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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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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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3
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Zhang Y, Huang R, Iepure M, Merriman S, Min Y. Geocolloidal interactions and relaxation dynamics under nanoconfinement: Effects of salinity and particle concentration. J Colloid Interface Sci 2023; 656:200-213. [PMID: 37989053 DOI: 10.1016/j.jcis.2023.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
HYPOTHESIS Energy-related contaminants are frequently associated with geocolloids that translocate in underground fissures with dimensions comparable with geocolloids. To assess the transport and impact of energy-related contaminants in geological systems, fundamental understandings of interfacial behaviors of nanoparticles under confinement is imperative. We hypothesize that the dynamic properties of geocolloids, as well as their dependence on aqueous medium conditions would deviate from bulk behaviors under nanoconfinement. EXPERIMENTS Force profiles and rheological properties of 50 nm silica nanoparticles in aqueous media confined between mica surfaces as a function of surface separation, particle concentrations, and salinity were measured utilizing the surface forces apparatus. FINDINGS Force profiles revealed the critical surface separation for nonlinear rheological behaviors coincides with the onset of exponential repulsion between mica surfaces. When salts were absent, the normal forces and viscosity values of colloidal suspensions resembled pure water. In contrast, with salts, the force profiles and corresponding critical length scales were found to be highly sensitive to the particle concentration and the degree of confinement. A Newtonian to shear-thinning transition was captured with increasing degrees of confinement. Our results show that the interplay among confinement, particle, and ionic concentrations can alter the interparticle forces and rheological responses of true nanosized-colloidal suspensions and thus their transport behaviors under nanoconfinement for the first time.
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Affiliation(s)
- Yuanzhong Zhang
- Department of Chemical and Environmental Engineering, University of California, Riverside 92521 CA, USA
| | - Rundong Huang
- Department of Chemical and Environmental Engineering, University of California, Riverside 92521 CA, USA
| | - Monica Iepure
- Department of Chemical and Environmental Engineering, University of California, Riverside 92521 CA, USA
| | - Stephen Merriman
- School of Polymer Science and Polymer Engineering, University of Akron, 44325 OH, USA
| | - Younjin Min
- Department of Chemical and Environmental Engineering, University of California, Riverside 92521 CA, USA; Material Science and Engineering Program, University of California, Riverside, 92521 CA, USA.
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4
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Lee JW. Transient protonic capacitor: Explaining the bacteriorhodopsin membrane experiment of Heberle et al. 1994. Biophys Chem 2023; 300:107072. [PMID: 37406610 DOI: 10.1016/j.bpc.2023.107072] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/07/2023]
Abstract
The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, it is now better explained how the bacteriorhodopsin-purple membrane-ATPase system functions. The bacteriorhodopsin pumping of protons across the membrane results in the formation of TELP around the halobacterial extracellular membrane surface that is perfectly positioned to drive ATP synthase for the synthesis of ATP from ADP and Pi. The bacteriorhodopsin purple membrane sheet experiment of Heberle et al. 1994 is now better explained here as a transient "protonic capacitor". During the lifetime of a flashlight-induced protonic bacteriorhodopsin purple membrane capacitor activity, there is at least a transient non-zero membrane potential (Δψ ≠ 0). The experimental results demonstrated that "after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase" exactly as predicted by the TELP theory, which is fundamentally important to the science of bioenergetics.
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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Sokolov VS, Tashkin VY, Zykova DD, Kharitonova YV, Galimzyanov TR, Batishchev OV. Electrostatic Potentials Caused by the Release of Protons from Photoactivated Compound Sodium 2-Methoxy-5-nitrophenyl Sulfate at the Surface of Bilayer Lipid Membrane. MEMBRANES 2023; 13:722. [PMID: 37623783 PMCID: PMC10456422 DOI: 10.3390/membranes13080722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/26/2023]
Abstract
Lateral transport and release of protons at the water-membrane interface play crucial roles in cell bioenergetics. Therefore, versatile techniques need to be developed for investigating as well as clarifying the main features of these processes at the molecular level. Here, we experimentally measured the kinetics of binding of protons released from the photoactivated compound sodium 2-methoxy-5-nitrophenyl sulfate (MNPS) at the surface of a bilayer lipid membrane (BLM). We developed a theoretical model of this process describing the damage of MNPS coupled with the release of the protons at the membrane surface, as well as the exchange of MNPS molecules and protons between the membrane and solution. We found that the total change in the boundary potential difference across the membrane, ∆ϕb, is the sum of opposing effects of adsorption of MNPS anions and release of protons at the membrane-water interface. Steady-state change in the ∆ϕb due to protons decreased with the concentration of the buffer and increased with the pH of the solution. The change in the concentration of protons evaluated from measurements of ∆ϕb was close to that in the unstirred water layer near the BLM. This result, as well as rate constants of the proton exchange between the membrane and the bulk solution, indicated that the rate-limiting step of the proton surface to bulk release is the change in the concentration of protons in the unstirred layer. This means that the protons released from MNPS remain in equilibrium between the BLM surface and an adjacent water layer.
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Affiliation(s)
- Valerij S. Sokolov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
| | - Vsevolod Yu. Tashkin
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
| | - Darya D. Zykova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
- Moscow Institute of Physics and Technology, Institutski Per., 9, Moscow Region, Dolgoprudny 141701, Russia
| | - Yulia V. Kharitonova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
| | - Timur R. Galimzyanov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
| | - Oleg V. Batishchev
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky Prospekt, 31, Moscow 119071, Russia (O.V.B.)
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Lee JW. Protonic conductor: Explaining the transient "excess protons" experiment of Pohl's group 2012. Biophys Chem 2023; 296:106983. [PMID: 36868162 DOI: 10.1016/j.bpc.2023.106983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/20/2023] [Accepted: 02/22/2023] [Indexed: 02/27/2023]
Abstract
The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, we can now better explain: the experimental results of Pohl's group (Zhang et al. 2012) as an effect of transient "excess protons" that can temporally form because of the difference between the fast protonic conduction in liquid water through the "hops and turns" mechanism and the relatively slow diffusion of chloride anions. This new understanding with the TELP theory agrees well with the independent analysis on the Pohl's lab group experiment results by Agmon and Gutman who also concluded that "the excess protons propagate as an advancing front".
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529, USA.
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7
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Novel In Silico Insights into Rv1417 and Rv2617c as Potential Protein Targets: The Importance of the Medium on the Structural Interactions with Exported Repetitive Protein (Erp) of Mycobacterium tuberculosis. Polymers (Basel) 2022; 14:polym14132577. [PMID: 35808623 PMCID: PMC9269478 DOI: 10.3390/polym14132577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/17/2022] Open
Abstract
Nowadays, tuberculosis is the second leading cause of death from a monopathogenic transmitted disease, only ahead of COVID-19. The role of exported repetitive protein (Erp) in the virulence of Mycobacterium tuberculosis has been extensively demonstrated. In vitro and in vivo assays have identified that Erp interacts with Rv1417 and Rv2617c proteins, forming putative transient molecular complexes prior to localization to the cell envelope. Although new insights into the interactions and functions of Erp have emerged over the years, knowledge about its structure and protein–protein interactions at the atomistic level has not been sufficiently explored. In this work, we have combined several in silico methodologies to gain new insights into the structural relationship between these proteins. Two system conditions were evaluated by MD simulations: Rv1417 and Rv2617c embedded in a lipid membrane and another with a semi-polar solvent to mimic the electrostatic conditions on the membrane surface. The Erp protein was simulated as an unanchored structure. Stabilized structures were docked, and complexes were evaluated to recognize the main residues involved in protein–protein interactions. Our results show the influence of the medium on the structural conformation of proteins. Globular conformations were favored under high polarity conditions and showed a higher energetic affinity in complex formation. Meanwhile, disordered conformations were favored under semi-polar conditions and an increase in the number of contacts between residues was observed. In addition, the electrostatic potential analysis showed remarkable changes in protein interactions due to the polarity of the medium, demonstrating the relevance of Erp protein in heterodimer formation. On the other hand, contact analysis showed that several C-terminal residues of Erp were involved in the protein interactions, which seems to contradict experimental observations; however, these complexes could be transient forms. The findings presented in this work are intended to open new perspectives in the studies of Erp protein molecular interactions and to improve the knowledge about its function and role in the virulence of Mycobacterium tuberculosis.
