1
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Benjamin I. Hydronium Ion Transport across the Liquid/Liquid Interface Assisted by a Phase-Transfer Catalyst: Structure and Thermodynamics Using Molecular Dynamics Simulation. J Phys Chem B 2024; 128:9613-9618. [PMID: 39302249 DOI: 10.1021/acs.jpcb.4c04983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Molecular dynamics simulations are used to examine the thermodynamic and structural aspects of the transfer of the classical hydronium ion (H3O+) across a water/1,2-dichloroethane (DCE) interface assisted by the phase-transfer catalyst (PTC) tetrakis(pentafluorophenyl) borate anion (TPFB-). The free energy of transfer from water to DCE of the H3O+-TPFB- ion pair is calculated to be 6 ± 1 kcal/mol, significantly less than that of the free hydronium ion (17 ± 1 kcal/mol). The ion pair is relatively stable at the interface and in the organic phase when it is accompanied by three water molecules with a small barrier to dissociation that supports its utility as a PTC. An examination of the hydration structure that accompanies the transfer of the ion pair shows that the ion pair, like the free hydronium ion, is transferred with the assistance of a finger-like water structure.
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Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
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2
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de Lucas M, Blazquez S, Troncoso J, Vega C, Gámez F. Dressing a Nonpolarizable Force Field for OH - in TIP4P/2005 Aqueous Solutions with Corrected Hirshfeld Charges. J Phys Chem Lett 2024; 15:9411-9418. [PMID: 39248393 PMCID: PMC11417996 DOI: 10.1021/acs.jpclett.4c02261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/22/2024] [Accepted: 08/28/2024] [Indexed: 09/10/2024]
Abstract
We present a rigid model for the OH- ion parametrized for binary mixtures with TIP4P/2005-type water molecules. Li+, Na+ and K+ were selected as counterions, hence mimicking the important and widely used solutions of soluble alkaline hydroxides. The optimized atomic charge distributions were obtained by scaling in a factor of 0.85 those derived from the atomic dipole corrected Hirshfeld approach. The agreement between experimental and Molecular Dynamics simulation results is remarkable for a set of properties, namely, the dependence of the density of the solutions on the hydroxide concentration and on temperature, the structure (i.e., positions of the atom-to-atom radial distribution functions and coordination numbers), the viscosity coefficients, the surface tension, or the freezing point depression. The proposed optimized potential parameters for OH- thus enlarge the set of models comprised within the Madrid-2019 force field and widen the potential applicability of the TIP4P/2005 water model in basic environments.
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Affiliation(s)
- Marcos de Lucas
- Departamento
de Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, España
| | - Samuel Blazquez
- Departamento
de Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, España
| | - Jacobo Troncoso
- Departamento
de Física Aplicada, Universidade
de Vigo, Escola de Enxeñaría Aeronaútica e do
Espazo, E 32004, Ourense, España
| | - Carlos Vega
- Departamento
de Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, España
| | - Francisco Gámez
- Departamento
de Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, España
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3
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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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4
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Ramanthrikkovil Variyam A, Rzycki M, Yucknovsky A, Stuchebrukhov AA, Drabik D, Amdursky N. Proton diffusion on the surface of mixed lipid membranes highlights the role of membrane composition. Biophys J 2024:S0006-3495(24)00441-7. [PMID: 38961623 DOI: 10.1016/j.bpj.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/13/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
Proton circuits within biological membranes, the foundation of natural bioenergetic systems, are significantly influenced by the lipid compositions of different biological membranes. In this study, we investigate the influence of mixed lipid membrane composition on the proton transfer (PT) properties on the surface of the membrane. We track the excited-state PT (ESPT) process from a tethered probe to the membrane with timescales and length scales of PT relevant to bioenergetic systems. Two processes can happen during ESPT: the initial PT from the probe to the membrane at short timescales, followed by diffusion of dissociated protons around the probe on the membrane, and the possible geminate recombination with the probe at longer timescales. Here, we use membranes composed of mixtures of phosphatidylcholine (PC) and phosphatidic acid (PA). We show that the changes in the ESPT properties are not monotonous with the concentration of the lipid mixture; at a low concentration of PA in PC, we find that the membrane is a poor proton acceptor. Molecular dynamics simulations indicate that the membrane is more structured at this specific lipid mixture, with the least number of defects. Accordingly, we suggest that the structure of the membrane is an important factor in facilitating PT. We further show that the composition of the membrane affects the geminate proton diffusion around the probe, whereas, on a timescale of tens of nanoseconds, the dissociated proton is mostly lateral restricted to the membrane plane in PA membranes, while in PC, the diffusion is less restricted by the membrane.
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Affiliation(s)
| | - Mateusz Rzycki
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Anna Yucknovsky
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, Israel
| | | | - Dominik Drabik
- Department of Biomedical Engineering, Wroclaw University of Science and Technology, Wroclaw, Poland
| | - Nadav Amdursky
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, Israel.
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5
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Gasanoff ES, Dagda RK. Cobra Venom Cytotoxins as a Tool for Probing Mechanisms of Mitochondrial Energetics and Understanding Mitochondrial Membrane Structure. Toxins (Basel) 2024; 16:287. [PMID: 39057927 PMCID: PMC11281317 DOI: 10.3390/toxins16070287] [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: 05/15/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
In this paper, we provide an overview of mitochondrial bioenergetics and specific conditions that lead to the formation of non-bilayer structures in mitochondria. Secondly, we provide a brief overview on the structure/function of cytotoxins and how snake venom cytotoxins have contributed to increasing our understanding of ATP synthesis via oxidative phosphorylation in mitochondria, to reconcile some controversial aspects of the chemiosmotic theory. Specifically, we provide an emphasis on the biochemical contribution of delocalized and localized proton movement, involving direct transport of protons though the Fo unit of ATP synthase or via the hydrophobic environment at the center of the inner mitochondrial membrane (proton circuit) on oxidative phosphorylation, and how this influences the rate of ATP synthesis. Importantly, we provide new insights on the molecular mechanisms through which cobra venom cytotoxins affect mitochondrial ATP synthesis, mitochondrial structure, and dynamics. Finally, we provide a perspective for the use of cytotoxins as novel pharmacological tools to study membrane bioenergetics and mitochondrial biology, how they can be used in translational research, and their potential therapeutic applications.
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Affiliation(s)
- Edward S. Gasanoff
- STEM Research Center, Chaoyang Kaiwen Academy, Beijing 100018, China;
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Ruben K. Dagda
- Department of Pharmacology, University of Nevada Medical School, Reno, NV 89557, USA
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6
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Ramanthrikkovil Variyam A, Stolov M, Feng J, Amdursky N. Solid-State Molecular Protonics Devices of Solid-Supported Biological Membranes Reveal the Mechanism of Long-Range Lateral Proton Transport. ACS NANO 2024; 18:5101-5112. [PMID: 38314693 PMCID: PMC10867892 DOI: 10.1021/acsnano.3c11990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Abstract
Lateral proton transport (PT) on the surface of biological membranes is a fundamental biochemical process in the bioenergetics of living cells, but a lack of available experimental techniques has resulted in a limited understanding of its mechanism. Here, we present a molecular protonics experimental approach to investigate lateral PT across membranes by measuring long-range (70 μm) lateral proton conduction via a few layers of lipid bilayers in a solid-state-like environment, i.e., without having bulk water surrounding the membrane. This configuration enables us to focus on lateral proton conduction across the surface of the membrane while decoupling it from bulk water. Hence, by controlling the relative humidity of the environment, we can directly explore the role of water in the lateral PT process. We show that proton conduction is dependent on the number of water molecules and their structure and on membrane composition, where we explore the role of the headgroup, the tail saturation, the membrane phase, and membrane fluidity. The measured PT as a function of temperature shows an inverse temperature dependency, which we explain by the desorption and adsorption of water molecules into the solid membrane platform. We explain our findings by discussing the role of percolating hydrogen bonding within the membrane structure in a Grotthuss-like mechanism.
