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Mallick S, Agmon N. Lateral diffusion of ions near membrane surface. Phys Chem Chem Phys 2024; 26:19433-19449. [PMID: 38973628 DOI: 10.1039/d3cp04112c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Biological membranes isolate living cells from their environment, while allowing selective molecular transport between the inner and outer realms. For example, Na+ and K+ permeability through ionic channels contributes to neural conduction. Whether the ionic currents arise directly from cations in the bulk, or from the interface, is currently unclear. There are only scant results concerning lateral diffusion of ions on aquated membrane surfaces (and strong belief that this occurs through binding to a diffusing lipid). We performed classical molecular dynamics (MD) simulations of monovalent ions, Na+, K+, and Cl-, near the surface of the zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) membrane. Realistic force-fields for lipids (Amber's Lipid17 and Lipid21) and water (TIP4P-Ew) are tested for the mass and charge densities and the electrostatic potential across the membrane. These calculations reveal that the chloride can bind to the choline moiety through an intervening water molecule by forming a CH⋯OH hydrogen bond, while cations bind to both the phosphatic and carbonyl oxygens of phosphatidylcholine moieties. Upon transitioning from the bulk to the interface, a cation sheds some of its hydration water, which are replaced by headgroup atoms. Notably, an interfacial cation can bind 1-4 headgroup atoms, which is a key to understanding its surface hopping mechanism. We find that cation binding to three headgroup atoms immobilizes it, while binding to four energizes it. Consequently, the lateral cation diffusion rate is only 15-25 times slower than in the bulk, and 4-5 times faster than lipid self-diffusion. K+ diffusion is notably more anomalous than Na+, switching from sub- to super-diffusion after about 2 ns.
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Affiliation(s)
- Subhasish Mallick
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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Kumari M, Khatoon N, Sharma R, Adusumilli S, Auerbach A, Kashyap HK, Nayak TK. Mechanism of hydrophobic gating in the acetylcholine receptor channel pore. J Gen Physiol 2024; 156:e202213189. [PMID: 38153395 PMCID: PMC10757554 DOI: 10.1085/jgp.202213189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
Neuromuscular acetylcholine receptors (AChRs) are hetero-pentameric, ligand-gated ion channels. The binding of the neurotransmitter acetylcholine (ACh) to two target sites promotes a global conformational change of the receptor that opens the channel and allows ion conduction through the channel pore. Here, by measuring free-energy changes from single-channel current recordings and using molecular dynamics simulations, we elucidate how a constricted hydrophobic region acts as a "gate" to regulate the channel opening in the pore of AChRs. Mutations of gate residues, including those implicated in congenital myasthenia syndrome, lower the permeation barrier of the channel substantially and increase the unliganded gating equilibrium constant (constitutive channel openings). Correlations between hydrophobicity and the observed free-energy changes, supported by calculations of water densities in the wild-type versus mutant channel pores, provide evidence for hydrophobic wetting-dewetting transition at the gate. The analysis of a coupled interaction network provides insight into the molecular mechanism of closed- versus open-state conformational changes at the gate. Studies of the transition state by "phi"(φ)-value analysis indicate that agonist binding serves to stabilize both the transition and the open state. Intersubunit interaction energy measurements and molecular dynamics simulations suggest that channel opening involves tilting of the pore-lining M2 helices, asymmetric outward rotation of amino acid side chains, and wetting transition of the gate region that lowers the barrier to ion permeation and stabilizes the channel open conformation. Our work provides new insight into the hydrophobic gate opening and shows why the gate mutations result in constitutive AChR channel activity.
