reduced (scaled) charges do better for solution diffusivities and viscosities but encounter issues describing other dynamic phenomena such as nucleation rates of crystals from solution. Polarizable models show promise, especially when appropriately parametrized, but may still miss important physical effects such as charge transfer. First-principles calculations are starting to emerge for these properties that are in principle able to capture polarization, charge transfer, and chemical transformations in solution. While direct ab initio simulations are still too slow for simulations of large systems over long time scales, machine-learning models trained on appropriate first-principles data show significant promise for accurate and transferable modeling of electrolyte solution dynamics.
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Affiliation(s)
| | - Shuwen Yue
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Pluhařová E, Stirnemann G, Laage D. On water reorientation dynamics in cation hydration shells. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Shaimardanov AR, Shulga DA, Palyulin VA. Is an Inductive Effect Explicit Account Required for Atomic Charges Aimed at Use within the Force Fields? J Phys Chem A 2022; 126:6278-6294. [PMID: 36054931 DOI: 10.1021/acs.jpca.2c02722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polarization and inductive effects are the concepts that have been widely used in qualitative and even quantitative descriptions of experimentally observed properties in chemistry. The polarization effect has proven to be important in cases of biomolecular modeling though still the vast majority of molecular simulations use the classical non-polarizable force fields. In the last few decades, a lot of effort has been put into promoting the polarization effect and incorporating it into modern force fields and charge calculation methods. In contrast, the inductive effect has not attracted such attention and is effectively absent in both classic and modern force fields. Thus, a question is whether this difference corresponds to the difference in the physical significance of the effects and their explicit account, or is an artifact that should be corrected in the next generation of force fields. The significance of the electronic effects is studied in this paper through the prism of performance of specific models for atomic charge calculation that take into explicit account a nested set of effects: the formal charge, the nearest neighbors, the inductive effect, and finally the model, which takes into account all effects, which are possible to account for using atomic charges. The specific choice for the methods is the following: formal charges, MMFF94 bond charge increments, Dynamic Electronegativity Relaxation (DENR), and RESP. We propose a special scheme for the separate estimation of each particular effect contribution. By pairwise comparing the residual molecular electrostatic potential (MEP) errors of those charge models (aimed at best reproducing the quantum chemical reference MEP), we sequentially revealed how the account of each effect contributes to the better-quality MEP reproduction. The following relative importance of effects was estimated; thus, the natural hierarchy of the effects was established. First, the account of formal charges is of primordial importance. Second, the nearest neighbors account is the next in significance. Third, the explicit account of inductive effect in empirical charge calculation schemes was shown to significantly─both qualitatively and quantitatively─improve the quality of MEP reproduction. Fourth, the contribution of polarization is indirectly assessed. Surprisingly, it is of the order of magnitude of the inductive effect even for the molecular systems, for which it is anticipated to be more significant. Finally, the relative importance of anisotropic effects in neutral molecules was additionally reviewed.
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Affiliation(s)
- Arslan R Shaimardanov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Dmitry A Shulga
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Vladimir A Palyulin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
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Opoku RA, Toubin C, Gomes ASP. Simulating core electron binding energies of halogenated species adsorbed on ice surfaces and in solution via relativistic quantum embedding calculations. Phys Chem Chem Phys 2022; 24:14390-14407. [PMID: 35647703 DOI: 10.1039/d1cp05836c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we investigate the effects of the environment on the X-ray photoelectron spectra of hydrogen chloride and chloride ions adsorbed on ice surfaces, as well as of chloride ions in water droplets. In our approach, we combine a density functional theory (DFT) description of the ice surface with that of halogen species using the recently developed relativistic core-valence separation equation of motion coupled cluster (CVS-EOM-IP-CCSD) via the frozen density embedding formalism (FDE), to determine the K and L1,2,3 edges of chlorine. Our calculations, which incorporate temperature effects through snapshots from classical molecular dynamics simulations, are shown to reproduce experimental trends in the change of the core binding energies of Cl- upon moving from a liquid (water droplets) to an interfacial (ice quasi-liquid layer) environment. Our simulations yield water valence band binding energies in good agreement with experiment, which vary little between the droplets and the ice surface. For halide core binding energies there is an overall trend for overestimating experimental values, though good agreement between theory and experiment is found for Cl- in water droplets and on ice. For HCl on the other hand there are significant discrepancies between experimental and calculated core binding energies when we consider structural models that maintain the H-Cl bond more or less intact. An analysis of models that allow for pre-dissociated and dissociated structures suggests that experimentally observed chemical shifts in binding energies between Cl- and HCl would require that H+ (in the form of H3O+) and Cl- are separated by roughly 4-6 Å.
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Affiliation(s)
- Richard A Opoku
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
| | - Céline Toubin
- Univ. Lille, CNRS, UMR 8523 - PhLAM - Physique des Lasers Atomes et Molécules, F-59000 Lille, France.
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Velez C, Acevedo O. Simulation of deep eutectic solvents: Progress to promises. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1598] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Caroline Velez
- Department of Chemistry University of Miami Coral Gables Florida USA
| | - Orlando Acevedo
- Department of Chemistry University of Miami Coral Gables Florida USA
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