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Ebrahimi A, Ergün T, Kaygusuz İzgördü Ö, Darcan C, Avci H, Öztürk B, Güner HR, Ghorbanpoor H, Doğan Güzel F. Revealing the single-channel characteristics of OprD (OccAB1) porins from hospital strains of Acinetobacter baumannii. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023:10.1007/s00249-023-01651-2. [PMID: 37052656 DOI: 10.1007/s00249-023-01651-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 03/28/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023]
Abstract
Nowadays, reports of antimicrobial resistance (AMR) against many antibiotics are increasing because of their misapplication. With this rise, there is a serious decrease in the discovery and development of new types of antibiotics amid an increase in multi-drug resistance. Unfermented Acinetobacter baumannii from gram-negative bacteria, which is one of the main causes of nosocomial infections and multi-drug resistance, has 4 main kinds of antibiotic resistance mechanism: inactivating antibiotics by enzymes, reduced numbers of porins and changing of their target or cellular functions due to mutations, and efflux pumps. In this study, characterization of the possible mutations in OprD (OccAB1) porins from hospital strains of A. baumannii were investigated using single channel electrophysiology and compared with the standard OprD isolated from wild type ATCC 19,606. For this aim, 5 A. baumannii bacteria samples were obtained from patients infected with A. baumannii, after which OprD porins were isolated from these A. baumannii strains. OprD porins were then inserted in an artificial lipid bilayer and the current-voltage curves were obtained using electrical recordings through a pair of Ag/AgCl electrodes. We observed that each porin has a characteristic conductance and single channel recording, which then leads to differences in channel diameter. Finally, the single channel data have been compared with the gene sequences of each porin. It was interesting to find out that each porin isolated has a unique porin diameter and decreased anion selectivity compared to the wild type.
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Affiliation(s)
- Aliakbar Ebrahimi
- Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
- Cellular Therapy and Stem Cell Research Center and Translational Medicine Research and Clinical Center (ESTEM), Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Tuğçe Ergün
- Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey
- Department of Biotechnology and Biosafety, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Özge Kaygusuz İzgördü
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, Bilecik, Turkey
| | - Cihan Darcan
- Faculty of Science and Literature, Department of Molecular Biology and Genetics, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Hüseyin Avci
- Cellular Therapy and Stem Cell Research Center and Translational Medicine Research and Clinical Center (ESTEM), Eskisehir Osmangazi University, Eskisehir, Turkey
- Faculty of Engineering and Architecture, Department of Metallurgical and Material Engineering, Eskisehir Osmangazi University, Eskisehir, Turkey
- Department of Stem Cell, Institute of Health Sciences, Eskisehir Osmangazi University, Eskisehir, Turkey
- Translational Medicine Research and Clinical Center (TATUM), Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Barçin Öztürk
- Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, Adnan Menderes University, Aydin, Turkey
| | - Hatice Rahmet Güner
- Faculty of Medicine, Department of Infectious Diseases and Clinical Microbiology, Ankara Yildirim Beyazit University, Ankara, Turkey
| | - Hamed Ghorbanpoor
- Cellular Therapy and Stem Cell Research Center and Translational Medicine Research and Clinical Center (ESTEM), Eskisehir Osmangazi University, Eskisehir, Turkey
- Department of Biomedical Engineering, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Fatma Doğan Güzel
- Faculty of Engineering and Natural Sciences, Department of Biomedical Engineering, Ankara Yildirim Beyazit University, Ankara, Turkey.
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2
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R-Type Fonticins Produced by Pragia fontium Form Large Pores with High Conductance. J Bacteriol 2023; 205:e0031522. [PMID: 36541812 PMCID: PMC9879110 DOI: 10.1128/jb.00315-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Fonticins are phage tail-like bacteriocins produced by the Gram-negative bacterium Pragia fontium from the family Budviciaceae. This bacterium produces contractile-type particles that adsorb on the surface of sensitive bacteria and penetrate the cell wall, probably during contraction, in a way similar to the type VI secretion system. We characterized the pore-forming activity of fonticins using both living cells and in vitro model membranes. Using a potassium leakage assay, we show that fonticins are able to permeabilize sensitive cells. On black lipid membranes, single-pore conductance is about 0.78 nS in 1 M NaCl and appears to be linearly dependent on the increasing molar strength of NaCl solution, which is a property of considerably large pores. In agreement with these findings, fonticins are not ion selective for Na+, K+, and Cl-. Polyethylene glycol 3350 (PEG 3350) molecules of about 3.5 nm in diameter can enter the fonticin pore lumen, whereas the larger molecules cannot pass the pore. The size of fonticin pores was confirmed by transmission electron microscopy. The terminal membrane-piercing complex of the fonticin tube probably creates a selective barrier restricting passage of macromolecules. IMPORTANCE Phage tail-like bacteriocins are now the subject of research as potent antibacterial agents due to their narrow host specificity and single-hit mode of action. In this work, we focused on the structure and mode of action of fonticins. According to some theories, related particles were initially adapted for passage of double-stranded DNA (dsDNA) molecules, but fonticins changed their function during the evolution; they are able to form large pores through the bacterial envelope of Gram-negative bacteria. As various pore-forming proteins are extensively used for nanopore sequencing and stochastic sensing, we decided to investigate the pore-forming properties of fonticin protein complexes on artificial lipid membranes. Our research revealed remarkable structural properties of these particles that may have a potential application as a nanodevice.
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Ulhuq FR, Mariano G. Bacterial pore-forming toxins. MICROBIOLOGY (READING, ENGLAND) 2022; 168:001154. [PMID: 35333704 PMCID: PMC9558359 DOI: 10.1099/mic.0.001154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/03/2022] [Indexed: 12/11/2022]
Abstract
Pore-forming toxins (PFTs) are widely distributed in both Gram-negative and Gram-positive bacteria. PFTs can act as virulence factors that bacteria utilise in dissemination and host colonisation or, alternatively, they can be employed to compete with rival microbes in polymicrobial niches. PFTs transition from a soluble form to become membrane-embedded by undergoing large conformational changes. Once inserted, they perforate the membrane, causing uncontrolled efflux of ions and/or nutrients and dissipating the protonmotive force (PMF). In some instances, target cells intoxicated by PFTs display additional effects as part of the cellular response to pore formation. Significant progress has been made in the mechanistic description of pore formation for the different PFTs families, but in several cases a complete understanding of pore structure remains lacking. PFTs have evolved recognition mechanisms to bind specific receptors that define their host tropism, although this can be remarkably diverse even within the same family. Here we summarise the salient features of PFTs and highlight where additional research is necessary to fully understand the mechanism of pore formation by members of this diverse group of protein toxins.