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8
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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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9
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Silverstein TP. The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry. Front Mol Biosci 2021; 8:764099. [PMID: 34901158 PMCID: PMC8661011 DOI: 10.3389/fmolb.2021.764099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pK a and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H+. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.
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Affiliation(s)
- Todd P Silverstein
- Chemistry Department (emeritus), Willamette University, Salem, OR, United States
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10
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Nesterov SV, Ilyinsky NS, Uversky VN. Liquid-liquid phase separation as a common organizing principle of intracellular space and biomembranes providing dynamic adaptive responses. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119102. [PMID: 34293345 DOI: 10.1016/j.bbamcr.2021.119102] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 02/07/2023]
Abstract
This work is devoted to the phenomenon of liquid-liquid phase separation (LLPS), which has come to be recognized as fundamental organizing principle of living cells. We distinguish separation processes with different dimensions. Well-known 3D-condensation occurs in aqueous solution and leads to membraneless organelle (MLOs) formation. 2D-films may be formed near membrane surfaces and lateral phase separation (membrane rafts) occurs within the membranes themselves. LLPS may also occur on 1D structures like DNA and the cyto- and nucleoskeleton. Phase separation provides efficient transport and sorting of proteins and metabolites, accelerates the assembly of metabolic and signaling complexes, and mediates stress responses. In this work, we propose a model in which the processes of polymerization (1D structures), phase separation in membranes (2D structures), and LLPS in the volume (3D structures) influence each other. Disordered proteins and whole condensates may provide membrane raft separation or polymerization of specific proteins. On the other hand, 1D and 2D structures with special composition or embedded IDRs can nucleate condensates. We hypothesized that environmental change may trigger a LLPS which can propagate within the cell interior moving along the cytoskeleton or as an autowave. New phase propagation quickly and using a low amount of energy adjusts cell signaling and metabolic systems to new demands. Cumulatively, the interconnected phase separation phenomena in different dimensions represent a previously unexplored system of intracellular communication and regulation which cannot be ignored when considering both physiological and pathological cell processes.
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Affiliation(s)
- Semen V Nesterov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Kurchatov Complex of NBICS-Technologies, National Research Center Kurchatov Institute, Moscow 123182, Russia.
| | - Nikolay S Ilyinsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia
| | - Vladimir N Uversky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny 141700, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL 33612, USA.
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11
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Alav I, Kobylka J, Kuth MS, Pos KM, Picard M, Blair JMA, Bavro VN. Structure, Assembly, and Function of Tripartite Efflux and Type 1 Secretion Systems in Gram-Negative Bacteria. Chem Rev 2021; 121:5479-5596. [PMID: 33909410 PMCID: PMC8277102 DOI: 10.1021/acs.chemrev.1c00055] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Indexed: 12/11/2022]
Abstract
Tripartite efflux pumps and the related type 1 secretion systems (T1SSs) in Gram-negative organisms are diverse in function, energization, and structural organization. They form continuous conduits spanning both the inner and the outer membrane and are composed of three principal components-the energized inner membrane transporters (belonging to ABC, RND, and MFS families), the outer membrane factor channel-like proteins, and linking the two, the periplasmic adaptor proteins (PAPs), also known as the membrane fusion proteins (MFPs). In this review we summarize the recent advances in understanding of structural biology, function, and regulation of these systems, highlighting the previously undescribed role of PAPs in providing a common architectural scaffold across diverse families of transporters. Despite being built from a limited number of basic structural domains, these complexes present a staggering variety of architectures. While key insights have been derived from the RND transporter systems, a closer inspection of the operation and structural organization of different tripartite systems reveals unexpected analogies between them, including those formed around MFS- and ATP-driven transporters, suggesting that they operate around basic common principles. Based on that we are proposing a new integrated model of PAP-mediated communication within the conformational cycling of tripartite systems, which could be expanded to other types of assemblies.
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Affiliation(s)
- Ilyas Alav
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Jessica Kobylka
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Miriam S. Kuth
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Klaas M. Pos
- Institute
of Biochemistry, Biocenter, Goethe Universität
Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Martin Picard
- Laboratoire
de Biologie Physico-Chimique des Protéines Membranaires, CNRS
UMR 7099, Université de Paris, 75005 Paris, France
- Fondation
Edmond de Rothschild pour le développement de la recherche
Scientifique, Institut de Biologie Physico-Chimique, 75005 Paris, France
| | - Jessica M. A. Blair
- Institute
of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Vassiliy N. Bavro
- School
of Life Sciences, University of Essex, Colchester, CO4 3SQ United Kingdom
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12
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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13
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Wang C, Sensale S, Pan Z, Senapati S, Chang HC. Slowing down DNA translocation through solid-state nanopores by edge-field leakage. Nat Commun 2021; 12:140. [PMID: 33420061 PMCID: PMC7794543 DOI: 10.1038/s41467-020-20409-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/23/2020] [Indexed: 01/26/2023] Open
Abstract
Solid-state nanopores allow high-throughput single-molecule detection but identifying and even registering all translocating small molecules remain key challenges due to their high translocation speeds. We show here the same electric field that drives the molecules into the pore can be redirected to selectively pin and delay their transport. A thin high-permittivity dielectric coating on bullet-shaped polymer nanopores permits electric field leakage at the pore tip to produce a voltage-dependent surface field on the entry side that can reversibly edge-pin molecules. This mechanism renders molecular entry an activated process with sensitive exponential dependence on the bias voltage and molecular rigidity. This sensitivity allows us to selectively prolong the translocation time of short single-stranded DNA molecules by up to 5 orders of magnitude, to as long as minutes, allowing discrimination against their double-stranded duplexes with 97% confidence.
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Affiliation(s)
- Ceming Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Sebastian Sensale
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Zehao Pan
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, USA.
- Department of Aerospace and Mechanical Engineering, University of Notre Dame, Notre Dame, IN, USA.