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Affiliation(s)
| | - Mikhail Stolov
- Wolfson
Department of Chemical Engineering, Technion
− Israel Institute of Technology, Haifa 3200003, Israel
| | - Jiajun Feng
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
| | - Nadav Amdursky
- Schulich
Faculty of Chemistry, Technion −
Israel Institute of Technology, Haifa 3200003, Israel
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7
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Knyazev DG, Silverstein TP, Brescia S, Maznichenko A, Pohl P. A New Theory about Interfacial Proton Diffusion Revisited: The Commonly Accepted Laws of Electrostatics and Diffusion Prevail. Biomolecules 2023; 13:1641. [PMID: 38002323 PMCID: PMC10669390 DOI: 10.3390/biom13111641] [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: 09/26/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The high propensity of protons to stay at interfaces has attracted much attention over the decades. It enables long-range interfacial proton diffusion without relying on titratable residues or electrostatic attraction. As a result, various phenomena manifest themselves, ranging from spillover in material sciences to local proton circuits between proton pumps and ATP synthases in bioenergetics. In an attempt to replace all existing theoretical and experimental insight into the origin of protons' preference for interfaces, TELP, the "Transmembrane Electrostatically-Localized Protons" hypothesis, has been proposed. The TELP hypothesis envisions static H+ and OH- layers on opposite sides of interfaces that are up to 75 µm thick. Yet, the separation at which the electrostatic interaction between two elementary charges is comparable in magnitude to the thermal energy is more than two orders of magnitude smaller and, as a result, the H+ and OH- layers cannot mutually stabilize each other, rendering proton accumulation at the interface energetically unfavorable. We show that (i) the law of electroneutrality, (ii) Fick's law of diffusion, and (iii) Coulomb's law prevail. Using them does not hinder but helps to interpret previously published experimental results, and also helps us understand the high entropy release barrier enabling long-range proton diffusion along the membrane surface.
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Affiliation(s)
- Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (D.G.K.); (S.B.); (A.M.)
| | | | - Stefania Brescia
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (D.G.K.); (S.B.); (A.M.)
| | - Anna Maznichenko
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (D.G.K.); (S.B.); (A.M.)
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University, 4020 Linz, Austria; (D.G.K.); (S.B.); (A.M.)
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8
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Maurer M, Lazaridis T. Comparison of classical and ab initio simulations of hydronium and aqueous proton transfer. J Chem Phys 2023; 159:134506. [PMID: 37795787 DOI: 10.1063/5.0166596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Proton transport in aqueous systems occurs by making and breaking covalent bonds, a process that classical force fields cannot reproduce. Various attempts have been made to remedy this deficiency, by valence bond theory or instantaneous proton transfers, but the ability of such methods to provide a realistic picture of this fundamental process has not been fully evaluated. Here we compare an ab initio molecular dynamics (AIMD) simulation of an excess proton in water to a simulation of a classical H3O+ in TIP3P water. The energy gap upon instantaneous proton transfer from H3O+ to an acceptor water molecule is much higher in the classical simulation than in the AIMD configurations evaluated with the same classical potential. The origins of this discrepancy are identified by comparing the solvent structures around the excess proton in the two systems. One major structural difference is in the tilt angle of the water molecules that accept an hydrogen bond from H3O+. The lack of lone pairs in TIP3P produces a tilt angle that is too large and generates an unfavorable geometry after instantaneous proton transfer. This problem can be alleviated by the use of TIP5P, which gives a tilt angle much closer to the AIMD result. Another important factor that raises the energy gap is the different optimal distance in water-water vs H3O+-water H-bonds. In AIMD the acceptor is gradually polarized and takes a hydronium-like configuration even before proton transfer actually happens. Ways to remedy some of these problems in classical simulations are discussed.
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Affiliation(s)
- Manuela Maurer
- Department of Chemistry, City College of New York/CUNY, 160 Convent Ave., New York, New York 10031, USA
| | - Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY, 160 Convent Ave., New York, New York 10031, USA
- Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Ave., New York, New York 10016, USA
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9
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Ledesma-Durán A, Juárez-Valencia LH. Diffusion coefficients and MSD measurements on curved membranes and porous media. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:70. [PMID: 37578670 DOI: 10.1140/epje/s10189-023-00329-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/28/2023] [Indexed: 08/15/2023]
Abstract
We study some geometric aspects that influence the transport properties of particles that diffuse on curved surfaces. We compare different approaches to surface diffusion based on the Laplace-Beltrami operator adapted to predict concentration along entire membranes, confined subdomains along surfaces, or within porous media. Our goal is to summarize, firstly, how diffusion in these systems results in different types of diffusion coefficients and mean square displacement measurements, and secondly, how these two factors are affected by the concavity of the surface, the shape of the possible barriers or obstacles that form the available domains, the sinuosity, tortuosity, and constrictions of the trajectories and even how the observation plane affects the measurements of the diffusion. In addition to presenting a critical and organized comparison between different notions of MSD, in this review, we test the correspondence between theoretical predictions and numerical simulations by performing finite element simulations and illustrate some situations where diffusion theory can be applied. We briefly reviewed computational schemes for understanding surface diffusion and finally, discussed how this work contributes to understanding the role of surface diffusion transport properties in porous media and their relationship to other transport processes.
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Affiliation(s)
- Aldo Ledesma-Durán
- Departmento de Matemáticas, Universidad Autónoma Metropolitana, CDMX, Mexico
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10
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Weichselbaum E, Galimzyanov T, Batishchev OV, Akimov SA, Pohl P. Proton Migration on Top of Charged Membranes. Biomolecules 2023; 13:352. [PMID: 36830721 PMCID: PMC9953355 DOI: 10.3390/biom13020352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/23/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Proton relay between interfacial water molecules allows rapid two-dimensional diffusion. An energy barrier, ΔGr‡, opposes proton-surface-to-bulk release. The ΔGr‡-regulating mechanism thus far has remained unknown. Here, we explored the effect interfacial charges have on ΔGr‡'s enthalpic and entropic constituents, ΔGH‡ and ΔGS‡, respectively. A light flash illuminating a micrometer-sized membrane patch of a free-standing planar lipid bilayer released protons from an adsorbed hydrophobic caged compound. A lipid-anchored pH-sensitive dye reported protons' arrival at a distant membrane patch. Introducing net-negative charges to the bilayer doubled ΔGH‡, while positive net charges decreased ΔGH‡. The accompanying variations in ΔGS‡ compensated for the ΔGH‡ modifications so that ΔGr‡ was nearly constant. The increase in the entropic component of the barrier is most likely due to the lower number and strength of hydrogen bonds known to be formed by positively charged residues as compared to negatively charged moieties. The resulting high ΔGr‡ ensured interfacial proton diffusion for all measured membranes. The observation indicates that the variation in membrane surface charge alone is a poor regulator of proton traffic along the membrane surface.
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Affiliation(s)
- Ewald Weichselbaum
- Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Timur Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology “MISiS”, Moscow 119991, Russia
| | - Oleg V. Batishchev
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Sergey A. Akimov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology “MISiS”, Moscow 119991, Russia
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
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11
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Local Attraction of Substrates and Co-Substrates Enhances Weak Acid and Base Transmembrane Transport. Biomolecules 2022; 12:biom12121794. [PMID: 36551222 PMCID: PMC9775063 DOI: 10.3390/biom12121794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
The transmembrane transport of weak acid and base metabolites depends on the local pH conditions that affect the protonation status of the substrates and the availability of co-substrates, typically protons. Different protein designs ensure the attraction of substrates and co-substrates to the transporter entry sites. These include electrostatic surface charges on the transport proteins and complexation with seemingly transport-unrelated proteins that provide substrate and/or proton antenna, or enzymatically generate substrates in place. Such protein assemblies affect transport rates and directionality. The lipid membrane surface also collects and transfers protons. The complexity in the various systems enables adjustability and regulation in a given physiological or pathophysiological situation. This review describes experimentally shown principles in the attraction and facilitation of weak acid and base transport substrates, including monocarboxylates, ammonium, bicarbonate, and arsenite, plus protons as a co-substrate.