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Affiliation(s)
- Fatima R. Ulhuq
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
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4
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Queralt-Martín M, Bergdoll L, Teijido O, Munshi N, Jacobs D, Kuszak AJ, Protchenko O, Reina S, Magrì A, De Pinto V, Bezrukov SM, Abramson J, Rostovtseva TK. A lower affinity to cytosolic proteins reveals VDAC3 isoform-specific role in mitochondrial biology. J Gen Physiol 2021; 152:133600. [PMID: 31935282 PMCID: PMC7062508 DOI: 10.1085/jgp.201912501] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 11/20/2019] [Indexed: 01/30/2023] Open
Abstract
Voltage-dependent anion channel (VDAC) is the major pathway for the transport of ions and metabolites across the mitochondrial outer membrane. Among the three known mammalian VDAC isoforms, VDAC3 is the least characterized, but unique functional roles have been proposed in cellular and animal models. Yet, a high-sequence similarity between VDAC1 and VDAC3 is indicative of a similar pore-forming structure. Here, we conclusively show that VDAC3 forms stable, highly conductive voltage-gated channels that, much like VDAC1, are weakly anion selective and facilitate metabolite exchange, but exhibit unique properties when interacting with the cytosolic proteins α-synuclein and tubulin. These two proteins are known to be potent regulators of VDAC1 and induce similar characteristic blockages (on the millisecond time scale) of VDAC3, but with 10- to 100-fold reduced on-rates and altered α-synuclein blocking times, indicative of an isoform-specific function. Through cysteine scanning mutagenesis, we found that VDAC3's cysteine residues regulate its interaction with α-synuclein, demonstrating VDAC3-unique functional properties and further highlighting a general molecular mechanism for VDAC isoform-specific regulation of mitochondrial bioenergetics.
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Affiliation(s)
- María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Lucie Bergdoll
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Oscar Teijido
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Nabill Munshi
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Daniel Jacobs
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Adam J Kuszak
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Olga Protchenko
- Liver Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Simona Reina
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Andrea Magrì
- Department of Biological, Geological and Environmental Sciences, University of Catania, Catania, Italy
| | - Vito De Pinto
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD
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Transport mechanisms of SARS-CoV-E viroporin in calcium solutions: Lipid-dependent Anomalous Mole Fraction Effect and regulation of pore conductance. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183590. [PMID: 33621516 PMCID: PMC7896491 DOI: 10.1016/j.bbamem.2021.183590] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/04/2021] [Accepted: 02/06/2021] [Indexed: 02/06/2023]
Abstract
The envelope protein E of the SARS-CoV coronavirus is an archetype of viroporin. It is a small hydrophobic protein displaying ion channel activity that has proven highly relevant in virus-host interaction and virulence. Ion transport through E channel was shown to alter Ca2+ homeostasis in the cell and trigger inflammation processes. Here, we study transport properties of the E viroporin in mixed solutions of potassium and calcium chloride that contain a fixed total concentration (mole fraction experiments). The channel is reconstituted in planar membranes of different lipid compositions, including a lipid mixture that mimics the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane where the virus localizes within the cell. We find that the E ion conductance changes non-monotonically with the total ionic concentration displaying an Anomalous Mole Fraction Effect (AMFE) only when charged lipids are present in the membrane. We also observe that E channel insertion in ERGIC-mimic membranes – including lipid with intrinsic negative curvature – enhances ion permeation at physiological concentrations of pure CaCl2 or KCl solutions, with a preferential transport of Ca2+ in mixed KCl-CaCl2 solutions. Altogether, our findings demonstrate that the presence of calcium modulates the transport properties of the E channel by interacting preferentially with charged lipids through different mechanisms including direct Coulombic interactions and possibly inducing changes in membrane morphology.
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6
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Xin P, Zhao L, Mao L, Xu L, Hou S, Kong H, Fang H, Zhu H, Jiang T, Chen CP. Effect of charge status on the ion transport and antimicrobial activity of synthetic channels. Chem Commun (Camb) 2020; 56:13796-13799. [DOI: 10.1039/d0cc05730d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge status of channels formed by pillararene–gramicidin hybrid molecules has a significant impact on their trans-membrane transport properties, membrane-association abilities and antimicrobial activities.
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7
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Colicin U from Shigella boydii Forms Voltage-Dependent Pores. J Bacteriol 2019; 201:JB.00493-19. [PMID: 31548276 DOI: 10.1128/jb.00493-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/19/2019] [Indexed: 12/30/2022] Open
Abstract
Colicin U is a protein produced by the bacterium Shigella boydii (serovars 1 and 8). It exerts antibacterial activity against strains of the enterobacterial genera Shigella and Escherichia Here, we report that colicin U forms voltage-dependent pores in planar lipid membranes; its single-pore conductance was found to be about 22 pS in 1 M KCl at pH 6 under 80 mV in asolectin bilayers. In agreement with the high degree of homology between their C-terminal domains, colicin U shares some pore characteristics with the related colicins A and B. Colicin U pores are strongly pH dependent, and as we deduced from the activity of colicin U in planar membranes at different protein concentrations, they have a monomeric pore structure. However, in contrast to related colicins, we observed a very low cationic selectivity of colicin U pores (1.5/1 of K+/Cl- at pH 6) along with their atypical voltage gating. Finally, using nonelectrolytes, we determined the inner diameter of the pores to be in the range of 0.7 to 1 nm, which is similar to colicin Ia, but with a considerably different inner profile.IMPORTANCE Currently, a dramatic increase in antibiotic resistance is driving researchers to find new antimicrobial agents. The large group of toxins called bacteriocins appears to be very promising from this point of view, especially because their narrow killing spectrum allows specific targeting against selected bacterial strains. Colicins are a subgroup of bacteriocins that act on Gram-negative bacteria. To date, some colicins are commercially used for the treatment of animals (1) and tested as a component of engineered species-specific antimicrobial peptides, which are studied for the potential treatment of humans (2). Here, we present a thorough single-molecule study of colicin U which leads to a better understanding of its mode of action. It extends the range of characterized colicins available for possible future medical applications.
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8
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Abstract
BACKGROUND Coronaviruses (CoVs) primarily cause enzootic infections in birds and mammals but, in the last few decades, have shown to be capable of infecting humans as well. The outbreak of severe acute respiratory syndrome (SARS) in 2003 and, more recently, Middle-East respiratory syndrome (MERS) has demonstrated the lethality of CoVs when they cross the species barrier and infect humans. A renewed interest in coronaviral research has led to the discovery of several novel human CoVs and since then much progress has been made in understanding the CoV life cycle. The CoV envelope (E) protein is a small, integral membrane protein involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. Recent studies have expanded on its structural motifs and topology, its functions as an ion-channelling viroporin, and its interactions with both other CoV proteins and host cell proteins. MAIN BODY This review aims to establish the current knowledge on CoV E by highlighting the recent progress that has been made and comparing it to previous knowledge. It also compares E to other viral proteins of a similar nature to speculate the relevance of these new findings. Good progress has been made but much still remains unknown and this review has identified some gaps in the current knowledge and made suggestions for consideration in future research. CONCLUSIONS The most progress has been made on SARS-CoV E, highlighting specific structural requirements for its functions in the CoV life cycle as well as mechanisms behind its pathogenesis. Data shows that E is involved in critical aspects of the viral life cycle and that CoVs lacking E make promising vaccine candidates. The high mortality rate of certain CoVs, along with their ease of transmission, underpins the need for more research into CoV molecular biology which can aid in the production of effective anti-coronaviral agents for both human CoVs and enzootic CoVs.