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14
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Cardiolipin, Perhydroxyl Radicals, and Lipid Peroxidation in Mitochondrial Dysfunctions and Aging. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:1323028. [PMID: 32963690 PMCID: PMC7499269 DOI: 10.1155/2020/1323028] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 02/19/2020] [Indexed: 01/09/2023]
Abstract
Mitochondrial dysfunctions caused by oxidative stress are currently regarded as the main cause of aging. Accumulation of mutations and deletions of mtDNA is a hallmark of aging. So far, however, there is no evidence that most studied oxygen radicals are directly responsible for mutations of mtDNA. Oxidative damages to cardiolipin (CL) and phosphatidylethanolamine (PEA) are also hallmarks of oxidative stress, but the mechanisms of their damage remain obscure. CL is the only phospholipid present almost exclusively in the inner mitochondrial membrane (IMM) where it is responsible, together with PEA, for the maintenance of the superstructures of oxidative phosphorylation enzymes. CL has negative charges at the headgroups and due to specific localization at the negative curves of the IMM, it creates areas with the strong negative charge where local pH may be several units lower than in the surrounding bulk phases. At these sites with the higher acidity, the chance of protonation of the superoxide radical (O2•), generated by the respiratory chain, is much higher with the formation of the highly reactive hydrophobic perhydroxyl radical (HO2•). HO2• specifically reacts with the double bonds of polyunsaturated fatty acids (PUFA) initiating the isoprostane pathway of lipid peroxidation. Because HO2• is formed close to CL aggregates and PEA, it causes peroxidation of the linoleic acid in CL and also damages PEA. This causes disruption of the structural and functional integrity of the respirosomes and ATP synthase. We provide evidence that in elderly individuals with metabolic syndrome (MetS), fatty acids become the major substrates for production of ATP and this may increase several-fold generation of O2• and thus HO2•. We conclude that MetS accelerates aging and the mitochondrial dysfunctions are caused by the HO2•-induced direct oxidation of CL and the isoprostane pathway of lipid peroxidation (IPLP). The toxic products of IPLP damage not only PEA, but also mtDNA and OXPHOS proteins. This results in gradual disruption of the structural and functional integrity of mitochondria and cells.
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Lee JW. Protonic Capacitor: Elucidating the biological significance of mitochondrial cristae formation. Sci Rep 2020; 10:10304. [PMID: 32601276 PMCID: PMC7324581 DOI: 10.1038/s41598-020-66203-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/17/2020] [Indexed: 11/12/2022] Open
Abstract
For decades, it was not entirely clear why mitochondria develop cristae? The work employing the transmembrane-electrostatic proton localization theory reported here has now provided a clear answer to this fundamental question. Surprisingly, the transmembrane-electrostatically localized proton concentration at a curved mitochondrial crista tip can be significantly higher than that at the relatively flat membrane plane regions where the proton-pumping respiratory supercomplexes are situated. The biological significance for mitochondrial cristae has now, for the first time, been elucidated at a protonic bioenergetics level: 1) The formation of cristae creates more mitochondrial inner membrane surface area and thus more protonic capacitance for transmembrane-electrostatically localized proton energy storage; and 2) The geometric effect of a mitochondrial crista enhances the transmembrane-electrostatically localized proton density to the crista tip where the ATP synthase can readily utilize the localized proton density to drive ATP synthesis.
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA.
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16
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Whiteley JP. An evaluation of some assumptions underpinning the bidomain equations of electrophysiology. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2020; 37:262-302. [PMID: 31680135 DOI: 10.1093/imammb/dqz014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/11/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022]
Abstract
Tissue level cardiac electrophysiology is usually modelled by the bidomain equations, or the monodomain simplification of the bidomain equations. One assumption made when deriving the bidomain equations is that both the intracellular and extracellular spaces are in electrical equilibrium. This assumption neglects the disturbance of this equilibrium in thin regions close to the cell membrane known as Debye layers. We first demonstrate that the governing equations at the cell, or microscale, level may be adapted to take account of these Debye layers with little additional complexity, provided the permittivity within the Debye layers satisfies certain conditions that are believed to be satisfied for biological cells. We then homogenize the microscale equations using a technique developed for an almost periodic microstructure. Cardiac tissue is usually modelled as sheets of cardiac fibres stacked on top of one another. A common assumption is that an orthogonal coordinate system can be defined at each point of cardiac tissue, where the first axis is in the fibre direction, the second axis is orthogonal to the first axis but lies in the sheet of cardiac fibres and the third axis is orthogonal to the cardiac sheet. It is assumed further that both the intracellular and extracellular conductivity tensors are diagonal with respect to these axes and that the diagonal entries of these tensors are constant across the whole tissue. Using the homogenization technique we find that this assumption is usually valid for cardiac tissue, but highlight situations where the assumption may not be valid.
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Affiliation(s)
- Jonathan P Whiteley
- Department of Computer Science, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, UK
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Kinetic coupling of the respiratory chain with ATP synthase, but not proton gradients, drives ATP production in cristae membranes. Proc Natl Acad Sci U S A 2020; 117:2412-2421. [PMID: 31964824 DOI: 10.1073/pnas.1917968117] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mitochondria have a characteristic ultrastructure with invaginations of the inner membrane called cristae that contain the protein complexes of the oxidative phosphorylation system. How this particular morphology of the respiratory membrane impacts energy conversion is currently unknown. One proposed role of cristae formation is to facilitate the establishment of local proton gradients to fuel ATP synthesis. Here, we determined the local pH values at defined sublocations within mitochondria of respiring yeast cells by fusing a pH-sensitive GFP to proteins residing in different mitochondrial subcompartments. Only a small proton gradient was detected over the inner membrane in wild type or cristae-lacking cells. Conversely, the obtained pH values did barely permit ATP synthesis in a reconstituted system containing purified yeast F1F0 ATP synthase, although, thermodynamically, a sufficiently high driving force was applied. At higher driving forces, where robust ATP synthesis was observed, a P-side pH value of 6 increased the ATP synthesis rate 3-fold compared to pH 7. In contrast, when ATP synthase was coreconstituted with an active proton-translocating cytochrome oxidase, ATP synthesis readily occurred at the measured, physiological pH values. Our study thus reveals that the morphology of the inner membrane does not influence the subcompartmental pH values and is not necessary for robust oxidative phosphorylation in mitochondria. Instead, it is likely that the dense packing of the oxidative phosphorylation complexes in the cristae membranes assists kinetic coupling between proton pumping and ATP synthesis.
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18
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Lee JW. Electrostatically localized proton bioenergetics: better understanding membrane potential. Heliyon 2019; 5:e01961. [PMID: 31367684 PMCID: PMC6646885 DOI: 10.1016/j.heliyon.2019.e01961] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/28/2019] [Accepted: 06/12/2019] [Indexed: 11/03/2022] Open
Abstract
In Mitchell's chemiosmotic theory, membrane potential Δ ψ was given as the electric potential difference across the membrane. However, its physical origin for membrane potential Δ ψ was not well explained. Using the Lee proton electrostatic localization model with a newly formulated equation for protonic motive force (pmf) that takes electrostatically localized protons into account, membrane potential has now been better understood as the voltage difference contributed by the localized surface charge density ( [ H L + ] + ∑ i = 1 n [ M L i + ] ) at the liquid-membrane interface as in an electrostatically localized protons/cations-membrane-anions capacitor. That is, the origin of membrane potential Δ ψ is now better understood as the electrostatic formation of the localized surface charge density that is the sum of the electrostatically localized proton concentration [ H L + ] and the localized non-proton cations density ∑ i = 1 n [ M L i + ] at the liquid membrane interface. The total localized surface charge density equals to the ideal localized proton population density [ H L + ] 0 before the cation-proton exchange process; since the cation-proton exchange process does not change the total localized charges density, neither does it change to the membrane potential Δ ψ . The localized proton concentration [ H L + ] represents the dominant component, which accounts about 78% of the total localized surface charge density at the cation-proton exchange equilibrium state in animal mitochondria. Liquid water as a protonic conductor may play a significant role in the biological activities of membrane potential formation and utilization.