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12
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Stuchebrukhov AA, Variyam AR, Amdursky N. Using Proton Geminate Recombination as a Probe of Proton Migration on Biological Membranes. J Phys Chem B 2022; 126:6026-6038. [PMID: 35921517 DOI: 10.1021/acs.jpcb.2c00953] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton migration on biological membranes plays a major role in cellular respiration and photosynthesis, but it is not yet fully understood. Here we show that proton dissociation kinetics and related geminate recombination can be used as a probe of such proton migration mechanisms. We develop a simple model for the process and apply it to analyze the results obtained using a photo-induced proton release probe (chemically modified photoacid) tethered to phosphatidylcholine membranes. In our theoretical model, we apply approximate treatment for the diffusional cloud of the geminate proton around the dissociated photoacid and consider arbitrary dimension of the system, 1 < d < 3. We observe that in d > 2, there is a kinetic phase transition between an exponential and a power-law kinetic phases. The existence of an exponential decay phase at the beginning of the proton dissociation is a signature of d > 2 systems. In most other cases, the exponential decay phase is not present, and the kinetics follows a diffusional power-law P(t) ∼ t-d/2 that develops after a short initiation time. Specifically, in a 1D case, which corresponds to the desorption of a proton from the surface, the dissociation occurs by the slow power-law ∼1/t and explains the abnormally slow desorption rate reported recently in experiments.
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Affiliation(s)
- Alexei A Stuchebrukhov
- Department of Chemistry, University of California at Davis, One Shields Avenue, Davis, California 95616, United States
| | | | - Nadav Amdursky
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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13
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Du Z, Piguet J, Baryshnikov G, Tornmalm J, Demirbay B, Ågren H, Widengren J. Imaging Fluorescence Blinking of a Mitochondrial Localization Probe: Cellular Localization Probes Turned into Multifunctional Sensors. J Phys Chem B 2022; 126:3048-3058. [PMID: 35417173 PMCID: PMC9059120 DOI: 10.1021/acs.jpcb.2c01271] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Indexed: 11/29/2022]
Abstract
Mitochondrial membranes and their microenvironments directly influence and reflect cellular metabolic states but are difficult to probe on site in live cells. Here, we demonstrate a strategy, showing how the widely used mitochondrial membrane localization fluorophore 10-nonyl acridine orange (NAO) can be transformed into a multifunctional probe of membrane microenvironments by monitoring its blinking kinetics. By transient state (TRAST) studies of NAO in small unilamellar vesicles (SUVs), together with computational simulations, we found that NAO exhibits prominent reversible singlet-triplet state transitions and can act as a light-induced Lewis acid forming a red-emissive doublet radical. The resulting blinking kinetics are highly environment-sensitive, specifically reflecting local membrane oxygen concentrations, redox conditions, membrane charge, fluidity, and lipid compositions. Here, not only cardiolipin concentration but also the cardiolipin acyl chain composition was found to strongly influence the NAO blinking kinetics. The blinking kinetics also reflect hydroxyl ion-dependent transitions to and from the fluorophore doublet radical, closely coupled to the proton-transfer events in the membranes, local pH, and two- and three-dimensional buffering properties on and above the membranes. Following the SUV studies, we show by TRAST imaging that the fluorescence blinking properties of NAO can be imaged in live cells in a spatially resolved manner. Generally, the demonstrated blinking imaging strategy can transform existing fluorophore markers into multiparametric sensors reflecting conditions of large biological relevance, which are difficult to retrieve by other means. This opens additional possibilities for fundamental membrane studies in lipid vesicles and live cells.
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Affiliation(s)
- Zhixue Du
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Joachim Piguet
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Glib Baryshnikov
- Laboratory
of Organic Electronics, Department of Science and Technology, Linköping University, SE-60174 Norrköping, Sweden
| | - Johan Tornmalm
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Baris Demirbay
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
| | - Hans Ågren
- Department
of Physics and Astronomy, Uppsala University, P.O. Box 516, SE-751 20 Uppsala, Sweden
| | - Jerker Widengren
- Royal
Institute of Technology (KTH), Experimental Biomolecular Physics,
Department Applied Physics, Albanova Univ
Center, 106 91 Stockholm, Sweden
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14
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Silverstein TP. A critique of the capacitor-based "Transmembrane Electrostatically Localized Proton" hypothesis. J Bioenerg Biomembr 2022; 54:59-65. [PMID: 35190945 DOI: 10.1007/s10863-022-09931-w] [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: 12/02/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
In his Transmembrane Electrostatically Localized Proton hypothesis (TELP), James W. Lee has modeled the bioenergetic membrane as a simple capacitor. According to this model, the surface concentration of protons is completely independent of proton concentration in the bulk phase, and is linearly proportional to the transmembrane potential. Such a proportionality runs counter to the results of experimental measurements, molecular dynamics simulations, and electrostatics calculations. We show that the TELP model dramatically overestimates the surface concentration of protons, and we discuss the electrostatic reasons why a simple capacitor is not an appropriate model for the bioenergetic membrane.
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15
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Chen Y, Fu X, Yu S, Quan K, Zhao C, Shao Z, Ye D, Qi H, Chen P. Parameterization of classical nonpolarizable force field for hydroxide toward the large‐scale molecular dynamics simulation of cellulose in pre‐cooled alkali/urea aqueous solution. J Appl Polym Sci 2021. [DOI: 10.1002/app.51477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yu Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Xiaotong Fu
- Key Laboratory of Eco‐Textiles, Ministry of Education Jiangnan University Wuxi Jiangsu Province China
| | - Shuxian Yu
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Kun Quan
- China Institute of Marine Technology and Economy Beijing China
| | - Changjun Zhao
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Ziqiang Shao
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
| | - Dongdong Ye
- School of Textile Materials and Engineering Wuyi University Jiangmen Guangdong Province China
| | - Haisong Qi
- State Key Laboratory of Pulp and Paper Engineering South China University of Technology Guangzhou Guangdong Province China
| | - Pan Chen
- Beijing Engineering Research Centre of Cellulose and Its Derivatives School of Materials Science and Engineering, Beijing Institute of Technology Beijing China
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16
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Hossain SI, Saha SC, Deplazes E. Phenolic compounds alter the ion permeability of phospholipid bilayers via specific lipid interactions. Phys Chem Chem Phys 2021; 23:22352-22366. [PMID: 34604899 DOI: 10.1039/d1cp03250j] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This study aims to understand the role of specific phenolic-lipid interactions in the membrane-altering properties of phenolic compounds. We combine tethered lipid bilayer (tBLM) electrical impedance spectroscopy (EIS) with all-atom molecular dynamics (MD) simulations to study the membrane interactions of six phenolic compounds: caffeic acid methyl ester, caffeic acid, 3,4 dihydroxybenzoic acid, chlorogenic acid, syringic acid and p-coumaric acid. tBLM/EIS experiments showed that caffeic acid methyl ester, caffeic acid and 3,4 dihydroxybenzoic acid significantly increase the permeability of phospholipid bilayers to Na+ ions. In contrast, chlorogenic acid, syringic acid and p-coumaric acid showed no effect. Experiments with lipids lacking the phosphate group show a significant decrease in the membrane-altering effects indicating that specific phenolic-lipid interactions are critical in altering ion permeability. MD simulations confirm that compounds that alter ion permeability form stable interactions with the phosphate oxygen. In contrast, inactive phenolic compounds are superficially bound to the membrane surface and primarily interact with interfacial water. Our combined results show that compounds with similar structures can have very different effects on ion permeability in membranes. These effects are governed by specific interactions at the water-lipid interface and show no correlation with lipophilicity. Furthermore, none of the compounds alter the overall structure of the phospholipid bilayer as determined by area per lipid and order parameters. Based on data from this study and previous findings, we propose that phenolic compounds can alter membrane ion permeability by causing local changes in lipid packing that subsequently reduce the energy barrier for ion-induced pores.