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Affiliation(s)
- Dewald Schoeman
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Burtram C Fielding
- Molecular Biology and Virology Research Laboratory, Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa.
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9
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Pierdominici-Sottile G, Racigh V, Ormazábal A, Palma J. Charge Discrimination in P2X 4 Receptors Occurs in Two Consecutive Stages. J Phys Chem B 2019; 123:1017-1025. [PMID: 30624928 DOI: 10.1021/acs.jpcb.8b10249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
P2X receptors are a group of trimeric cationic channels that are activated by adenosine 5'-triphosphate. They perform critical roles in the membranes of mammalian cells, and their improper functioning is associated with numerous diseases. Despite the vast amount of research devoted to them, several aspects of their operation are currently unclear, including the causes of their charge selectivity. We present the results of molecular dynamics simulation, which shed light on this issue for the case of P2X4 channels. We examined in detail the behavior of Na+ and Cl- ions inside the receptor. The examination reveals that charge discrimination occurs in two stages. First, cations bear precedence over anions to enter the extracellular vestibule. Then, cations at the extracellular vestibule are more likely to cross the pore than anions in an equivalent position. In this manner, a thorough but straightforward analysis of computational simulations suggests a stepwise mechanism, without a unique determinant factor.
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Affiliation(s)
- Gustavo Pierdominici-Sottile
- Departamento de Ciencia y Tecnología, Consejo Nacional de Investigaciones Científicas y Técnicas , Universidad Nacional de Quilmes , Sáenz Peña 352 , Bernal B1876BXD , Argentina
| | - Vanesa Racigh
- Departamento de Ciencia y Tecnología, Consejo Nacional de Investigaciones Científicas y Técnicas , Universidad Nacional de Quilmes , Sáenz Peña 352 , Bernal B1876BXD , Argentina
| | - Agustín Ormazábal
- Departamento de Ciencia y Tecnología, Consejo Nacional de Investigaciones Científicas y Técnicas , Universidad Nacional de Quilmes , Sáenz Peña 352 , Bernal B1876BXD , Argentina
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Consejo Nacional de Investigaciones Científicas y Técnicas , Universidad Nacional de Quilmes , Sáenz Peña 352 , Bernal B1876BXD , Argentina
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10
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Ahumada JC, Alemán C, Soto-Delgado J, Torras J. Ion–Ion Repulsions and Charge-Shielding Effects Dominate the Permeation Mechanism through the OmpF Porin Channel. J Phys Chem B 2018; 123:86-94. [DOI: 10.1021/acs.jpcb.8b09549] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juan Carlos Ahumada
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
- Departamento de Química, Universidad Técnica Federico Santa María, Casilla 110-V, 2390123 Valparaíso, Chile
| | - Carlos Alemán
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
| | - Jorge Soto-Delgado
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andrés Bello, Quillota 980, 2531015 Viña del Mar, Chile
| | - Juan Torras
- Department of Chemical Engineering (EEBE) and Barcelona Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany 10−14, 08019 Barcelona, Spain
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11
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Queralt-Martín M, López ML, Aguilella-Arzo M, Aguilella VM, Alcaraz A. Scaling Behavior of Ionic Transport in Membrane Nanochannels. NANO LETTERS 2018; 18:6604-6610. [PMID: 30178677 PMCID: PMC6242701 DOI: 10.1021/acs.nanolett.8b03235] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Ionic conductance in membrane channels exhibits a power-law dependence on electrolyte concentration ( G ∼ cα). The many scaling exponents, α, reported in the literature usually require detailed interpretations concerning each particular system under study. Here, we critically evaluate the predictive power of scaling exponents by analyzing conductance measurements in four biological channels with contrasting architectures. We show that scaling behavior depends on several interconnected effects whose contributions change with concentration so that the use of oversimplified models missing critical factors could be misleading. In fact, the presence of interfacial effects could give rise to an apparent universal scaling that hides the channel distinctive features. We complement our study with 3D structure-based Poisson-Nernst-Planck (PNP) calculations, giving results in line with experiments and validating scaling arguments. Our findings not only provide a unified framework for the study of ion transport in confined geometries but also highlight that scaling arguments are powerful and simple tools with which to offer a comprehensive perspective of complex systems, especially those in which the actual structure is unknown.
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Affiliation(s)
- María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver
NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - M. Lidón López
- Laboratory of Molecular Biophysics, Department of Physics,
Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071 Castellón, Spain
| | - Marcel Aguilella-Arzo
- Laboratory of Molecular Biophysics, Department of Physics,
Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071 Castellón, Spain
| | - Vicente M. Aguilella
- Laboratory of Molecular Biophysics, Department of Physics,
Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071 Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics,
Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071 Castellón, Spain
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12
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Puiggalí-Jou A, Pawlowski J, del Valle LJ, Michaux C, Perpète EA, Sek S, Alemán C. Properties of Omp2a-Based Supported Lipid Bilayers: Comparison with Polymeric Bioinspired Membranes. ACS OMEGA 2018; 3:9003-9019. [PMID: 31459033 PMCID: PMC6645002 DOI: 10.1021/acsomega.8b00913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 07/19/2018] [Indexed: 05/31/2023]
Abstract
Omp2a β-barrel outer membrane protein has been reconstituted into supported lipid bilayers (SLBs) to compare the nanomechanical properties (elastic modulus, adhesion forces, and deformation) and functionality of the resulting bioinspired system with those of Omp2a-based polymeric nanomembranes (NMs). Protein reconstitution into lipid bilayers has been performed using different strategies, the most successful one consisting of a detergent-mediated process into preformed liposomes. The elastic modulus obtained for the lipid bilayer and Omp2a are ∼19 and 10.5 ± 1.7 MPa, respectively. Accordingly, the protein is softer than the lipid bilayer, whereas the latter exhibits less mechanical strength than polymeric NMs. Besides, the function of Omp2a in the SLB is similar to that observed for Omp2a-based polymeric NMs. Results open the door to hybrid bioinspired substrates based on the integration of Omp2a-proteoliposomes and nanoperforated polymeric freestanding NMs.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Jan Pawlowski
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Luis J. del Valle
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
| | - Catherine Michaux
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A. Perpète
- Laboratoire
de Chimie Physique des Biomolécules, University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Slawomir Sek
- Biological
and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Carlos Alemán
- Departament
d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. I2, 08019 Barcelona, Spain
- Barcelona
Research Center for Multiscale Science and Engineering, Universitat Politècnica de Catalunya, C/Eduard Maristany, 10-14, Ed. C, 08019 Barcelona, Spain
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13
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Role of Severe Acute Respiratory Syndrome Coronavirus Viroporins E, 3a, and 8a in Replication and Pathogenesis. mBio 2018; 9:mBio.02325-17. [PMID: 29789363 PMCID: PMC5964350 DOI: 10.1128/mbio.02325-17] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Viroporins are viral proteins with ion channel (IC) activity that play an important role in several processes, including virus replication and pathogenesis. While many coronaviruses (CoVs) encode two viroporins, severe acute respiratory syndrome CoV (SARS-CoV) encodes three: proteins 3a, E, and 8a. Additionally, proteins 3a and E have a PDZ-binding motif (PBM), which can potentially bind over 400 cellular proteins which contain a PDZ domain, making them potentially important for the control of cell function. In the present work, a comparative study of the functional motifs included within the SARS-CoV viroporins was performed, mostly focusing on the roles of the IC and PBM of E and 3a proteins. Our results showed that the full-length E and 3a proteins were required for maximal SARS-CoV replication and virulence, whereas viroporin 8a had only a minor impact on these activities. A virus missing both the E and 3a proteins was not viable, whereas the presence of either protein with a functional PBM restored virus viability. E protein IC activity and the presence of its PBM were necessary for virulence in mice. In contrast, the presence or absence of the homologous motifs in protein 3a did not influence virus pathogenicity. Therefore, dominance of the IC and PBM of protein E over those of protein 3a was demonstrated in the induction of pathogenesis in mice.IMPORTANCE Collectively, these results demonstrate key roles for the ion channel and PBM domains in optimal virus replication and pathogenesis and suggest that the viral viroporins and PBMs are suitable targets for antiviral therapy and for mutation in attenuated SARS-CoV vaccines.