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Affiliation(s)
- James Weifu Lee
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA 23529 USA
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19
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Oh MI, Gupta M, Weaver DF. Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface. J Phys Chem B 2019; 123:3945-3954. [DOI: 10.1021/acs.jpcb.9b01331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myong In Oh
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Donald F. Weaver
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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20
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Lee J, Lee TH. How Protein Binding Sensitizes the Nucleosome to Histone H3K56 Acetylation. ACS Chem Biol 2019; 14:506-515. [PMID: 30768236 DOI: 10.1021/acschembio.9b00018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The nucleosome, the fundamental gene-packing unit comprising an octameric histone protein core wrapped with DNA, has a flexible structure that enables dynamic gene regulation mechanisms. Histone lysine acetylation at H3K56 removes a positive charge from the histone core where it interacts with the termini of the nucleosomal DNA and acts as a critical gene regulatory signal that is implicated in transcription initiation and elongation. The predominant proposal for the biophysical role of H3K56 acetylation (H3K56ac) is that weakened electrostatic interaction between DNA termini and the histone core results in facilitated opening and subsequent disassembly of the nucleosome. However, this effect alone is too weak to account for the strong coupling between H3K56ac and its regulatory outcomes. Here we utilized a semisynthetically modified nucleosome with H3K56ac in order to address this discrepancy. Based on the results, we propose an innovative mechanism by which the charge neutralization effect of H3K56ac is significantly amplified via protein binding. We employed three-color single-molecule fluorescence resonance energy transfer (smFRET) to monitor the opening rate of nucleosomal DNA termini induced by binding of histone chaperone Nap1. We observed an elevated opening rate upon H3K56ac by 5.9-fold, which is far larger than the 1.5-fold previously reported for the spontaneous opening dynamics in the absence of Nap1. Our proposed mechanism successfully reconciles this discrepancy because DNA opening for Nap1 binding must be larger than the average spontaneous opening. This is a novel mechanism that can explain how a small biophysical effect of histone acetylation results in a significant change in protein binding rate.
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Affiliation(s)
- Jaehyoun Lee
- Department of Chemistry, the Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Tae-Hee Lee
- Department of Chemistry, the Pennsylvania State University, University Park, Pennsylvania 16802, United States
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21
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Fealey ME, Binder BP, Uversky VN, Hinderliter A, Thomas DD. Structural Impact of Phosphorylation and Dielectric Constant Variation on Synaptotagmin's IDR. Biophys J 2019; 114:550-561. [PMID: 29414700 DOI: 10.1016/j.bpj.2017.12.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/21/2017] [Accepted: 12/04/2017] [Indexed: 11/28/2022] Open
Abstract
We used time-resolved Förster resonance energy transfer, circular dichroism, and molecular dynamics simulation to investigate the structural dependence of synaptotagmin 1's intrinsically disordered region (IDR) on phosphorylation and dielectric constant. We found that a peptide corresponding to the full-length IDR sequence, a ∼60-residue strong polyampholyte, can sample structurally collapsed states in aqueous solution, consistent with its κ-predicted behavior, where κ is a sequence-dependent parameter that is used to predict IDR compaction. In implicit solvent simulations of this same sequence, lowering the dielectric constant to more closely mimic the environment near a lipid bilayer surface promoted further sampling of collapsed structures. We then examined the structural tendencies of central region residues of the IDR in isolation. We found that the exocytosis-modulating phosphorylation of Thr112 disrupts a local disorder-to-order transition induced by trifluoroethanol/water mixtures that decrease the solution dielectric constant and stabilize helical structure. Implicit solvent simulations on these same central region residues testing the impact of dielectric constant alone converge on a similar result, showing that helical structure is formed with higher probability at a reduced dielectric. In these helical conformers, lysine-aspartic acid salt bridges contribute to stabilization of transient secondary structure. In contrast, phosphorylation results in formation of salt bridges unsuitable for helix formation. Collectively, these results suggest a model in which phosphorylation and compaction of the IDR sequence regulate structural transitions that in turn modulate neuronal exocytosis.
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Affiliation(s)
- Michael E Fealey
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Benjamin P Binder
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, Florida
| | - Anne Hinderliter
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota.
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22
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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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23
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Sweeney DC, Davalos RV. Discontinuous Galerkin Model of Cellular Electroporation. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2018; 2018:5850-5853. [PMID: 30441666 DOI: 10.1109/embc.2018.8513541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Electroporation (EP) is a phenomenon involving both nonlinear biophysical processes and complex geometries. When exposed to strong electric fields, the formation of pores within a cell membrane increases the membrane permeability. Discontinuous Galerkin (DG) finite element methods can directly enforce these flux jumps across the thin cell membrane interface. We implement a DG finite element method to model the electric field, pore formation, and transmembrane flux of charged solutes during EP. Our model is readily extensible for parallel computation on high performance clusters and agrees with previous reports.
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24
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Maldonado Vidaurri E, Chavez-Montes A, Garza Tapia M, Castro-Rios R, Gonzalez-Horta A. Differential interaction of α-synuclein N-terminal segment with mitochondrial model membranes. Int J Biol Macromol 2018; 119:1286-1293. [DOI: 10.1016/j.ijbiomac.2018.08.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 08/08/2018] [Accepted: 08/09/2018] [Indexed: 01/27/2023]
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25
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The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior. Sci Rep 2018; 8:15690. [PMID: 30356074 PMCID: PMC6200761 DOI: 10.1038/s41598-018-33955-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 10/06/2018] [Indexed: 12/25/2022] Open
Abstract
GRASPs are proteins involved in cell processes that seem paradoxical: responsible for shaping the Golgi cisternae and involved in unconventional secretion mechanisms that bypass the Golgi. Despite its physiological relevance, there is still a considerable lack of studies on full-length GRASPs. Our group has previously reported an unexpected behavior of the full-length GRASP from the fungus C. neoformans: its intrinsically-disordered characteristic. Here, we generalize this finding by showing that it is also observed in the GRASP from S. cerevisae (Grh1), which strongly suggests it might be a general property within the GRASP family. Furthermore, Grh1 is also able to form amyloid-like fibrils either upon heating or when submitted to changes in the dielectric constant of its surroundings, a condition that is experienced by the protein when in close contact with membranes of cell compartments, such as the Golgi apparatus. Intrinsic disorder and fibril formation can thus be two structural properties exploited by GRASP during its functional cycle.
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26
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Yang S, Su Y, Xu Y, Wu Q, Zhang Y, Raschke MB, Ren M, Chen Y, Wang J, Guo W, Ron Shen Y, Tian C. Mechanism of Electric Power Generation from Ionic Droplet Motion on Polymer Supported Graphene. J Am Chem Soc 2018; 140:13746-13752. [DOI: 10.1021/jacs.8b07778] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Shanshan Yang
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
| | - Yudan Su
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
| | - Ying Xu
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
| | - Qiong Wu
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
| | - Yuanbo Zhang
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
| | - Markus B. Raschke
- Department of Physics, Department of Chemistry, and JILA, University of Colorado, Boulder, Colorado 80309, United States
| | - Mengxin Ren
- School of Physics and TEDA Applied Physics Institute, Nankai University, Tianjin 300071, China
| | - Yan Chen
- National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Jianlu Wang
- National Laboratory for Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai 200083, China
| | - Wanlin Guo
- Institute of Nanoscience, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Y. Ron Shen
- Department of Physics, University of California, Berkeley, Berkeley, California 94720, United States
| | - Chuanshan Tian
- Department of Physics, State Key Laboratory of Surface Physics and Key Laboratory of Micro- and Nano-Photonic Structures (MOE), Fudan University, Shanghai 200433, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, China
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27
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Takahashi T, Krulwich TA, Ito M. A Hydrophobic Small Protein, BpOF4_01690, Is Critical for Alkaliphily of Alkaliphilic Bacillus pseudofirmus OF4. Front Microbiol 2018; 9:1994. [PMID: 30210472 PMCID: PMC6120979 DOI: 10.3389/fmicb.2018.01994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/08/2018] [Indexed: 11/17/2022] Open
Abstract
A monocistronic small protein, BpOF4_01690, was annotated in alkaliphilic Bacillus pseudofirmus OF4. It comprises 59 amino acids and is hydrophobic. Importantly, homologs of this protein were identified only in alkaliphiles. In this study, a mutant with a BpOF4_01690 gene deletion (designated Δ01690) exhibited weaker growth than that of the wild type in both malate-based defined and glucose-based defined media under low-sodium conditions at pH 10.5. Additionally, the enzymatic activity of the respiratory chain of Δ01690 was much lower than that of the wild type. These phenotypes were similar to those of a ctaD deletion mutant and an atpB-F deletion mutant. Therefore, we hypothesize that BpOF4_01690 plays a critical role in oxidative phosphorylation under highly alkaline conditions.