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Affiliation(s)
- Sheikh I Hossain
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia.
| | - Suvash C Saha
- School of Mechanical and Mechatronic Engineering, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia. .,School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD 4072, Australia
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17
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Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Water molecules play a key role in all biochemical processes. They help define the shape of proteins, and they are reactant or product in many reactions and are released as ligands are bound. They facilitate the transfer of protons through transmembrane proton channel, pump and transporter proteins. Continuum electrostatics (CE) force fields used by program Multiconformation CE (MCCE) capture electrostatic interactions in biomolecules with an implicit solvent, which captures the averaged solvent water equilibrium properties. Hybrid CE methods can use explicit water molecules within the protein surrounded by implicit solvent. These hybrid methods permit the study of explicit hydrogen bond networks within the protein and allow analysis of processes such as proton transfer reactions. Yet hybrid CE methods have not been rigorously tested. Here, we present an explicit treatment of water molecules in the Gramicidin A (gA) channel using MCCE and compare the resulting distributions of water molecules and key hydration features against those obtained with explicit solvent Molecular Dynamics (MD) simulations with the nonpolarizable CHARMM36 and polarizable Drude force fields. CHARMM36 leads to an aligned water wire in the channel characterized by a large absolute net water dipole moment; the MCCE and Drude analysis lead to a small net dipole moment as the water molecules change orientation within the channel. The correct orientation is not as yet known, so these calculations identify an open question.
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Affiliation(s)
- Yingying Zhang
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Kamran Haider
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
| | - Divya Kaur
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Van A. Ngo
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Xiuhong Cai
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Junjun Mao
- Levich Institute, School of Engineering, City College of New York, City University of New York, New York, NY 10031, USA
| | - Umesh Khaniya
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Xuyu Zhu
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Sergei Noskov
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, Calgary, AB, Canada
| | - Themis Lazaridis
- Department of Chemistry, The Graduate Center, City University of New York, New York, NY 10016, USA
- Department of Chemistry, City College of New York, City University of New York, New York, NY 10031, USA
| | - M. R. Gunner
- Department of Physics, City College of New York, City University of New York, New York, NY 10031, USA
- Department of Physics, The Graduate Center, City University of New York, New York, NY 10016, USA
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18
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Morelli AM, Ravera S, Panfoli I. The aerobic mitochondrial ATP synthesis from a comprehensive point of view. Open Biol 2020; 10:200224. [PMID: 33081639 PMCID: PMC7653358 DOI: 10.1098/rsob.200224] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Most of the ATP to satisfy the energetic demands of the cell is produced by the F1Fo-ATP synthase (ATP synthase) which can also function outside the mitochondria. Active oxidative phosphorylation (OxPhos) was shown to operate in the photoreceptor outer segment, myelin sheath, exosomes, microvesicles, cell plasma membranes and platelets. The mitochondria would possess the exclusive ability to assemble the OxPhos molecular machinery so to share it with the endoplasmic reticulum (ER) and eventually export the ability to aerobically synthesize ATP in true extra-mitochondrial districts. The ER lipid rafts expressing OxPhos components is indicative of the close contact of the two organelles, bearing different evolutionary origins, to maximize the OxPhos efficiency, exiting in molecular transfer from the mitochondria to the ER. This implies that its malfunctioning could trigger a generalized oxidative stress. This is consistent with the most recent interpretations of the evolutionary symbiotic process whose necessary prerequisite appears to be the presence of the internal membrane system inside the eukaryote precursor, of probable archaeal origin allowing the engulfing of the α-proteobacterial precursor of mitochondria. The process of OxPhos in myelin is here studied in depth. A model is provided contemplating the biface arrangement of the nanomotor ATP synthase in the myelin sheath.
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Affiliation(s)
- Alessandro Maria Morelli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | - Silvia Ravera
- Experimental Medicine Department (DIMES), University of Genova, Via De Toni, 14, 16132 Genova, Italy
| | - Isabella Panfoli
- Pharmacy Department (DIFAR), Biochemistry Laboratory, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
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19
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Benjamin I. Molecular Dynamics Studies on the Effect of Surface Roughness and Surface Tension on the Thermodynamics and Dynamics of Hydronium Ion Transfer Across the Liquid/Liquid Interface. J Phys Chem B 2020; 124:8711-8718. [PMID: 32902279 DOI: 10.1021/acs.jpcb.0c06304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Molecular dynamics simulations are used to examine the effect of surface roughness and surface tension on the transfer of the classical hydronium ion (H3O+) across the water/1,2-dichloroethane interface. Free energy of transfer, hydration structure, and dynamics as a function of the ion location along the interface normal are calculated with six different values of a control parameter whose variation modifies the surface tension without impacting the bulk properties of the two solvents. Transfer of the classical hydronium ion across the water/1,2-dichloroethan interface involves the cotransfer of three hydration shell water molecules, independent of the surface tension. However, as the interaction between the two liquids weakens, a rise in interfacial tension and decrease in intrinsic water fingering and capillary fluctuations result in fewer water molecules cotransported with the ion in the second shell and a reduction in the length of the finger that the ion is attached to, consistent with the reduced size of the second hydration shell. First shell water residence time and lateral ion diffusion constants vary with the surface tension in a way that is consistent with the abovementioned structural insight.
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Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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20
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Affiliation(s)
- Nadav Amdursky
- Schulich Faculty of ChemistryTechnion – Israel Institute of Technology Haifa 3200003 Israel
| | - Yiyang Lin
- State Key Laboratory of Organic-Inorganic Composites Beijing Laboratory of Biomedical MaterialsBeijing University of Chemical Technology Beijing 100029 China
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21
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Singh S. Dynamics of the mixtures of fullerene‐60 and aromatic solvents: A molecular dynamics approach. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Satnam Singh
- Department of Physical Sciences Indian Institute of Science Education & Research (IISER) Mohali Sector 81 SAS Nagar, Manauli Punjab 140306 India
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22
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Li Z, Voth GA. Interfacial solvation and slow transport of hydrated excess protons in non-ionic reverse micelles. Phys Chem Chem Phys 2020; 22:10753-10763. [PMID: 32154815 DOI: 10.1039/d0cp00378f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work employs molecular dynamics simulations to investigate the solvation and transport properties of hydrated excess protons (with a hydronium-like core structure) in non-ionic Igepal CO-520 reverse micelles of various sizes in a non-polar solvent. Multiscale Reactive Molecular Dynamics (MS-RMD) simulations were used to describe vehicular and hopping diffusion during the proton transport process. As detailed herein, an excess proton shows a marked tendency to localize in the interfacial region of micellar water pools. Slow proton transport was observed which becomes faster with increasing micellar size. Further analysis reveals that the slow diffusion of an excess proton is a combined result of slow water diffusion and the low proton hopping rate. This study also confirms that a low proton hopping rate in reverse micelles stems from the interfacial solvation of hydrated excess protons and the immobilization of interfacial water. The low water density in the interfacial region makes it difficult to form a complete hydrogen bond network near the hydrated excess proton, and therefore locks in the orientation of hydrated proton cations. The immobilization of the interfacial water also slows the relaxation of the overall hydrogen bond network.
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Affiliation(s)
- Zhefu Li
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, USA.