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Largo E, Gladue DP, Torralba J, Aguilella VM, Alcaraz A, Borca MV, Nieva JL. Mutation-induced changes of transmembrane pore size revealed by combined ion-channel conductance and single vesicle permeabilization analyses. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1015-1021. [PMID: 29317201 DOI: 10.1016/j.bbamem.2018.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 11/25/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Abstract
Permeabilization of the Endoplasmic Reticulum (ER) is instrumental in the progression of host-cell infection by many viral pathogens. We have described that permeabilization of ER model membranes by the pore-forming domain of the Classical Swine Fever Virus (CSFV) p7 protein depends on two sequence determinants: the C-terminal transmembrane helix, and the preceding polar loop that regulates its activity. Here, by combining ion-channel activity measurements in planar lipid bilayers with imaging of single Giant Unilamellar Vesicles (GUVs), we demonstrate that point substitutions directed to conserved residues within these regions affect ER-like membrane permeabilization following distinct mechanisms. Whereas the polar loop appeared to be involved in protein insertion and oligomerization, substitution of residues predicted to face the lumen of the pore inhibited large conducting channels (>1 nS) over smaller ones (120 pS). Quantitative analyses of the ER-GUV distribution as a function of the solute size revealed a selective inhibition for the permeation of solutes with sizes larger than 4 kDa, further demonstrating that the mutation targeting the transmembrane helix prevented formation of the large pores. Collectively, our data support the idea that the pore-forming domain of p7 may assemble into finite pores with approximate diameters of 1 and 5 nm. Moreover, the observation that the mutation interfering with formation of the larger pores can hamper virus production without affecting ER localization or homo-oligomerization, suggests prospective strategies to block/attenuate pestiviruses.
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Affiliation(s)
- Eneko Largo
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Douglas P Gladue
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - Johana Torralba
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain
| | - Vicente M Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, University Jaume I, 12071 Castellón, Spain
| | - Manuel V Borca
- Plum Island Animal Disease Center, ARS, USDA, Greenport, NY 11944, USA
| | - José L Nieva
- Biofisika Institute (CSIC, UPV/EHU), Biochemistry and Molecular Biology Department, University of the Basque Country (UPV/EHU), P.O. Box 644, 48080 Bilbao, Spain.
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15
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Hernández S, Porter C, Zhang X, Wei Y, Bhattacharyya D. Layer-by-layer Assembled Membranes with Immobilized Porins. RSC Adv 2017; 7:56123-56136. [PMID: 29391943 PMCID: PMC5788187 DOI: 10.1039/c7ra08737c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With the synthesis and functionalization of membranes for selective separations, reactivity, and stimuli responsive behavior arises new and advanced opportunities. The integration of bio-based channels is one of these advancements in membrane technologies. By a layer-by-layer (LbL) assembly of polyelectrolytes, outer membrane protein F trimers (OmpF) or "porins" from Escherichia coli with a central pore of ~2 nm diameter at its opening and ~0.7 × 1.1 nm at its constricted region are immobilized within the pores of poly(vinylidene fluoride) microfiltration membranes, as opposed to traditional ruptured lipid bilayer or vesicles processes. These OmpF-membranes demonstrate selective rejections of non-charged organics over ionic solutes, allowing the passage of salts up to 2 times higher than traditional nanofiltration membranes starting with rejections of 84% for 0.4-1.0 kDa organics. The presence of charged groups in OmpF membranes also leads to pH-dependent salt rejection through Donnan exclusion. These OmpF-membranes also show exceptional durability and stability, delivering consistent and constant permeability and recovery for over 160 h of operation. Characterization of solutions containing OmpF, and membranes were conducted during each stage of the process, including detection by fluorescence labelling (FITC), zeta potential, pH responsiveness, flux changes, and rejections of organic-inorganic solutions.
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Affiliation(s)
- Sebastián Hernández
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
| | - Cassandra Porter
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
| | - Xinyi Zhang
- Department of Chemistry, University of Kentucky, Lexington, KY
| | - Yinan Wei
- Department of Chemistry, University of Kentucky, Lexington, KY
| | - Dibakar Bhattacharyya
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY
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16
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Alcaraz A, López ML, Queralt-Martín M, Aguilella VM. Ion Transport in Confined Geometries below the Nanoscale: Access Resistance Dominates Protein Channel Conductance in Diluted Solutions. ACS NANO 2017; 11:10392-10400. [PMID: 28930428 DOI: 10.1021/acsnano.7b05529] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Synthetic nanopores and mesoscopic protein channels have common traits like the importance of electrostatic interactions between the permeating ions and the nanochannel. Ion transport at the nanoscale occurs under confinement conditions so that the usual assumptions made in microfluidics are challenged, among others, by interfacial effects such as access resistance (AR). Here, we show that a sound interpretation of electrophysiological measurements in terms of channel ion selective properties requires the consideration of interfacial effects, up to the point that they dominate protein channel conductance in diluted solutions. We measure AR in a large ion channel, the bacterial porin OmpF, by means of single-channel conductance measurements in electrolyte solutions containing varying concentrations of high molecular weight PEG, sterically excluded from the pore. Comparison of experiments performed in charged and neutral planar membranes shows that lipid surface charges modify the ion distribution and determine the value of AR, indicating that lipid molecules are more than passive scaffolds even in the case of large transmembrane proteins. We also found that AR may reach up to 80% of the total channel conductance in diluted solutions, where electrophysiological recordings register essentially the AR of the system and depend marginally on the pore characteristics. These findings may have implications for several low aspect ratio biological channels that perform their physiological function in a low ionic strength and macromolecule crowded environment, just the two conditions enhancing the AR contribution.