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Affiliation(s)
| | - Terry A. Krulwich
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
- Bio-Nano Electronics Research Centre, Toyo University, Kawagoe, Japan
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28
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Panov A. Perhydroxyl Radical (HO2•) as Inducer of the Isoprostane Lipid Peroxidation in Mitochondria. Mol Biol 2018. [DOI: 10.1134/s0026893318020097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Neuberger A, Du D, Luisi BF. Structure and mechanism of bacterial tripartite efflux pumps. Res Microbiol 2018; 169:401-413. [PMID: 29787834 DOI: 10.1016/j.resmic.2018.05.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/20/2018] [Accepted: 05/14/2018] [Indexed: 12/22/2022]
Abstract
Efflux pumps are membrane proteins which contribute to multi-drug resistance. In Gram-negative bacteria, some of these pumps form complex tripartite assemblies in association with an outer membrane channel and a periplasmic membrane fusion protein. These tripartite machineries span both membranes and the periplasmic space, and they extrude from the bacterium chemically diverse toxic substrates. In this chapter, we summarise current understanding of the structural architecture, functionality, and regulation of tripartite multi-drug efflux assemblies.
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Affiliation(s)
- Arthur Neuberger
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Dijun Du
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK.
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30
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Dreier LB, Nagata Y, Lutz H, Gonella G, Hunger J, Backus EHG, Bonn M. Saturation of charge-induced water alignment at model membrane surfaces. SCIENCE ADVANCES 2018; 4:eaap7415. [PMID: 29670939 PMCID: PMC5903901 DOI: 10.1126/sciadv.aap7415] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/15/2018] [Indexed: 05/23/2023]
Abstract
The electrical charge of biological membranes and thus the resulting alignment of water molecules in response to this charge are important factors affecting membrane rigidity, transport, and reactivity. We tune the surface charge density by varying lipid composition and investigate the charge-induced alignment of water molecules using surface-specific vibrational spectroscopy and molecular dynamics simulations. At low charge densities, the alignment of water increases proportionally to the charge. However, already at moderate, physiologically relevant charge densities, water alignment starts to saturate despite the increase in the nominal surface charge. The saturation occurs in both the Stern layer, directly at the surface, and in the diffuse layer, yet for distinctly different reasons. Our results show that the soft nature of the lipid interface allows for a marked reduction of the surface potential at high surface charge density via both interfacial molecular rearrangement and permeation of monovalent ions into the interface.
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Affiliation(s)
- Lisa B. Dreier
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudingerweg 9, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Helmut Lutz
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Grazia Gonella
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ellen H. G. Backus
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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31
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Sharma SK, Seven ES, Micic M, Li S, Leblanc RM. Surface Chemistry and Spectroscopic Study of a Cholera Toxin B Langmuir Monolayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:2557-2564. [PMID: 29378405 DOI: 10.1021/acs.langmuir.7b04252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In this article, we explored the surface chemistry properties of a cholera toxin B (CTB) monolayer at the air-subphase interface and investigated the change in interfacial properties through in situ spectroscopy. The study showed that the impact of the blue shift was negligible, suggesting that the CTB molecules were minimally affected by the subphase molecules. The stability of the CTB monolayer was studied by maintaining the constant surface pressure for a long time and also by using the compression-decompression cycle experiments. The high stability of the Langmuir monolayer of CTB clearly showed that the driving force of CTB going to the amphiphilic membrane was its amphiphilic nature. In addition, no major change was detected in the various in situ spectroscopy results (such as UV-vis, fluorescence, and IR ER) of the CTB Langmuir monolayer with the increase in surface pressure. This indicates that no aggregation occurs in the Langmuir monolayer of CTB.
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Affiliation(s)
- Shiv K Sharma
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Elif S Seven
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
| | - Miodrag Micic
- MP Biomedicals LLC, 3 Hutton Center, Santa Ana, California 92707, United States
- Department of Engineering Design Technology, Cerritos College , 11110 Alondra Boulevard, Norwalk, California 90650, United States
| | - Shanghao Li
- MP Biomedicals LLC, 3 Hutton Center, Santa Ana, California 92707, United States
| | - Roger M Leblanc
- Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States
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Mendes LFS, Basso LGM, Kumagai PS, Fonseca-Maldonado R, Costa-Filho AJ. Disorder-to-order transitions in the molten globule-like Golgi Reassembly and Stacking Protein. Biochim Biophys Acta Gen Subj 2018; 1862:855-865. [PMID: 29339081 DOI: 10.1016/j.bbagen.2018.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/14/2017] [Accepted: 01/11/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Golgi Reassembly and Stacking Proteins (GRASPs) are widely spread among eukaryotic cells (except plants) and are considered as key components in both the stacking of the Golgi cisternae and its lateral connection. Furthermore, GRASPs were also proved essential in the unconventional secretion pathway of several proteins, even though the mechanism remains obscure. It was previously observed that the GRASP homologue in Cryptococcus neoformans has a molten globule-like behavior in solution. METHODS We used circular dichroism, synchrotron radiation circular dichroism and steady-state as well as time-resolved fluorescence. RESULTS We report the disorder-to-order transition propensities for a native molten globule-like protein in the presence of different mimetics of cell conditions. Changes in the dielectric constant (such as those experienced close to the membrane surface) seem to be the major factor in inducing multiple disorder-to-order transitions in GRASP, which shows very distinct behavior when in conditions that mimic the vicinity of the membrane surface as compared to those found when free in solution. Other folding factors such as molecular crowding, counter ions, pH and phosphorylation exhibit lower or no effect on GRASP secondary structure and/or stability. GENERAL SIGNIFICANCE To the best of our knowledge, this is the first study focusing on understanding the disorder-to-order transitions of a molten globule structure without the need of any mild denaturing condition. A model is also introduced aiming at describing how the cell could manipulate the GRASP sensitivity to changes in the dielectric constant during different cell-cycle periods.