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23
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Morelli AM, Ravera S, Calzia D, Panfoli I. An update of the chemiosmotic theory as suggested by possible proton currents inside the coupling membrane. Open Biol 2020; 9:180221. [PMID: 30966998 PMCID: PMC6501646 DOI: 10.1098/rsob.180221] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Understanding how biological systems convert and store energy is a primary purpose of basic research. However, despite Mitchell's chemiosmotic theory, we are far from the complete description of basic processes such as oxidative phosphorylation (OXPHOS) and photosynthesis. After more than half a century, the chemiosmotic theory may need updating, thanks to the latest structural data on respiratory chain complexes. In particular, up-to date technologies, such as those using fluorescence indicators following proton displacements, have shown that proton translocation is lateral rather than transversal with respect to the coupling membrane. Furthermore, the definition of the physical species involved in the transfer (proton, hydroxonium ion or proton currents) is still an unresolved issue, even though the latest acquisitions support the idea that protonic currents, difficult to measure, are involved. Moreover, FoF1-ATP synthase ubiquitous motor enzyme has the peculiarity (unlike most enzymes) of affecting the thermodynamic equilibrium of ATP synthesis. It seems that the concept of diffusion of the proton charge expressed more than two centuries ago by Theodor von Grotthuss is to be taken into consideration to resolve these issues. All these uncertainties remind us that also in biology it is necessary to consider the Heisenberg indeterminacy principle, which sets limits to analytical questions.
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Affiliation(s)
- Alessandro Maria Morelli
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Silvia Ravera
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
| | - Daniela Calzia
- 1 Pharmacy Department, Biochemistry Lab, University of Genova , Viale Benedetto XV 3, 16132 Genova , Italy
| | - Isabella Panfoli
- 2 Experimental Medicine Department, University of Genova , Via De Toni 14, 16132 Genova , Italy
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24
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Deplazes E, Sarrami F, Poger D. Effect of H3O+ on the Structure and Dynamics of Water at the Interface with Phospholipid Bilayers. J Phys Chem B 2020; 124:1361-1373. [DOI: 10.1021/acs.jpcb.9b10169] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
- School of Pharmacy and Biomedical Sciences, Curtin Institute for Computation, Curtin University, Perth, Western Australia 6845, Australia
| | - Farzaneh Sarrami
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Benjamin I. Hydronium ion at the water/1,2-dichloroethane interface: Structure, thermodynamics, and dynamics of ion transfer. J Chem Phys 2019; 151:094701. [DOI: 10.1063/1.5116008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ilan Benjamin
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, USA
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26
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Deplazes E, White J, Murphy C, Cranfield CG, Garcia A. Competing for the same space: protons and alkali ions at the interface of phospholipid bilayers. Biophys Rev 2019; 11:483-490. [PMID: 31115866 DOI: 10.1007/s12551-019-00541-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022] Open
Abstract
Maintaining gradients of solvated protons and alkali metal ions such as Na+ and K+ across membranes is critical for cellular function. Over the last few decades, both the interactions of protons and alkali metal ions with phospholipid membranes have been studied extensively and the reported interactions of these ions with phospholipid headgroups are very similar, yet few studies have investigated the potential interdependence between proton and alkali metal ion binding at the water-lipid interface. In this short review, we discuss the similarities between the proton-membrane and alkali ion-membrane interactions. Such interactions include cation attraction to the phosphate and carbonyl oxygens of the phospholipid headgroups that form strong lipid-ion and lipid-ion-water complexes. We also propose potential mechanisms that may modulate the affinities of these cationic species to the water-phospholipid interfacial oxygen moieties. This review aims to highlight the potential interdependence between protons and alkali metal ions at the membrane surface and encourage a more nuanced understanding of the complex nature of these biologically relevant processes.
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Affiliation(s)
- Evelyne Deplazes
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia. .,School of Pharmacy and Biomedical Sciences, Curtin University, Perth, WA, 6845, Australia.
| | - Jacqueline White
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Christopher Murphy
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Charles G Cranfield
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Alvaro Garcia
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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27
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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28
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Exploring fast proton transfer events associated with lateral proton diffusion on the surface of membranes. Proc Natl Acad Sci U S A 2019; 116:2443-2451. [PMID: 30679274 DOI: 10.1073/pnas.1812351116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Proton diffusion (PD) across biological membranes is a fundamental process in many biological systems, and much experimental and theoretical effort has been employed for deciphering it. Here, we report on a spectroscopic probe, which can be tightly tethered to the membrane, for following fast (nanosecond) proton transfer events on the surface of membranes. Our probe is composed of a photoacid that serves as our light-induced proton source for the initiation of the PD process. We use our probe to follow PD, and its pH dependence, on the surface of lipid vesicles composed of a zwitterionic headgroup, a negative headgroup, a headgroup that is composed only from the negative phosphate group, or a positive headgroup without the phosphate group. We reveal that the PD kinetic parameters are highly sensitive to the nature of the lipid headgroup, ranging from a fast lateral diffusion at some membranes to the escape of protons from surface to bulk (and vice versa) at others. By referring to existing theoretical models for membrane PD, we found that while some of our results confirm the quasi-equilibrium model, other results are in line with the nonequilibrium model.
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29
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The effect of H 3O + on the membrane morphology and hydrogen bonding of a phospholipid bilayer. Biophys Rev 2018; 10:1371-1376. [PMID: 30219992 DOI: 10.1007/s12551-018-0454-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/06/2018] [Indexed: 12/30/2022] Open
Abstract
At the 2017 meeting of the Australian Society for Biophysics, we presented the combined results from two recent studies showing how hydronium ions (H3O+) modulate the structure and ion permeability of phospholipid bilayers. In the first study, the impact of H3O+ on lipid packing had been identified using tethered bilayer lipid membranes in conjunction with electrical impedance spectroscopy and neutron reflectometry. The increased presence of H3O+ (i.e. lower pH) led to a significant reduction in membrane conductivity and increased membrane thickness. A first-order explanation for the effect was assigned to alterations in the steric packing of the membrane lipids. Changes in packing were described by a critical packing parameter (CPP) related to the interfacial area and volume and shape of the membrane lipids. We proposed that increasing the concentraton of H3O+ resulted in stronger hydrogen bonding between the phosphate oxygens at the water-lipid interface leading to a reduced area per lipid and slightly increased membrane thickness. At the meeting, a molecular model for these pH effects based on the result of our second study was presented. Multiple μs-long, unrestrained molecular dynamic (MD) simulations of a phosphatidylcholine lipid bilayer were carried out and showed a concentration dependent reduction in the area per lipid and an increase in bilayer thickness, in agreement with experimental data. Further, H3O+ preferentially accumulated at the water-lipid interface, suggesting the localised pH at the membrane surface is much lower than the bulk bathing solution. Another significant finding was that the hydrogen bonds formed by H3O+ ions with lipid headgroup oxygens are, on average, shorter in length and longer-lived than the ones formed in bulk water. In addition, the H3O+ ions resided for longer periods in association with the carbonyl oxygens than with either phosphate oxygen in lipids. In summary, the MD simulations support a model where the hydrogen bonding capacity of H3O+ for carbonyl and phosphate oxygens is the origin of the pH-induced changes in lipid packing in phospholipid membranes. These molecular-level studies are an important step towards a better understanding of the effect of pH on biological membranes.
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30
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Rigler R, Widengren J. Fluorescence-based monitoring of electronic state and ion exchange kinetics with FCS and related techniques: from T-jump measurements to fluorescence fluctuations. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2018; 47:479-492. [PMID: 29260269 PMCID: PMC5982452 DOI: 10.1007/s00249-017-1271-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/30/2017] [Accepted: 12/03/2017] [Indexed: 11/01/2022]
Abstract
In this review, we give a historical view of how our research in the development and use of fluorescence correlation spectroscopy (FCS) and related techniques has its roots and how it originally evolved from the pioneering work of Manfred Eigen, his colleagues, and coworkers. Work on temperature-jump (T-jump) experiments, conducted almost 50 years ago, led on to the development of the FCS technique. The pioneering work in the 1970s, introducing and demonstrating the concept for FCS, in turn formed the basis for the breakthrough use of FCS more than 15 years later. FCS can be used for monitoring reaction kinetics, based on fluctuations at thermodynamic equilibrium, rather than on relaxation measurements following perturbations. In this review, we more specifically discuss FCS measurements on photodynamic, electronic state transitions in fluorophore molecules, and on proton exchange dynamics in solution and on biomembranes. In the latter case, FCS measurements have proven capable of casting new light on the mechanisms of proton exchange at biological membranes, of central importance to bioenergetics and signal transduction. Finally, we describe the transient-state (TRAST) spectroscopy/imaging technique, sharing features with both relaxation (T-jump) and equilibrium fluctuation (FCS) techniques. TRAST is broadly applicable for cellular and molecular studies, and we briefly outline how TRAST can provide unique information from fluorophore blinking kinetics, reflecting e.g., cellular metabolism, rare molecular encounters, and molecular stoichiometries.