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Affiliation(s)
- Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - M Lidón López
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
| | - Vicente M Aguilella
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , Av. Vicent Sos Baynat s/n, 12071 Castellón, Spain
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17
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Zhekova HR, Ngo V, da Silva MC, Salahub D, Noskov S. Selective ion binding and transport by membrane proteins – A computational perspective. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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18
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Fluctuation-Driven Transport in Biological Nanopores. A 3D Poisson–Nernst–Planck Study. ENTROPY 2017. [DOI: 10.3390/e19030116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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19
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Hong S, Constans C, Surmani Martins MV, Seow YC, Guevara Carrió JA, Garaj S. Scalable Graphene-Based Membranes for Ionic Sieving with Ultrahigh Charge Selectivity. NANO LETTERS 2017; 17:728-732. [PMID: 28005372 DOI: 10.1021/acs.nanolett.6b03837] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nanostructured graphene-oxide (GO) laminate membranes, exhibiting ultrahigh water flux, are excellent candidates for next generation nanofiltration and desalination membranes, provided the ionic rejection could be further increased without compromising the water flux. Using microscopic drift-diffusion experiments, we demonstrated the ultrahigh charge selectivity for GO membranes, with more than order of magnitude difference in the permeabilities of cationic and anionic species of equivalent hydration radii. Measuring diffusion of a wide range of ions of different size and charge, we were able to clearly disentangle different physical mechanisms contributing to the ionic sieving in GO membranes: electrostatic repulsion between ions and charged chemical groups; and the compression of the ionic hydration shell within the membrane's nanochannels, following the activated behavior. The charge-selectivity allows us to rationally design membranes with increased ionic rejection and opens up the field of ion exchange and electrodialysis to the GO membranes.
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Affiliation(s)
- Seunghyun Hong
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
| | - Charlotte Constans
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
- Department of Physics, National University of Singapore , Singapore 117551
| | - Marcos Vinicius Surmani Martins
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
- Department of Materials Science and Engineering, National University of Singapore , Singapore 117575
| | - Yong Chin Seow
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
| | - Juan Alfredo Guevara Carrió
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
- Engineering School, Presbyterian University Mackenzie , São Paulo 01302-907, Brazil
| | - Slaven Garaj
- Centre for Advanced 2D Materials, National University of Singapore , Singapore 117542
- Department of Physics, National University of Singapore , Singapore 117551
- NUS Nanoscience & Nanotechnology Institute, National University of Singapore , Singapore 117581
- Department of Biomedical Engineering, National University of Singapore , Singapore 117583
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20
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Patel DS, Re S, Wu EL, Qi Y, Klebba PE, Widmalm G, Yeom MS, Sugita Y, Im W. Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability. Biophys J 2016; 110:930-8. [PMID: 26910429 DOI: 10.1016/j.bpj.2016.01.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/13/2022] Open
Abstract
The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K(+) and Cl(-)), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.
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Affiliation(s)
- Dhilon S Patel
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Emilia L Wu
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Yifei Qi
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas
| | - Phillip E Klebba
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas
| | - Göran Widmalm
- Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
| | - Min Sun Yeom
- Korean Institute of Science and Technology Information, Yuseong-gu, Daejeon, Korea
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, Hirosawa, Wako, Saitama, Japan; RIKEN Quantitative Biology Center (QBiC), IMDA 6F, Chuo-ku, Kobe, Hyogo Prefecture, Japan; RIKEN Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo Prefecture, Japan
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, Lawrence, Kansas.
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21
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Puiggalí-Jou A, Pérez-Madrigal MM, Del Valle LJ, Armelin E, Casas MT, Michaux C, Perpète EA, Estrany F, Alemán C. Confinement of a β-barrel protein in nanoperforated free-standing nanomembranes for ion transport. NANOSCALE 2016; 8:16922-16935. [PMID: 27714137 DOI: 10.1039/c6nr04948f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Bioinspired free-standing nanomembranes (FSNMs) for selective ion transport have been tailored by immobilizing the Omp2a β-barrel membrane protein inside nanoperforations created in flexible poly(lactic acid) (PLA) nanomembranes. Perforated PLA FSNMs have been prepared by spin-coating a 99 : 1 PLA : poly(vinyl alcohol) mixture, and through a phase segregation process nanofeatures with dimensions similar to the entire nanomembrane thickness (∼110 nm) were induced. These nanofeatures have subsequently been transformed into nanoperforations (diameter: ∼51 nm) by selective solvent etching. The protein confined inside the nanopores of PLA FSNMs preserves the β-barrel structure and organizes in ovoid aggregates. The transport properties of Na+, K+, and Ca2+ across non-perforated PLA, nanoperforated PLA, and Omp2a-filled nanoperforated PLA have been monitored by measuring the nanomembrane resistance with electrochemical impedance spectroscopy (EIS). The incorporation of nanoperforations enhances the transport of ions across PLA nanomembranes, whereas the functionality of immobilized Omp2a is essential to exhibit effects similar to those observed in biological nanomembranes. Indeed, Omp2a-filled nanoperforated PLA nanomembranes exhibit stronger affinity towards Na+ and Ca2+ ions than towards K+. In summary, this work provides a novel bioinspired strategy to develop mechanically stable and flexible FSNMs with channels for ion transport, which are precisely located inside artificial nanoperforations, thus holding great potential for applications in biofiltration and biosensing.
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Affiliation(s)
- Anna Puiggalí-Jou
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Maria M Pérez-Madrigal
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Luis J Del Valle
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - Elaine Armelin
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| | - María T Casas
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain.
| | - Catherine Michaux
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Eric A Perpète
- Laboratoire de Chimie Physique des Biomolécules, Unité de Chimie Physique Théorique et Structurale (UCPTS), University of Namur, Rue de Bruxelles, 61, 5000 Namur, Belgium
| | - Francesc Estrany
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain and Departament d'Enginyeria Química, Escola Universitària d'Enginyeria Tècnica Industrial de Barcelona, Universitat Politècnica de Catalunya, Comte d'Urgell 187, 08036 Barcelona, Spain
| | - Carlos Alemán
- Departament d'Enginyeria Química, ETSEIB, Universitat Politècnica de Catalunya, Avda. Diagonal 647, Barcelona E-08028, Spain. and Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C', C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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22
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López ML, Queralt-Martín M, Alcaraz A. Stochastic pumping of ions based on colored noise in bacterial channels under acidic stress. NANOSCALE 2016; 8:13422-8. [PMID: 27349445 DOI: 10.1039/c6nr02638a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fluctuation-driven ion transport can be obtained in bacterial channels with the aid of different types of colored noise including the biologically relevant Lorentzian one. Using the electrochemical rectification of the channel current as a ratchet mechanism we observe transport of ions up to their concentration gradient under conditions similar to that met in vivo, namely moderate pH gradients and asymmetrically charged lipid membranes. We find that depending on the direction of the concentration gradient the channel can pump either cations or anions from the diluted side to the concentrated one. We discuss the possible relevance of this phenomenon for the pH homeostasis of bacterial cells.
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Affiliation(s)
- M Lidón López
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, Av. Vicent Sos Baynat s/n 12071, Castellón, Spain.