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Affiliation(s)
- Luís F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis G M Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Patricia S Kumagai
- Grupo de Biofísica Molecular "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Raquel Fonseca-Maldonado
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil; Instituto Federal de São Paulo, Campus Jacareí, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Microwave measurement of giant unilamellar vesicles in aqueous solution. Sci Rep 2018; 8:497. [PMID: 29323157 PMCID: PMC5764977 DOI: 10.1038/s41598-017-18806-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/18/2017] [Indexed: 11/26/2022] Open
Abstract
A microwave technique is demonstrated to measure floating giant unilamellar vesicle (GUV) membranes in a 25 μm wide and 18.8 μm high microfluidic channel. The measurement is conducted at 2.7 and 7.9 GHz, at which a split-ring resonator (SRR) operates at odd modes. A 500 nm wide and 100 μm long SRR split gap is used to scan GUVs that are slightly larger than 25 μm in diameter. The smaller fluidic channel induces flattened GUV membrane sections, which make close contact with the SRR gap surface. The used GUVs are synthesized with POPC (16:0–18:1 PC 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine), SM (16:0 Egg Sphingomyelin) and cholesterol at different molecular compositions. It is shown that SM and POPC bilayers have different dielectric permittivity values, which also change with measurement frequencies. The obtained membrane permittivity values, e.g. 73.64-j6.13 for POPC at 2.7 GHz, are more than 10 times larger than previously reported results. The discrepancy is likely due to the measurement of dielectric polarization parallel with, other than perpendicular to, the membrane surface. POPC and SM-rich GUV surface sections are also clearly identified. Further work is needed to verify the obtained large permittivity values and enable accurate analysis of membrane composition.
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Cherepanov DA, Milanovsky GE, Petrova AA, Tikhonov AN, Semenov AY. Electron Transfer through the Acceptor Side of Photosystem I: Interaction with Exogenous Acceptors and Molecular Oxygen. BIOCHEMISTRY (MOSCOW) 2018; 82:1249-1268. [PMID: 29223152 DOI: 10.1134/s0006297917110037] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review considers the state-of-the-art on mechanisms and alternative pathways of electron transfer in photosynthetic electron transport chains of chloroplasts and cyanobacteria. The mechanisms of electron transport control between photosystems (PS) I and II and the Calvin-Benson cycle are considered. The redistribution of electron fluxes between the noncyclic, cyclic, and pseudocyclic pathways plays an important role in the regulation of photosynthesis. Mathematical modeling of light-induced electron transport processes is considered. Particular attention is given to the electron transfer reactions on the acceptor side of PS I and to interactions of PS I with exogenous acceptors, including molecular oxygen. A kinetic model of PS I and its interaction with exogenous electron acceptors has been developed. This model is based on experimental kinetics of charge recombination in isolated PS I. Kinetic and thermodynamic parameters of the electron transfer reactions in PS I are scrutinized. The free energies of electron transfer between quinone acceptors A1A/A1B in the symmetric redox cofactor branches of PS I and iron-sulfur clusters FX, FA, and FB have been estimated. The second-order rate constants of electron transfer from PS I to external acceptors have been determined. The data suggest that byproduct formation of superoxide radical in PS I due to the reduction of molecular oxygen in the A1 site (Mehler reaction) can exceed 0.3% of the total electron flux in PS I.
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Affiliation(s)
- D A Cherepanov
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Moscow, 119992, Russia.
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Sjöholm J, Bergstrand J, Nilsson T, Šachl R, Ballmoos CV, Widengren J, Brzezinski P. The lateral distance between a proton pump and ATP synthase determines the ATP-synthesis rate. Sci Rep 2017; 7:2926. [PMID: 28592883 PMCID: PMC5462737 DOI: 10.1038/s41598-017-02836-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/19/2017] [Indexed: 11/09/2022] Open
Abstract
We have investigated the effect of lipid composition on interactions between cytochrome bo 3 and ATP-synthase, and the ATP-synthesis activity driven by proton pumping. The two proteins were labeled by fluorescent probes and co-reconstituted in large (d ≅ 100 nm) or giant (d ≅ 10 µm) unilamellar lipid vesicles. Interactions were investigated using fluorescence correlation/cross-correlation spectroscopy and the activity was determined by measuring ATP production, driven by electron-proton transfer, as a function of time. We found that conditions that promoted direct interactions between the two proteins in the membrane (higher fraction DOPC lipids or labeling by hydrophobic molecules) correlated with an increased activity. These data indicate that the ATP-synthesis rate increases with decreasing distance between cytochrome bo 3 and the ATP-synthase, and involves proton transfer along the membrane surface. The maximum distance for lateral proton transfer along the surface was found to be ~80 nm.
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Affiliation(s)
- Johannes Sjöholm
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Jan Bergstrand
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), SE-106 91, Stockholm, Sweden
| | - Tobias Nilsson
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Radek Šachl
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | | | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 2: Computer controlled pH gradients in the presence of urea provide improved separation of proteins: Stability influenced anion and cation exchange chromatography. J Chromatogr A 2017; 1495:22-30. [DOI: 10.1016/j.chroma.2017.03.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/08/2017] [Accepted: 03/13/2017] [Indexed: 11/21/2022]
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Plecitá-Hlavatá L, Ježek P. Integration of superoxide formation and cristae morphology for mitochondrial redox signaling. Int J Biochem Cell Biol 2016; 80:31-50. [PMID: 27640755 DOI: 10.1016/j.biocel.2016.09.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/09/2016] [Accepted: 09/12/2016] [Indexed: 12/16/2022]
Abstract
The mitochondrial network provides the central cell's energetic and regulatory unit, which besides ATP and metabolite production participates in cellular signaling through regulated reactive oxygen species (ROS) production and various protein/ion fluxes. The inner membrane forms extensive folds, called cristae, i.e. cavities enfolded from and situated perpendicularly to its inner boundary membrane portion, which encompasses an inner cylinder within the outer membrane tubule. Mitochondrial cristae ultramorphology reflects various metabolic, physiological or pathological states. Since the mitochondrion is typically a predominant superoxide source and generated ROS also serve for the creation of information redox signals, we review known relationships between ROS generation within the respiratory chain complexes of cristae and cristae morphology. Notably, it is emphasized that cristae shape is governed by ATP-synthase dimers, MICOS complexes, OPA1 isoforms and the umbrella of their regulation, and also dependent on local protonmotive force (electrical potential component) in cristae. Cristae are also affected by redox-sensitive kinases/phosphatases or p66SHC. ATP-synthase dimers decrease in the inflated intracristal space, diminishing pH and hypothetically having minimal superoxide formation. Matrix-released signaling superoxide/H2O2 is predominantly integrated along mitochondrial tubules, whereas the diffusion of intracristal signaling ROS species is controlled by crista junctions, the widening of which enables specific retrograde redox signaling such as during hypoxic cell adaptation. Other physiological cases of H2O2 release from the mitochondrion include the modulation of insulin release in pancreatic β-cells, enhancement of insulin signaling in peripheral tissues, signaling by T-cell receptors, retrograde signaling during the cell cycle and cell differentiation, specifically that of adipocytes.
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Affiliation(s)
- Lydie Plecitá-Hlavatá
- Department of Membrane Transport Biophysics, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Ježek
- Department of Membrane Transport Biophysics, No.75, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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38
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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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39
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Wang Y, Xu Z. Water Intercalation for Seamless, Electrically Insulating, and Thermally Transparent Interfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:1970-1976. [PMID: 26720217 DOI: 10.1021/acsami.5b10173] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The interface between functional nanostructures and host substrates is of pivotal importance in the design of their nanoelectronic applications because it conveys energy and information between the device and environment. We report here an interface-engineering approach to establish a seamless, electrically insulating, while thermally transparent interface between graphene and metal substrates by introducing water intercalation. Molecular dynamics simulations and first-principles calculations are performed to demonstrate this concept of design, showing that the presence of the interfacial water layer helps to unfold wrinkles formed in the graphene membrane, insulate the electronic coupling between graphene and the substrate, and elevate the interfacial thermal conductance. The findings here lay the ground for a new class of nanoelectronic setups through interface engineering, which could lead to significant improvement in the performance of nanodevices, such as the field-effect transistors.