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Affiliation(s)
- Rudolf Rigler
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics/ Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm, Sweden.
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31
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Dynamic Water Hydrogen-Bond Networks at the Interface of a Lipid Membrane Containing Palmitoyl-Oleoyl Phosphatidylglycerol. J Membr Biol 2018. [DOI: 10.1007/s00232-018-0023-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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32
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Nguyen TH, Zhang C, Weichselbaum E, Knyazev DG, Pohl P, Carloni P. Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion. PLoS One 2018; 13:e0193454. [PMID: 29474432 PMCID: PMC5825111 DOI: 10.1371/journal.pone.0193454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/26/2018] [Indexed: 11/19/2022] Open
Abstract
Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence. Hence, the specific water-proton interaction may help explain the proton mobility experimentally observed at the membrane interface.
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Affiliation(s)
- Trung Hai Nguyen
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
| | - Chao Zhang
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
- * E-mail: (CZ); (PC)
| | | | - Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Paolo Carloni
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
- * E-mail: (CZ); (PC)
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33
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Daldrop JO, Saita M, Heyden M, Lorenz-Fonfria VA, Heberle J, Netz RR. Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism. Nat Commun 2018; 9:311. [PMID: 29358659 PMCID: PMC5778031 DOI: 10.1038/s41467-017-02669-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal. Protein-bound water clusters play a key role for proton transport and storage in molecular biology. Here, the authors show by simulations and experiments that the orientation of non-spherical protonated water clusters in bacteriorhodopsin is unveiled by polarization-resolved infrared spectroscopy.
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Affiliation(s)
- Jan O Daldrop
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Mattia Saita
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | | | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
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34
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Deplazes E, Poger D, Cornell B, Cranfield CG. The effect of hydronium ions on the structure of phospholipid membranes. Phys Chem Chem Phys 2018; 20:357-366. [DOI: 10.1039/c7cp06776c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work studies the mechanisms by which hydronium ions modulate the structure of phospholipid bilayers.
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Affiliation(s)
- Evelyne Deplazes
- School of Biomedical Sciences
- Curtin Health Innovation Research Institute and Curtin Institute for Computation
- Curtin University
- Perth
- Australia
| | - David Poger
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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35
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Gennis RB. Proton Dynamics at the Membrane Surface. Biophys J 2017; 110:1909-11. [PMID: 27166799 DOI: 10.1016/j.bpj.2016.04.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 11/16/2022] Open
Affiliation(s)
- Robert B Gennis
- Department of Biochemistry, University of Illinois, Urbana, Illinois.
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36
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Sato T, Tsukamoto M, Yamamoto S, Mitsuishi M, Miyashita T, Nagano S, Matsui J. Acid-Group-Content-Dependent Proton Conductivity Mechanisms at the Interlayer of Poly(N-dodecylacrylamide-co-acrylic acid) Copolymer Multilayer Nanosheet Films. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12897-12902. [PMID: 29058441 DOI: 10.1021/acs.langmuir.7b03160] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The effect of the content of acid groups on the proton conductivity at the interlayer of polymer-nanosheet assemblies was investigated. For that purpose, amphiphilic poly(N-dodecylacrylamide-co-acrylic acid) copolymers [p(DDA/AA)] with varying contents of AA were synthesized by free radical polymerization. Surface pressure (π)-area (A) isotherms of these copolymers indicated that stable polymer monolayers are formed at the air/water interface for AA mole fraction (n) ≤ 0.49. In all cases, a uniform dispersion of the AA groups in the polymer monolayer was observed. Subsequently, polymer monolayers were transferred onto solid substrates using the Langmuir-Blodgett (LB) technique. X-ray diffraction (XRD) analyses of the multilayer films showed strong Bragg diffraction peaks, suggesting a highly uniform lamellar structure for the multilayer films. The proton conductivity of the multilayer films parallel to the direction of the layer planes were measured by impedance spectroscopy, which revealed that the conductivity increased with increasing values of n. Activation energies for proton conduction of ∼0.3 and 0.42 eV were observed for n ≥ 0.32 and n = 0.07, respectively. Interestingly, the proton conductivity of a multilayer film with n = 0.19 did not follow the Arrhenius equation. These results were interpreted in terms of the average distance between the AA groups (lAA), and it was concluded that, for n ≥ 0.32, an advanced 2D hydrogen bonding network was formed, while for n = 0.07, lAA is too long to form such hydrogen bonding networks. The lAA for n = 0.19 is intermediate to these extremes, resulting in the formation of hydrogen bonding networks at low temperatures, and disruption of these networks at high temperatures due to thermally induced motion. These results indicate that a high proton conductivity with low activation energy can be achieved, even under weakly acidic conditions, by arranging the acid groups at an optimal distance.
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Affiliation(s)
- Takuma Sato
- Graduate School of Science and Engineering, Yamagata University , 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Mayu Tsukamoto
- Graduate School of Science and Engineering, Yamagata University , 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
| | - Shunsuke Yamamoto
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University , 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Masaya Mitsuishi
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University , 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tokuji Miyashita
- Institute for Multidisciplinary Research for Advanced Materials, Tohoku University , 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Shusaku Nagano
- Nagoya University Venture Business Laboratory, Nagoya University , Furo-cho, Chikusa, Nagoya 464-8603, Japan
| | - Jun Matsui
- Faculty of Science, Yamagata University , 1-4-12 Kojirakawa-machi, Yamagata 990-8560, Japan
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37
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Abstract
An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.
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Affiliation(s)
- Themis Lazaridis
- Department of Chemistry, City College of New York/CUNY , 160 Convent Avenue, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry & Physics, Graduate Center, City University of New York , 365 Fifth Ave, New York, New York 10016, United States
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
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38
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Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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39
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Delpuech JJ, Dupont-Leclercq L, Parant S, Henry B. NMR Evidence for Grotthuss-like Proton Diffusion on the Surface of N-Alkyl-ammonium Micelles in Acidic Aqueous Solution. J SOLUTION CHEM 2017. [DOI: 10.1007/s10953-017-0672-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Weichselbaum E, Österbauer M, Knyazev DG, Batishchev OV, Akimov SA, Hai Nguyen T, Zhang C, Knör G, Agmon N, Carloni P, Pohl P. Origin of proton affinity to membrane/water interfaces. Sci Rep 2017; 7:4553. [PMID: 28674402 PMCID: PMC5495794 DOI: 10.1038/s41598-017-04675-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 05/18/2017] [Indexed: 11/21/2022] Open
Abstract
Proton diffusion along biological membranes is vitally important for cellular energetics. Here we extended previous time-resolved fluorescence measurements to study the time and temperature dependence of surface proton transport. We determined the Gibbs activation energy barrier ΔG ‡r that opposes proton surface-to-bulk release from Arrhenius plots of (i) protons' surface diffusion constant and (ii) the rate coefficient for proton surface-to-bulk release. The large size of ΔG ‡r disproves that quasi-equilibrium exists in our experiments between protons in the near-membrane layers and in the aqueous bulk. Instead, non-equilibrium kinetics describes the proton travel between the site of its photo-release and its arrival at a distant membrane patch at different temperatures. ΔG ‡r contains only a minor enthalpic contribution that roughly corresponds to the breakage of a single hydrogen bond. Thus, our experiments reveal an entropic trap that ensures channeling of highly mobile protons along the membrane interface in the absence of potent acceptors.