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23
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Alcaraz A, Queralt-Martín M. On the different sources of cooperativity in pH titrating sites of a membrane protein channel. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:29. [PMID: 26987733 PMCID: PMC7087919 DOI: 10.1140/epje/i2016-16029-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Cooperative interactions play a central role in the regulation of protein functions. Here we show that in multi-site systems like ion channels the application of the Hill formalism could require a combination of different experiments, even involving site-directed mutagenesis, to identify the different sources of cooperativity and to discriminate between genuine and apparent cooperativity. We discuss the implications for the channel function in the bacterial porins PorA (N. meningitidis) and OmpF (E. coli) and the viroporin SARS-CoV E.
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Affiliation(s)
- Antonio Alcaraz
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, 12080, Castellón, Spain.
| | - María Queralt-Martín
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, 12080, Castellón, Spain
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24
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Queralt-Martín M, Peiró-González C, Aguilella-Arzo M, Alcaraz A. Effects of extreme pH on ionic transport through protein nanopores: the role of ion diffusion and charge exclusion. Phys Chem Chem Phys 2016; 18:21668-75. [DOI: 10.1039/c6cp04180a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We combine electrophysiological experiments with the structure-based Poisson–Nernst–Planck 3D calculations to investigate the transport properties of the bacterial porin OmpF under large pH gradients and particularly low salt concentrations.
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Affiliation(s)
| | | | | | - Antonio Alcaraz
- Laboratory of Molecular Biophysics
- Department of Physics
- 12071 Castellón
- Spain
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25
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Pothula KR, Solano CJF, Kleinekathöfer U. Simulations of outer membrane channels and their permeability. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:1760-71. [PMID: 26721326 DOI: 10.1016/j.bbamem.2015.12.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/15/2015] [Accepted: 12/17/2015] [Indexed: 12/25/2022]
Abstract
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. Most antibiotics have to pass through these membrane channels to either reach cytoplasmic bound targets or to further cross the hydrophobic inner membrane. Considering the pharmaceutical significance of antibiotics, understanding the functional role and mechanism of these channels is of fundamental importance in developing strategies to design new drugs with enhanced permeation abilities. Due to the biological complexity of membrane channels and experimental limitations, computer simulations have proven to be a powerful tool to investigate the structure, dynamics and interactions of membrane channels. Considerable progress has been made in computer simulations of membrane channels during the last decade. The goal of this review is to provide an overview of the computational techniques and their roles in modeling the transport across outer membrane channels. A special emphasis is put on all-atom molecular dynamics simulations employed to better understand the transport of molecules. Moreover, recent molecular simulations of ion, substrate and antibiotics translocation through membrane pores are briefly summarized. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- Karunakar R Pothula
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Carlos J F Solano
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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26
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García-Giménez E, Alcaraz A, Aguilella-Arzo M, Aguilella VM. Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations. J Phys Chem B 2015; 119:8475-9. [PMID: 26091047 DOI: 10.1021/acs.jpcb.5b03547] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The preference of large protein ion channels for cations or anions is mainly determined by the electrostatic interactions of mobile ions with charged residues of the protein. Here we discuss the widely spread paradigm that the charges determining the channel selectivity are only those that can be considered solvent-accessible because of their location near the permeation pathways of ions and water molecules. Theoretical predictions for the electric potential and average ion densities inside the pore are presented using several approaches of increasing resolution: from analytical and numerical solutions of electrostatic equations in a model channel up to all-atom molecular dynamics simulations and continuum electrostatic calculations performed in a particular biological channel, the bacterial porin OmpF. The results highlight the role of protein dieletric properties and the importance of the initial choice of the residue ionization states in the understanding of the molecular basis of large channel selectivity irrespective of the level of resolution of the computational approach used.
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Affiliation(s)
- Elena García-Giménez
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Antonio Alcaraz
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Marcel Aguilella-Arzo
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
| | - Vicente M Aguilella
- Department of Physics. Laboratory of Molecular Biophysics, Universitat Jaume I, 12080 Castellón, Spain
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27
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Hydrogen peroxide and hypochlorous acid influx through the major S. Typhimurium porin OmpD is affected by substitution of key residues of the channel. Arch Biochem Biophys 2015; 568:38-45. [DOI: 10.1016/j.abb.2015.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 11/23/2022]
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Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc 2014; 135:16561-8. [PMID: 24106986 DOI: 10.1021/ja407783a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, favorable anion locations in the OmpF pore were mapped by anomalous X-ray scattering of Br(–) ions from four different crystal structures and compared with Mg(2+) sites and Rb(+) sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.
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Affiliation(s)
- Balasundaresan Dhakshnamoorthy
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Brigitte K Ziervogel
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Lydia Blachowicz
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago Chicago, IL 60637, USA
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29
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YgaE regulates out membrane proteins in Salmonella enterica serovar Typhi under hyperosmotic stress. ScientificWorldJournal 2014; 2014:374276. [PMID: 24592164 PMCID: PMC3921978 DOI: 10.1155/2014/374276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 10/30/2013] [Indexed: 11/27/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is a human-specific pathogen that causes typhoid fever. In this study, we constructed ΔygaE mutant and a microarray was performed to investigate the role of ygaE in regulation of gene expression changes in response to hyperosmotic stress in S. Typhi. qRT-PCR was performed to validate the microarray results. Our data indicated that ygaE was the repressor of gab operon in S. Typhi as in Escherichia coli (E. coli), though the sequence of ygaE is totally different from gabC (formerly ygaE) in E. coli. OmpF, OmpC, and OmpA are the most abundant out membrane proteins in S. Typhi. Here we report that YgaE is a repressor of both OmpF and OmpC at the early stage of hyperosmotic stress. Two-dimensional electrophoresis was applied to analyze proteomics of total proteins in wild-type strain and ΔygaE strain and we found that YgaE represses the expression of OmpA at the late stage of hyperosmotic stress. Altogether, our results implied that YgaE regulates out membrane proteins in a time-dependent manner under hyperosmotic stress in S. Typhi.
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30
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Aguilella VM, Verdiá-Báguena C, Alcaraz A. Lipid charge regulation of non-specific biological ion channels. Phys Chem Chem Phys 2014; 16:3881-93. [DOI: 10.1039/c3cp54690j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lipid charge regulation effects in different protein–lipid conformations highlight the role of electrostatic interactions in conductance and selectivity of non-specific biological ion channels.
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Affiliation(s)
| | | | - Antonio Alcaraz
- Dept. Physics
- Lab. Molecular Biophysics
- Universitat Jaume I
- 12080 Castellón, Spain
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31
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Queralt-Martín M, Verdiá-Báguena C, Aguilella VM, Alcaraz A. Electrostatic interactions drive the nonsteric directional block of OmpF channel by La3+. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:15320-15327. [PMID: 24256306 DOI: 10.1021/la402700m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Ion channels regulate the transport of molecules and the electric signal transduction in living cells by means of complex and even highly sophisticated mechanisms. We focus here on the crucial role that polyvalent ions, well-known modulators of many biological nanosystems, play in ion channel function. In particular, we show that trace amounts of lanthanum are able to block the bacterial porin OmpF, a large biological pore of Escherichia coli wide enough to exchange antibiotics and other larger molecules. The underlying mechanism has a strong directional character: it is sensitive to the sign of the applied voltage and to the side of the blocker addition. We explore these channel features by combining planar lipid bilayer electrophysiology at the single channel level, site-directed mutagenesis, and inductively coupled plasma mass spectrometry (ICP-MS). In contrast to other well-described channel blockers, which seem to occlude the narrower part of the pore, we envisage a nonsteric mechanism based on electrostatic interactions.