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Affiliation(s)
- Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Nadira Khatoon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Rachita Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Sushanth Adusumilli
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Anthony Auerbach
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Tapan K. Nayak
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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Da-yang TE, Lai CH. Potential energy surfaces of the Cu2+(NH3)n=1−10 clusters in solvent phase: A DFT study. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2023.111902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Miller SL, Gaidamauskas E, Altaf AA, Crans DC, Levinger NE. Where Are Sodium Ions in AOT Reverse Micelles? Fluoride Anion Probes Nanoconfined Ions by 19F Nuclear Magnetic Resonance Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37219990 DOI: 10.1021/acs.langmuir.3c00649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Confining water to nanosized spaces creates a unique environment that can change water's structural and dynamic properties. When ions are present in these nanoscopic spaces, the limited number of water molecules and short screening length can dramatically affect how ions are distributed compared to the homogeneous distribution assumed in bulk aqueous solution. Here, we demonstrate that the chemical shift observed in 19F NMR spectroscopy of fluoride anion, F-, probes the location of sodium ions, Na+, confined in reverse micelles prepared from AOT (sodium dioctyl sulfosuccinate) surfactants. Our measurements show that the nanoconfined environment of reverse micelles can lead to extremely high apparent ion concentrations and ionic strength, beyond the limit in bulk aqueous solutions. Most notably, the 19F NMR chemical shift trends we observe for F- in the reverse micelles indicate that the AOT sodium counterions remain at or near the interior interface between surfactant and water, thus providing the first experimental support for this hypothesis.
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Affiliation(s)
- Samantha L Miller
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ernestas Gaidamauskas
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Ataf Ali Altaf
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Chemistry, University of Okara, Okara 56300, Pakistan
| | - Debbie C Crans
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Cell and Molecular Biology Program, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Nancy E Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, United States
- Department of Electrical and Computer Engineering, Colorado State University, Fort Collins, Colorado 80523, United States
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Malloum A, Conradie J. Solvation of Manganese(III) Ion in Water and in Ammonia. J Phys Chem A 2023; 127:1103-1111. [PMID: 36716408 DOI: 10.1021/acs.jpca.2c05913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In this work, we have studied the solvation of manganese(III) ion in water and in ammonia using three levels of theory: MP2, MN15, and ωB97XD associated with the aug-cc-pVDZ basis set. The studied systems are constituted of Mn3+(H2O)6 and Mn3+(NH3)6 in gas and solvent phases as well as Mn3+(H2O)18 and Mn3+(NH3)18 in the gas phase. Four aspects of the solvation of manganese(III) ion have been examined for the aforementioned systems at the three levels of theory. First, we started by locating the Jahn-Teller elongated and compressed configuration in Mn3+(H2O)6 and Mn3+(NH3)6. Second, we calculated the spin state energies and the spin state free energies for temperatures ranging from 50 to 400 K to look at possible spin crossover in the studied systems. Third, we carried out a quantum theory of atoms in molecules (QTAIM) analysis, and we determined the ionic radii of manganese(III) ion in water and in ammonia. Fourth, we calculated the solvation free energies and the solvation enthalpies of manganese(III) ion in water and in ammonia using the cluster continuum solvation model. For these four aspects of the solvation of manganese(III) ion, most of the reported properties are provided in this work for the first time. We particularly found that the calculated solvation enthalpy of the manganese(III) ion in water is in good agreement with an experimental estimate.
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Affiliation(s)
- Alhadji Malloum
- Department of Chemistry, University of the Free State, Bloemfontein9300, South Africa.,Department of Physics, Faculty of Science, University of Maroua, Maroua, Cameroon
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, Bloemfontein9300, South Africa.,Department of Chemistry, UiT - The Arctic University of Norway, N-9037Tromsø, Norway
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Zhuang D, Riera M, Zhou R, Deary A, Paesani F. Hydration Structure of Na + and K + Ions in Solution Predicted by Data-Driven Many-Body Potentials. J Phys Chem B 2022; 126:9349-9360. [PMID: 36326071 DOI: 10.1021/acs.jpcb.2c05674] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The hydration structure of Na+ and K+ ions in solution is systematically investigated using a hierarchy of molecular models that progressively include more accurate representations of many-body interactions. We found that a conventional empirical pairwise additive force field that is commonly used in biomolecular simulations is unable to reproduce the extended X-ray absorption fine structure (EXAFS) spectra for both ions. In contrast, progressive inclusion of many-body effects rigorously derived from the many-body expansion of the energy allows the MB-nrg potential energy functions (PEFs) to achieve nearly quantitative agreement with the experimental EXAFS spectra, thus enabling the development of a molecular-level picture of the hydration structure of both Na+ and K+ in solution. Since the MB-nrg PEFs have already been shown to accurately describe isomeric equilibria and vibrational spectra of small ion-water clusters in the gas phase, the present study demonstrates that the MB-nrg PEFs effectively represent the long-sought-after models able to correctly predict the properties of ionic aqueous systems from the gas to the liquid phase, which has so far remained elusive.