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Affiliation(s)
- Ewald Weichselbaum
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Maria Österbauer
- 0000 0001 1941 5140grid.9970.7Institute of Inorganic Chemistry, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Denis G. Knyazev
- 0000 0001 1941 5140grid.9970.7Institute of Biophysics, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Oleg V. Batishchev
- 0000 0001 2192 9124grid.4886.2A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskiy pr. 31/4, Moscow, 119071 Russian Federation ,0000000092721542grid.18763.3bMoscow Institute of Physics and Technology, Institutsky lane, 9, 141700 Dolgoprudniy, Russian Federation
| | - Sergey A. Akimov
- 0000 0001 2192 9124grid.4886.2A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskiy pr. 31/4, Moscow, 119071 Russian Federation ,0000 0001 0010 3972grid.35043.31National University of Science and Technology “MISiS”, Leninskiy pr. 4, Moscow, 119991 Russian Federation
| | - Trung Hai Nguyen
- 0000 0001 0728 696Xgrid.1957.aComputational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, 52425 Jülich, Germany, RWTH Aachen University, 52056 Aachen, Germany
| | - Chao Zhang
- 0000 0001 0728 696Xgrid.1957.aComputational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, 52425 Jülich, Germany, RWTH Aachen University, 52056 Aachen, Germany ,0000000121885934grid.5335.0Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge, CB2 1EW United Kingdom
| | - Günther Knör
- 0000 0001 1941 5140grid.9970.7Institute of Inorganic Chemistry, Johannes Kepler University Linz, 4040 Linz, Austria
| | - Noam Agmon
- 0000 0004 1937 0538grid.9619.7Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401 Israel
| | - Paolo Carloni
- 0000 0001 0728 696Xgrid.1957.aComputational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, 52425 Jülich, Germany, RWTH Aachen University, 52056 Aachen, Germany
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, 4040, Linz, Austria.
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41
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Xu L, Öjemyr LN, Bergstrand J, Brzezinski P, Widengren J. Protonation Dynamics on Lipid Nanodiscs: Influence of the Membrane Surface Area and External Buffers. Biophys J 2017; 110:1993-2003. [PMID: 27166807 PMCID: PMC4939474 DOI: 10.1016/j.bpj.2016.03.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/11/2016] [Accepted: 03/07/2016] [Indexed: 11/29/2022] Open
Abstract
Lipid membrane surfaces can act as proton-collecting antennae, accelerating proton uptake by membrane-bound proton transporters. We investigated this phenomenon in lipid nanodiscs (NDs) at equilibrium on a local scale, analyzing fluorescence fluctuations of individual pH-sensitive fluorophores at the membrane surface by fluorescence correlation spectroscopy (FCS). The protonation rate of the fluorophores was ∼100-fold higher when located at 9- and 12-nm diameter NDs, compared to when in solution, indicating that the proton-collecting antenna effect is maximal already for a membrane area of ∼60 nm2. Fluorophore-labeled cytochrome c oxidase displayed a similar increase when reconstituted in 12 nm NDs, but not in 9 nm NDs, i.e., an acceleration of the protonation rate at the surface of cytochrome c oxidase is found when the lipid area surrounding the protein is larger than 80 nm2, but not when below 30 nm2. We also investigated the effect of external buffers on the fluorophore proton exchange rates at the ND membrane-water interfaces. With increasing buffer concentrations, the proton exchange rates were found to first decrease and then, at millimolar buffer concentrations, to increase. Monte Carlo simulations, based on a simple kinetic model of the proton exchange at the membrane-water interface, and using rate parameter values determined in our FCS experiments, could reconstruct both the observed membrane-size and the external buffer dependence. The FCS data in combination with the simulations indicate that the local proton diffusion coefficient along a membrane is ∼100 times slower than that observed over submillimeter distances by proton-pulse experiments (Ds ∼ 10−5cm2/s), and support recent theoretical studies showing that proton diffusion along membrane surfaces is time- and length-scale dependent.
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Affiliation(s)
- Lei Xu
- Experimental Biomolecular Physics, Department of Applied Physics, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Linda Näsvik Öjemyr
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Jan Bergstrand
- Experimental Biomolecular Physics, Department of Applied Physics, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, KTH-Royal Institute of Technology, AlbaNova University Center, Stockholm, Sweden.
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42
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Sezer D, Oruç T. Protonation Kinetics Compromise Liposomal Fluorescence Assay of Membrane Permeation. J Phys Chem B 2017; 121:5218-5227. [DOI: 10.1021/acs.jpcb.7b01881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Deniz Sezer
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
| | - Tuğçe Oruç
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
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43
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Lancaster CRD, Betz YM, Heit S, Lafontaine MA. Transmembrane Electron and Proton Transfer in Diheme-Containing Succinate : Quinone Oxidoreductases. Isr J Chem 2017. [DOI: 10.1002/ijch.201600139] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- C. Roy D. Lancaster
- Department of Structural Biology; Center of Human and Molecular Biology (ZHMB); Saarland University; Faculty of Medicine Building 60 D-66421 Homburg (Saar) Germany
| | - Yamila M. Betz
- Department of Structural Biology; Center of Human and Molecular Biology (ZHMB); Saarland University; Faculty of Medicine Building 60 D-66421 Homburg (Saar) Germany
| | - Sabine Heit
- Department of Structural Biology; Center of Human and Molecular Biology (ZHMB); Saarland University; Faculty of Medicine Building 60 D-66421 Homburg (Saar) Germany
| | - Michael A. Lafontaine
- Department of Structural Biology; Center of Human and Molecular Biology (ZHMB); Saarland University; Faculty of Medicine Building 60 D-66421 Homburg (Saar) Germany
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44
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Safdari H, Cherstvy AG, Chechkin AV, Bodrova A, Metzler R. Aging underdamped scaled Brownian motion: Ensemble- and time-averaged particle displacements, nonergodicity, and the failure of the overdamping approximation. Phys Rev E 2017; 95:012120. [PMID: 28208482 DOI: 10.1103/physreve.95.012120] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Indexed: 06/06/2023]
Abstract
We investigate both analytically and by computer simulations the ensemble- and time-averaged, nonergodic, and aging properties of massive particles diffusing in a medium with a time dependent diffusivity. We call this stochastic diffusion process the (aging) underdamped scaled Brownian motion (UDSBM). We demonstrate how the mean squared displacement (MSD) and the time-averaged MSD of UDSBM are affected by the inertial term in the Langevin equation, both at short, intermediate, and even long diffusion times. In particular, we quantify the ballistic regime for the MSD and the time-averaged MSD as well as the spread of individual time-averaged MSD trajectories. One of the main effects we observe is that, both for the MSD and the time-averaged MSD, for superdiffusive UDSBM the ballistic regime is much shorter than for ordinary Brownian motion. In contrast, for subdiffusive UDSBM, the ballistic region extends to much longer diffusion times. Therefore, particular care needs to be taken under what conditions the overdamped limit indeed provides a correct description, even in the long time limit. We also analyze to what extent ergodicity in the Boltzmann-Khinchin sense in this nonstationary system is broken, both for subdiffusive and superdiffusive UDSBM. Finally, the limiting case of ultraslow UDSBM is considered, with a mixed logarithmic and power-law dependence of the ensemble- and time-averaged MSDs of the particles. In the limit of strong aging, remarkably, the ordinary UDSBM and the ultraslow UDSBM behave similarly in the short time ballistic limit. The approaches developed here open ways for considering other stochastic processes under physically important conditions when a finite particle mass and aging in the system cannot be neglected.