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Affiliation(s)
- María Queralt-Martín
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I , 12071 Castellón, Spain
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32
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Dreyer J, Strodel P, Ippoliti E, Finnerty J, Eisenberg B, Carloni P. Ion permeation in the NanC porin from Escherichia coli: free energy calculations along pathways identified by coarse-grain simulations. J Phys Chem B 2013; 117:13534-42. [PMID: 24147565 DOI: 10.1021/jp4081838] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using the X-ray structure of a recently discovered bacterial protein, the N-acetylneuraminic acid-inducible channel (NanC), we investigate computationally K(+) and Cl(-) ions' permeation. We identify ion permeation pathways that are likely to be populated using coarse-grain Monte Carlo simulations. Next, we use these pathways as reaction coordinates for umbrella sampling-based free energy simulations. We find distinct tubelike pathways connecting specific binding sites for K(+) and, more pronounced, for Cl(-) ions. Both ions permeate the porin preserving almost all of their first hydration shell. The calculated free energy barriers are G(#) ≈ 4 kJ/mol and G(#) ≈ 8 kJ/mol for Cl(-) and K(+), respectively. Within the approximations associated with these values, discussed in detail in this work, we suggest that the porin is slightly selective for Cl(-) versus K(+). Our suggestion is consistent with the experimentally observed weak Cl(-) over K(+) selectivity. A rationale for the latter is suggested by a comparison with previous calculations on strongly anion selective porins.
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Affiliation(s)
- Jens Dreyer
- Computational Biophysics, German Research School for Simulation Sciences , D-52425 Jülich, Germany
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33
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Valade E, Davin-Regli A, Bolla JM, Pagès JM. Bacterial Membrane, a Key for Controlling Drug Influx and Efflux. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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34
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Masi M, Pagès JM. Structure, Function and Regulation of Outer Membrane Proteins Involved in Drug Transport in Enterobactericeae: the OmpF/C - TolC Case. Open Microbiol J 2013; 7:22-33. [PMID: 23569467 PMCID: PMC3617542 DOI: 10.2174/1874285801307010022] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 11/26/2022] Open
Abstract
Antibiotic translocation across membranes of Gram-negative bacteria is a key step for the activity on their specific intracellular targets. Resistant bacteria control their membrane permeability as a first line of defense to protect themselves against external toxic compounds such as antibiotics and biocides. On one hand, resistance to small hydrophilic antibiotics such as ß-lactams and fluoroquinolones frequently results from the « closing » of their way in: the general outer membrane porins. On the other hand, an effective way out for a wide range of antibiotics is provided by TolC-like proteins, which are outer membrane components of multidrug efflux pumps. Accordingly, altered membrane permeability, including porin modifications and/or efflux pumps’ overexpression, is always associated to multidrug resistance (MDR) in a number of clinical isolates. Several recent studies have highlighted our current understanding of porins/TolC structures and functions in Enterobacteriaceae. Here, we review the transport of antibiotics through the OmpF/C general porins and the TolC-like channels with regards to recent data on their structure, function, assembly, regulation and contribution to bacterial resistance. Because MDR strains have evolved global strategies to identify and fight our antibiotic arsenal, it is important to constantly update our global knowledge on antibiotic transport.
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Affiliation(s)
- Muriel Masi
- CNRS-UMR 8619, Institut de Biophysique et de Biochimie Moléculaire et Cellulaire (IBBMC), Université Paris Sud, Orsay, France
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35
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Parra E, Alcaraz A, Cruz A, Aguilella VM, Pérez-Gil J. Hydrophobic pulmonary surfactant proteins SP-B and SP-C induce pore formation in planar lipid membranes: evidence for proteolipid pores. Biophys J 2013; 104:146-55. [PMID: 23332067 DOI: 10.1016/j.bpj.2012.11.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/14/2012] [Accepted: 11/12/2012] [Indexed: 11/24/2022] Open
Abstract
Pulmonary surfactant is a complex mixture of lipids and specific surfactant proteins, including the hydrophobic proteins SP-B and SP-C, in charge of stabilizing the respiratory surface of mammalian lungs. The combined action of both proteins is responsible for the proper structure and dynamics of membrane arrays in the pulmonary surfactant network that covers the respiratory surface. In this study, we explore the possibility that proteins SP-B and SP-C induce the permeabilization of phospholipid membranes via pore formation. To this end, electrophysiological measurements have been carried out in planar lipid membranes prepared with different lipid/protein mixtures. Our main result is that channel-like structures are detected in the presence of SP-B, SP-C, or the native mixture of both proteins. Current traces show a high variety of conductance states (from pS to nS) that are dependent both on the lipid composition and the applied potential. We also show that the type of host lipid crucially determines the ionic selectivity of the observed pores: the anionic selectivity observed in zwitterionic membranes is inverted to cationic selectivity in the presence of negatively charged lipids. All those results suggest that SP-B and SP-C proteins promote the formation of proteolipid channels in which lipid molecules are functionally involved. We propose that proteolipidic membrane-permeabilizing structures may have an important role to tune ionic and lipidic flows through the pulmonary surfactant membrane network at the alveolar surfaces.
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Affiliation(s)
- Elisa Parra
- Department of Biochemistry and Molecular Biology, Faculty of Biology, Complutense University, Madrid, Spain
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36
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Bartsch P, Harsman A, Wagner R. Single channel analysis of membrane proteins in artificial bilayer membranes. Methods Mol Biol 2013; 1033:345-61. [PMID: 23996188 DOI: 10.1007/978-1-62703-487-6_22] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The planar lipid bilayer technique is a powerful experimental approach for electrical single channel recordings of pore-forming membrane proteins in a chemically well-defined and easily modifiable environment. Here we provide a general survey of the basic materials and procedures required to set up a robust bilayer system and perform electrophysiological single channel recordings of reconstituted proteins suitable for the in-depth characterization of their functional properties.