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Affiliation(s)
- Yanlei Wang
- Applied Mechanics Laboratory, Department of Engineering Mechanics and Center for Nano and Micro Mechanics, Tsinghua University , Beijing 100084, People's Republic of China
| | - Zhiping Xu
- Applied Mechanics Laboratory, Department of Engineering Mechanics and Center for Nano and Micro Mechanics, Tsinghua University , Beijing 100084, People's Republic of China
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40
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Olson EJ, Ma R, Sun T, Ebrish MA, Haratipour N, Min K, Aluru NR, Koester SJ. Capacitive Sensing of Intercalated H2O Molecules Using Graphene. ACS APPLIED MATERIALS & INTERFACES 2015; 7:25804-12. [PMID: 26502269 DOI: 10.1021/acsami.5b07731] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Understanding the interactions of ambient molecules with graphene and adjacent dielectrics is of fundamental importance for a range of graphene-based devices, particularly sensors, where such interactions could influence the operation of the device. It is well-known that water can be trapped underneath graphene and its host substrate; however, the electrical effect of water beneath graphene and the dynamics of how the interfacial water changes with different ambient conditions has not been quantified. Here, using a metal-oxide-graphene variable-capacitor (varactor) structure, we show that graphene can be used to capacitively sense the intercalation of water between graphene and HfO2 and that this process is reversible on a fast time scale. Atomic force microscopy is used to confirm the intercalation and quantify the displacement of graphene as a function of humidity. Density functional theory simulations are used to quantify the displacement of graphene induced by intercalated water and also explain the observed Dirac point shifts as being due to the combined effect of water and oxygen on the carrier concentration in the graphene. Finally, molecular dynamics simulations indicate that a likely mechanism for the intercalation involves adsorption and lateral diffusion of water molecules beneath the graphene.
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Affiliation(s)
- Eric J Olson
- Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities , 200 Union Street SE, Minneapolis, Minnesota 55455, United States
| | - Rui Ma
- Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities , 200 Union Street SE, Minneapolis, Minnesota 55455, United States
| | - Tao Sun
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Mona A Ebrish
- Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities , 200 Union Street SE, Minneapolis, Minnesota 55455, United States
| | - Nazila Haratipour
- Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities , 200 Union Street SE, Minneapolis, Minnesota 55455, United States
| | - Kyoungmin Min
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Narayana R Aluru
- Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61802, United States
| | - Steven J Koester
- Department of Electrical and Computer Engineering, University of Minnesota-Twin Cities , 200 Union Street SE, Minneapolis, Minnesota 55455, United States
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Yi X, Zhang Y, Gong M, Yu X, Darabedian N, Zheng J, Zhou F. Ca2+ Interacts with Glu-22 of Aβ(1–42) and Phospholipid Bilayers to Accelerate the Aβ(1–42) Aggregation Below the Critical Micelle Concentration. Biochemistry 2015; 54:6323-32. [DOI: 10.1021/acs.biochem.5b00719] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xinyao Yi
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
- College
of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Yi Zhang
- College
of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Ming Gong
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
| | - Xiang Yu
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Narek Darabedian
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
| | - Jie Zheng
- Department
of Chemical and Biomolecular Engineering, The University of Akron, Akron, Ohio 44325, United States
| | - Feimeng Zhou
- Department
of Chemistry and Biochemistry, California State University, Los Angeles, California 90032, United States
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42
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Wolf MG, Grubmüller H, Groenhof G. Anomalous surface diffusion of protons on lipid membranes. Biophys J 2015; 107:76-87. [PMID: 24988343 DOI: 10.1016/j.bpj.2014.04.062] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/06/2014] [Accepted: 04/07/2014] [Indexed: 11/30/2022] Open
Abstract
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.
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Affiliation(s)
- Maarten G Wolf
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Gerrit Groenhof
- Computational Biomolecular Chemistry Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Medvedev ES, Stuchebrukhov AA. Mechanisms of generation of local ΔpH in mitochondria and bacteria. BIOCHEMISTRY (MOSCOW) 2015; 79:425-34. [PMID: 24954593 DOI: 10.1134/s000629791405006x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The concepts of global and local coupling between proton generators, the enzymes of the respiratory chain, and the consumer, the ATP synthase, coexist in the theory of oxidative phosphorylation. Global coupling is trivial proton transport via the aqueous medium, whereas local coupling implies that the protons pumped are consumed before they escape to the bulk phase. In this work, the conditions for the occurrence of local coupling are explored. It is supposed that the membrane retains protons near its surface and that the proton current generated by the proton pumps rapidly decreases with increasing proton motive force (pmf). It is shown that the competition between the processes of proton translocation across the membrane and their dissipation from the surface to the bulk can result in transient generation of a local ΔpH in reply to a sharp change in pmf; the appearance of local ΔpH, in turn, leads to rapid recovery of the pmf, and hence, it provides for stabilization of the potential at the membrane. Two mechanisms of such kind are discussed: 1) pH changes in the surface area due to proton pumping develop faster than those due to proton escape to the bulk; 2) the former does not take place, but the protons leaving the surface do not equilibrate with the bulk immediately; rather, they give rise to a non-equilibrium concentration near the surface and, as a result, to a back proton flow to the surface. The first mechanism is more efficient, but it does not occur in mitochondria and neutrophilic bacteria, whereas the second can produce ΔpH on the order of unity. In the absence of proton retardation at the surface, local ΔpH does not arise, whereas the formation of global ΔpH is possible only at buffer concentration of less than 10 mM. The role of the mechanisms proposed in transitions between States 3 and 4 of the respiratory chain is discussed. The main conclusion is that surface protons, under conditions where they play a role, support stabilization of the membrane pmf and rapid communication between proton generators and consumers, while their contribution to the energetics is not significant.
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Affiliation(s)
- E S Medvedev
- Institute of Problems of Chemical Physics, Russian Academy of Sciences, Chernogolovka, Moscow Region, 142432, Russia.
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Preiner J, Horner A, Karner A, Ollinger N, Siligan C, Pohl P, Hinterdorfer P. High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties. NANO LETTERS 2015; 15:759-63. [PMID: 25516527 PMCID: PMC4296598 DOI: 10.1021/nl504478f] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/11/2014] [Indexed: 05/20/2023]
Abstract
The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.
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Affiliation(s)
- Johannes Preiner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
- E-mail:
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Andreas Karner
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
| | - Nicole Ollinger
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Peter Hinterdorfer
- Center
for Advanced Bioanalysis GmbH, Gruberstrasse 40, 4020 Linz, Austria
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstrasse 40, 4020 Linz, Austria
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45
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Li H, Lu B. An ionic concentration and size dependent dielectric permittivity Poisson-Boltzmann model for biomolecular solvation studies. J Chem Phys 2014; 141:024115. [DOI: 10.1063/1.4887342] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Xu Z, Ma M, Liu P. Self-energy-modified Poisson-Nernst-Planck equations: WKB approximation and finite-difference approaches. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:013307. [PMID: 25122410 DOI: 10.1103/physreve.90.013307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 06/03/2023]
Abstract
We propose a modified Poisson-Nernst-Planck (PNP) model to investigate charge transport in electrolytes of inhomogeneous dielectric environment. The model includes the ionic polarization due to the dielectric inhomogeneity and the ion-ion correlation. This is achieved by the self energy of test ions through solving a generalized Debye-Hückel (DH) equation. We develop numerical methods for the system composed of the PNP and DH equations. Particularly, toward the numerical challenge of solving the high-dimensional DH equation, we developed an analytical WKB approximation and a numerical approach based on the selective inversion of sparse matrices. The model and numerical methods are validated by simulating the charge diffusion in electrolytes between two electrodes, for which effects of dielectrics and correlation are investigated by comparing the results with the prediction by the classical PNP theory. We find that, at the length scale of the interface separation comparable to the Bjerrum length, the results of the modified equations are significantly different from the classical PNP predictions mostly due to the dielectric effect. It is also shown that when the ion self energy is in weak or mediate strength, the WKB approximation presents a high accuracy, compared to precise finite-difference results.