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Affiliation(s)
- Debbie Zhuang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Ruihan Zhou
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Alexander Deary
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California92093, United States.,Materials Science and Engineering, University of California San Diego, La Jolla, California92093, United States.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California92093, United States
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Wills A, Fernández-Serra M. Role of water model on ion dissociation at ambient conditions. J Chem Phys 2021; 154:194502. [PMID: 34240899 DOI: 10.1063/5.0046188] [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
We study ion pair dissociation in water at ambient conditions using a combination of classical and ab initio approaches. The goal of this study is to disentangle the sources of discrepancy observed in computed potentials of mean force. In particular, we aim to understand why some models favor the stability of solvent-separated ion pairs vs contact ion pairs. We found that some observed differences can be explained by non-converged simulation parameters. However, we also unveil that for some models, small changes in the solution density can have significant effects on modifying the equilibrium balance between the two configurations. We conclude that the thermodynamic stability of contact and solvent-separated ion pairs is very sensitive to the dielectric properties of the underlying simulation model. In general, classical models are very robust in providing a similar estimation of the contact ion pair stability, while this is much more variable in density functional theory-based models. The barrier to transition from the solvent-separated to contact ion pair is fundamentally dependent on the balance between electrostatic potential energy and entropy. This reflects the importance of water intra- and inter-molecular polarizability in obtaining an accurate description of the screened ion-ion interactions.
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Affiliation(s)
- Alec Wills
- Physics and Astronomy Department, Stony Brook University. Stony Brook, New York 11794-3800, USA
| | - Marivi Fernández-Serra
- Physics and Astronomy Department, Stony Brook University. Stony Brook, New York 11794-3800, USA
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Boukar O, Fifen JJ, Nsangou M, Ghalila H, Conradie J. Structures and relative stability of hydrated ferrous ion clusters and temperature effects. NEW J CHEM 2021. [DOI: 10.1039/d1nj01849c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Structures of solvated ferrous ion clusters have been investigated in the singlet and quintet spin states of the ferrous ion. Relative stabilities of isomers are also discussed at different temperatures.
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Affiliation(s)
- Ousman Boukar
- Department of Physics
- Faculty of Science
- University of Maroua
- Cameroon
| | - Jean Jules Fifen
- Quantum Theory and Aplications Unit
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
| | - Mama Nsangou
- Department of Physics
- Faculty of Science
- University of Maroua
- Cameroon
- Quantum Theory and Aplications Unit
| | - Hassen Ghalila
- Faculty of Science
- University of Tunis El Manar
- Tunis
- Tunisia
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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Da-yang TE, Fifen JJ, Malloum A, Lahmar S, Nsangou M, Conradie J. Structures of the solvated copper(ii) ion in ammonia at various temperatures. NEW J CHEM 2020. [DOI: 10.1039/c9nj05169d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated theoretically the structures and relative stabilities of the solvated copper(ii) ion in ammonia, Cu2+(NH3)n, n = 1–10.
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Affiliation(s)
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- The University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
- Department of Physics
| | - Souad Lahmar
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Mama Nsangou
- University of Maroua
- Maroua
- Cameroon
- Department of Physics
- Faculty of Science
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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Boukar O, Fifen JJ, Malloum A, Dhaouadi Z, Ghalila H, Conradie J. Structures of solvated ferrous ion clusters in ammonia and spin-crossover at various temperatures. NEW J CHEM 2019. [DOI: 10.1039/c9nj02462j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The solvated ferrous ion in ammonia is hexa-coordinated, irrespective of the temperature.
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Affiliation(s)
- Ousman Boukar
- Department of Physics
- Faculty of Science
- University of Maroua
- Maroua
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | | | - Hassen Ghalila
- Faculty of Science
- University of Tunis El Manar
- Tunis
- Tunisia
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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