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Affiliation(s)
- Hadiseh Safdari
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Department of Physics, Shahid Beheshti University, 19839 Tehran, Iran
| | - Andrey G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
| | - Aleksei V Chechkin
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
- Institute for Theoretical Physics, Kharkov Institute of Physics and Technology, 61108 Kharkov, Ukraine
- Department of Physics & Astronomy, University of Padova, "Galileo Galilei" - DFA, 35131 Padova, Italy
| | - Anna Bodrova
- Institute of Physics, Humboldt University Berlin, 12489 Berlin, Germany
- Faculty of Physics, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Ralf Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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45
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Oswald C, Tam HK, Pos KM. Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB. Nat Commun 2016; 7:13819. [PMID: 27982032 PMCID: PMC5171871 DOI: 10.1038/ncomms13819] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/01/2016] [Indexed: 12/16/2022] Open
Abstract
The deployment of multidrug efflux pumps is a powerful defence mechanism for Gram-negative bacterial cells when exposed to antimicrobial agents. The major multidrug efflux transport system in Escherichia coli, AcrAB–TolC, is a tripartite system using the proton-motive force as an energy source. The polyspecific substrate-binding module AcrB uses various pathways to sequester drugs from the periplasm and outer leaflet of the inner membrane. Here we report the asymmetric AcrB structure in complex with fusidic acid at a resolution of 2.5 Å and mutational analysis of the putative fusidic acid binding site at the transmembrane domain. A groove shaped by the interface between transmembrane helix 1 (TM1) and TM2 specifically binds fusidic acid and other lipophilic carboxylated drugs. We propose that these bound drugs are actively displaced by an upward movement of TM2 towards the AcrB periplasmic porter domain in response to protonation events in the transmembrane domain.
The AcrB module of the AcrAB-TolC multidrug efflux pump sequesters drugs from the periplasm and outer leaflet of the inner membrane. Here, Oswald et al. provide evidence that lipophilic carboxylated substrates bind to a groove between transmembrane helices TM1 and TM2, for further transport by an upward movement of TM2.
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Affiliation(s)
- Christine Oswald
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany.,Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Heng-Keat Tam
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
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46
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Yoshinaga MY, Kellermann MY, Valentine DL, Valentine RC. Phospholipids and glycolipids mediate proton containment and circulation along the surface of energy-transducing membranes. Prog Lipid Res 2016; 64:1-15. [PMID: 27448687 DOI: 10.1016/j.plipres.2016.07.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 05/29/2016] [Accepted: 07/13/2016] [Indexed: 01/06/2023]
Abstract
Proton bioenergetics provides the energy for growth and survival of most organisms in the biosphere ranging from unicellular marine phytoplankton to humans. Chloroplasts harvest light and generate a proton electrochemical gradient (proton motive force) that drives the production of ATP needed for carbon dioxide fixation and plant growth. Mitochondria, bacteria and archaea generate proton motive force to energize growth and other physiologies. Energy transducing membranes are at the heart of proton bioenergetics and are responsible for catalyzing the conversion of energy held in high-energy electrons→electron transport chain→proton motive force→ATP. Whereas the electron transport chain is understood in great detail there are major gaps in understanding mechanisms of proton transfer or circulation during proton bioenergetics. This paper is built on the proposition that phospho- and glyco-glycerolipids form proton transport circuitry at the membrane's surface. By this proposition, an emergent membrane property, termed the hyducton, confines active/unbound protons or hydronium ions to a region of low volume close to the membrane surface. In turn, a von Grotthuß mechanism rapidly moves proton substrate in accordance with nano-electrochemical poles on the membrane surface created by powerful proton pumps such as ATP synthase.
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Affiliation(s)
- Marcos Y Yoshinaga
- University of Bremen, MARUM - Center for Marine and Environmental Sciences, Germany.
| | - Matthias Y Kellermann
- University of California Santa Barbara - Department of Earth Science and Marine Science Institute, USA
| | - David L Valentine
- University of California Santa Barbara - Department of Earth Science and Marine Science Institute, USA
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47
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Agmon N, Bakker HJ, Campen RK, Henchman RH, Pohl P, Roke S, Thämer M, Hassanali A. Protons and Hydroxide Ions in Aqueous Systems. Chem Rev 2016; 116:7642-72. [PMID: 27314430 DOI: 10.1021/acs.chemrev.5b00736] [Citation(s) in RCA: 294] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the structure and dynamics of water's constituent ions, proton and hydroxide, has been a subject of numerous experimental and theoretical studies over the last century. Besides their obvious importance in acid-base chemistry, these ions play an important role in numerous applications ranging from enzyme catalysis to environmental chemistry. Despite a long history of research, many fundamental issues regarding their properties continue to be an active area of research. Here, we provide a review of the experimental and theoretical advances made in the last several decades in understanding the structure, dynamics, and transport of the proton and hydroxide ions in different aqueous environments, ranging from water clusters to the bulk liquid and its interfaces with hydrophobic surfaces. The propensity of these ions to accumulate at hydrophobic surfaces has been a subject of intense debate, and we highlight the open issues and challenges in this area. Biological applications reviewed include proton transport along the hydration layer of various membranes and through channel proteins, problems that are at the core of cellular bioenergetics.
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Affiliation(s)
- Noam Agmon
- The Fritz Haber Research Center, Institute of Chemistry, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Huib J Bakker
- FOM Institute AMOLF , Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - R Kramer Campen
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany
| | - Richard H Henchman
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, United Kingdom
| | - Peter Pohl
- Johannes Kepler University Linz , Institute of Biophysics, Gruberstrasse 40, 4020 Linz, Austria
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), and Institute of Material Science (IMX), School of Engineering (STI), and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015, Lausanne, Switzerland
| | - Martin Thämer
- Fritz Haber Institute of the Max Planck Society , Faradayweg 4-6, 14195 Berlin, Germany.,Department of Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago , Chicago, Illinois 60637, United States
| | - Ali Hassanali
- CMSP Section, The Abdus Salaam International Center for Theoretical Physics , I-34151 Trieste, Italy
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Amdursky N, Wang X, Meredith P, Bradley DDC, Stevens MM. Long-Range Proton Conduction across Free-Standing Serum Albumin Mats. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:2692-8. [PMID: 26840865 PMCID: PMC4862025 DOI: 10.1002/adma.201505337] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/28/2015] [Indexed: 05/26/2023]
Abstract
Free-standing serum-albumin mats can transport protons over millimetre length-scales. The results of photoinduced proton transfer and voltage-driven proton-conductivity measurements, together with temperature-dependent and isotope-effect studies, suggest that oxo-amino-acids of the protein serum albumin play a major role in the translocation of protons via an "over-the-barrier" hopping mechanism. The use of proton-conducting protein mats opens new possibilities for bioelectronic interfaces.
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Affiliation(s)
- Nadav Amdursky
- Departments of Materials, Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Xuhua Wang
- Department of Physics and Centre for Plastic Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Paul Meredith
- Centre for Organic Photonics and Electronics, School of Mathematics and Physics, University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Donal D C Bradley
- Department of Physics and Centre for Plastic Electronics, Imperial College London, London, SW7 2AZ, UK
| | - Molly M Stevens
- Departments of Materials, Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
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McDaniel JG, Yethiraj A. Importance of hydrophobic traps for proton diffusion in lyotropic liquid crystals. J Chem Phys 2016; 144:094705. [DOI: 10.1063/1.4943131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jesse G. McDaniel
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Metzler R, Jeon JH, Cherstvy AG. Non-Brownian diffusion in lipid membranes: Experiments and simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2451-2467. [PMID: 26826272 DOI: 10.1016/j.bbamem.2016.01.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/21/2016] [Accepted: 01/23/2016] [Indexed: 12/14/2022]
Abstract
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane-binding particles. We discuss how membrane compartmentalisation and the particle-membrane binding energy may impact the dynamics and response of lipid membranes. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- R Metzler
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany; Department of Physics, Tampere University of Technology, 33101 Tampere, Finland.
| | - J-H Jeon
- Korea Institute for Advanced Study (KIAS), Seoul, Republic of Korea
| | - A G Cherstvy
- Institute for Physics & Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany
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