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Affiliation(s)
- Zhenli Xu
- Department of Mathematics, Institute of Natural Sciences, and MoE Key Lab of Scientific and Engineering Computing, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Manman Ma
- Department of Mathematics, Institute of Natural Sciences, and MoE Key Lab of Scientific and Engineering Computing, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pei Liu
- Department of Mathematics, Institute of Natural Sciences, and MoE Key Lab of Scientific and Engineering Computing, Shanghai Jiao Tong University, Shanghai 200240, China
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Llorente-Garcia I, Lenn T, Erhardt H, Harriman OL, Liu LN, Robson A, Chiu SW, Matthews S, Willis NJ, Bray CD, Lee SH, Shin JY, Bustamante C, Liphardt J, Friedrich T, Mullineaux CW, Leake MC. Single-molecule in vivo imaging of bacterial respiratory complexes indicates delocalized oxidative phosphorylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:811-24. [DOI: 10.1016/j.bbabio.2014.01.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/22/2014] [Accepted: 01/30/2014] [Indexed: 02/04/2023]
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Jayant K, Auluck K, Rodriguez S, Cao Y, Kan EC. Programmable ion-sensitive transistor interfaces. III. Design considerations, signal generation, and sensitivity enhancement. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052817. [PMID: 25353854 DOI: 10.1103/physreve.89.052817] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 06/04/2023]
Abstract
We report on factors that affect DNA hybridization detection using ion-sensitive field-effect transistors (ISFETs). Signal generation at the interface between the transistor and immobilized biomolecules is widely ascribed to unscreened molecular charges causing a shift in surface potential and hence the transistor output current. Traditionally, the interaction between DNA and the dielectric or metal sensing interface is modeled by treating the molecular layer as a sheet charge and the ionic profile with a Poisson-Boltzmann distribution. The surface potential under this scenario is described by the Graham equation. This approximation, however, often fails to explain large hybridization signals on the order of tens of mV. More realistic descriptions of the DNA-transistor interface which include factors such as ion permeation, exclusion, and packing constraints have been proposed with little or no corroboration against experimental findings. In this study, we examine such physical models by their assumptions, range of validity, and limitations. We compare simulations against experiments performed on electrolyte-oxide-semiconductor capacitors and foundry-ready floating-gate ISFETs. We find that with weakly charged interfaces (i.e., low intrinsic interface charge), pertinent to the surfaces used in this study, the best agreement between theory and experiment exists when ions are completely excluded from the DNA layer. The influence of various factors such as bulk pH, background salinity, chemical reactivity of surface groups, target molecule concentration, and surface coatings on signal generation is studied. Furthermore, in order to overcome Debye screening limited detection, we suggest two signal enhancement strategies. We first describe frequency domain biosensing, highlighting the ability to sort short DNA strands based on molecular length, and then describe DNA biosensing in multielectrolytes comprising trace amounts of higher-valency salt in a background of monovalent saline. Our study provides guidelines for optimized interface design, signal enhancement, and the interpretation of FET-based biosensor signals.
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Affiliation(s)
- Krishna Jayant
- Electrical and Computer Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Kshitij Auluck
- Electrical and Computer Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Sergio Rodriguez
- Department of Biology, Randolph College, Lynchburg, Virginia 24503, USA
| | - Yingqiu Cao
- Electrical and Computer Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Edwin C Kan
- Electrical and Computer Engineering, Cornell University, Ithaca, New York 14853, USA
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Mosca S, Keller J, Azzouz N, Wagner S, Titz A, Seeberger PH, Brezesinski G, Hartmann L. Amphiphilic cationic β(3R3)-peptides: membrane active peptidomimetics and their potential as antimicrobial agents. Biomacromolecules 2014; 15:1687-95. [PMID: 24694059 DOI: 10.1021/bm500101w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We introduce a novel class of membrane active peptidomimetics, the amphiphilic cationic β(3R3)-peptides, and evaluate their potential as antimicrobial agents. The design criteria, the building block and oligomer synthesis as well as a detailed structure-activity relationship (SAR) study are reported. Specifically, infrared reflection absorption spectroscopy (IRRAS) was employed to investigate structural features of amphiphilic cationic β(3R3)-peptide sequences at the hydrophobic/hydrophilic air/liquid interface. Furthermore, Langmuir monolayers of anionic and zwitterionic phospholipids have been used to model the interactions of amphiphilic cationic β(3R3)-peptides with prokaryotic and eukaryotic cellular membranes in order to predict their membrane selectivity and elucidate their mechanism of action. Lastly, antimicrobial activity was tested against Gram-positive M. luteus and S. aureus as well as against Gram-negative E. coli and P. aeruginosa bacteria along with testing hemolytic activity and cytotoxicity. We found that amphiphilic cationic β(3R3)-peptide sequences combine high and selective antimicrobial activity with exceptionally low cytotoxicity in comparison to values reported in the literature. Overall, this study provides further insights into the SAR of antimicrobial peptides and peptidomimetics and indicates that amphiphilic cationic β(3R3)-peptides are strong candidates for further development as antimicrobial agents with high therapeutic index.
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Affiliation(s)
- Simone Mosca
- Department of Biomolecular Systems and ‡Department of Interfaces, Research Campus Golm, Max Planck Institute of Colloids and Interfaces , 14424 Potsdam, Germany
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Silverstein TP. An exploration of how the thermodynamic efficiency of bioenergetic membrane systems varies with c-subunit stoichiometry of F₁F₀ ATP synthases. J Bioenerg Biomembr 2014; 46:229-41. [PMID: 24706236 DOI: 10.1007/s10863-014-9547-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
Recently the F0 portion of the bovine mitochondrial F1F0-ATP synthase was shown to contain eight 'c' subunits (n = 8). This surprised many in the field, as previously, the only other mitochondrial F0 (for yeast) was shown to have ten 'c' subunits. The metabolic implications of 'c' subunit copy number explored in this paper lead to several surprising conclusions: (1) Aerobically respiring E. coli (n = 10) and animal mitochondria (n = 8) both have very high F1F0 thermodynamic efficiencies of ≈90% under typical conditions, whereas efficiency is only ≈65% for chloroplasts (n = 14). Reasons for this difference, including the importance of transmembrane potential (∆Ψ) as a rotational catalyst, as opposed to an energy source, are discussed. (2) Maximum theoretical P/O ratios in animal mitochondria (n = 8) are calculated to be 2.73 ATP/NADH and 1.64 ATP/FADH2, yielding 34.5 ATP/glucose (assuming NADH import via the malate/aspartate shuttle). The experimentally measured values of 2.44 (±0.15), 1.47 (±0.13), and 31.3 (±1.5), respectively, are only about 10% lower, suggesting very little energy depletion via transmembrane proton leakage. (3) Finally, the thermodynamic efficiency of oxidative phosphorylation is not lower than that of substrate level phosphorylation, as previously believed. The overall thermodynamic efficiencies of oxidative phosphorylation, glycolysis, and the citric acid cycle are ≈80% in all three processes.
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