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Affiliation(s)
- Philipp Bartsch
- Biophysics, Department of Biology/Chemistry, University of Osnabrueck, Osnabrueck, Germany
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37
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Maffeo C, Bhattacharya S, Yoo J, Wells D, Aksimentiev A. Modeling and simulation of ion channels. Chem Rev 2012; 112:6250-84. [PMID: 23035940 PMCID: PMC3633640 DOI: 10.1021/cr3002609] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Christopher Maffeo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Swati Bhattacharya
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Jejoong Yoo
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - David Wells
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois, 1110 W. Green St., Urbana, IL
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38
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Alcaraz A, Queralt-Martín M, García-Giménez E, Aguilella VM. Increased salt concentration promotes competitive block of OmpF channel by protons. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2777-82. [DOI: 10.1016/j.bbamem.2012.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 07/02/2012] [Accepted: 07/03/2012] [Indexed: 10/28/2022]
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39
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Divalent Metal Ion Transport across Large Biological Ion Channels and Their Effect on Conductance and Selectivity. Biochem Res Int 2012; 2012:245786. [PMID: 23008773 PMCID: PMC3449104 DOI: 10.1155/2012/245786] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Revised: 07/27/2012] [Accepted: 07/30/2012] [Indexed: 11/17/2022] Open
Abstract
Electrophysiological characterization of large protein channels, usually displaying multi-ionic transport and weak ion selectivity, is commonly performed at physiological conditions (moderate gradients of KCl solutions at decimolar concentrations buffered at neutral pH). We extend here the characterization of the OmpF porin, a wide channel of the outer membrane of E. coli, by studying the effect of salts of divalent cations on the transport properties of the channel. The regulation of divalent cations concentration is essential in cell metabolism and understanding their effects is of key importance, not only in the channels specifically designed to control their passage but also in other multiionic channels. In particular, in porin channels like OmpF, divalent cations modulate the efficiency of molecules having antimicrobial activity. Taking advantage of the fact that the OmpF channel atomic structure has been resolved both in water and in MgCl2 aqueous solutions, we analyze the single channel conductance and the channel selectivity inversion aiming to separate the role of the electrolyte itself, and the counterion accumulation induced by the protein channel charges and other factors (binding, steric effects, etc.) that being of minor importance in salts of monovalent cations become crucial in the case of divalent cations.
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40
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Verdiá-Báguena C, Nieto-Torres JL, Alcaraz A, DeDiego ML, Torres J, Aguilella VM, Enjuanes L. Coronavirus E protein forms ion channels with functionally and structurally-involved membrane lipids. Virology 2012; 432:485-94. [PMID: 22832120 PMCID: PMC3438407 DOI: 10.1016/j.virol.2012.07.005] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/06/2012] [Accepted: 07/06/2012] [Indexed: 12/28/2022]
Abstract
Coronavirus (CoV) envelope (E) protein ion channel activity was determined in channels formed in planar lipid bilayers by peptides representing either the transmembrane domain of severe acute respiratory syndrome CoV (SARS-CoV) E protein, or the full-length E protein. Both of them formed a voltage independent ion conductive pore with symmetric ion transport properties. Mutations N15A and V25F located in the transmembrane domain prevented the ion conductivity. E protein derived channels showed no cation preference in non-charged lipid membranes, whereas they behaved as pores with mild cation selectivity in negatively-charged lipid membranes. The ion conductance was also controlled by the lipid composition of the membrane. Lipid charge also regulated the selectivity of a HCoV-229E E protein derived peptide. These results suggested that the lipids are functionally involved in E protein ion channel activity, forming a protein-lipid pore, a novel concept for CoV E protein ion channel entity.
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Affiliation(s)
- Carmina Verdiá-Báguena
- Department of Physics, Laboratory of Molecular Biophysics, Universitat Jaume I, 12071 Castellón, Spain
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41
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Rostovtseva TK, Bezrukov SM. VDAC inhibition by tubulin and its physiological implications. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1818:1526-35. [PMID: 22100746 PMCID: PMC3302949 DOI: 10.1016/j.bbamem.2011.11.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/24/2011] [Accepted: 11/02/2011] [Indexed: 11/23/2022]
Abstract
Regulation of mitochondrial outer membrane (MOM) permeability has dual importance: in normal metabolite and energy exchange between mitochondria and cytoplasm, and thus in control of respiration, and in apoptosis by release of apoptogenic factors into the cytosol. However, the mechanism of this regulation involving the voltage-dependent anion channel (VDAC), the major channel of MOM, remains controversial. For example, one of the long-standing puzzles was that in permeabilized cells, adenine nucleotide translocase is less accessible to cytosolic ADP than in isolated mitochondria. Still another puzzle was that, according to channel-reconstitution experiments, voltage regulation of VDAC is limited to potentials exceeding 30mV, which are believed to be much too high for MOM. We have solved these puzzles and uncovered multiple new functional links by identifying a missing player in the regulation of VDAC and, hence, MOM permeability - the cytoskeletal protein tubulin. We have shown that, depending on VDAC phosphorylation state and applied voltage, nanomolar to micromolar concentrations of dimeric tubulin induce functionally important reversible blockage of VDAC reconstituted into planar phospholipid membranes. The voltage sensitivity of the blockage equilibrium is truly remarkable. It is described by an effective "gating charge" of more than ten elementary charges, thus making the blockage reaction as responsive to the applied voltage as the most voltage-sensitive channels of electrophysiology are. Analysis of the tubulin-blocked state demonstrated that although this state is still able to conduct small ions, it is impermeable to ATP and other multi-charged anions because of the reduced aperture and inversed selectivity. The findings, obtained in a channel reconstitution assay, were supported by experiments with isolated mitochondria and human hepatoma cells. Taken together, these results suggest a previously unknown mechanism of regulation of mitochondrial energetics, governed by VDAC interaction with tubulin at the mitochondria-cytosol interface. Immediate physiological implications include new insights into serine/threonine kinase signaling pathways, Ca(2+) homeostasis, and cytoskeleton/microtubule activity in health and disease, especially in the case of the highly dynamic microtubule network which is characteristic of cancerogenesis and cell proliferation. In the present review, we speculate how these findings may help to identify new mechanisms of mitochondria-associated action of chemotherapeutic microtubule-targeting drugs, and also to understand why and how cancer cells preferentially use inefficient glycolysis rather than oxidative phosphorylation (Warburg effect). This article is part of a Special Issue entitled: VDAC structure, function, and regulation of mitochondrial metabolism.
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Affiliation(s)
- Tatiana K Rostovtseva
- Laboratory of Physical and Structural Biology, Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Health, Bethesda, MD 20892, USA.
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42
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Parsons SP, Kunze WA, Huizinga JD. Maxi-channels recorded in situ from ICC and pericytes associated with the mouse myenteric plexus. Am J Physiol Cell Physiol 2011; 302:C1055-69. [PMID: 22159087 DOI: 10.1152/ajpcell.00334.2011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Ion channels are fundamental to gastrointestinal pacemaking by interstitial cells of Cajal (ICC). Previously, we have recorded a high-conductance chloride channel (HCCC) from ICC, both in culture and in situ, associated with the myenteric plexus. The biophysical properties of the HCCC (conductance, subconductances, voltage- and time-dependent inactivation) suggest it is a member of a class called the maxi-anion channels. In this study we further investigated the properties of the HCCC in situ. Our main finding was that the HCCC is not strictly a chloride channel but has a relative sodium-chloride permeability (P(Na/Cl)) of 0.76 to 1.64 (depending on the method of measurement). Therefore, we have renamed the HCCC the "maxi-channel." A maxi-channel was also expressed by pericytes associated with the vasculature near the myenteric plexus. This had a lower P(Na/Cl) (0.33 to 0.49, depending on the method of measurement) but similar conductance (326 ± 7 vs. 316 ± 24 pS for ICC). This is the first report of cation permeability equaling anion permeability in a maxi-anion channel. As such, the properties of the maxi-channels described in this article may have implications for the maxi-anion channel field, as well as for studies of their role in ICC and pericytes.
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Affiliation(s)
- Sean P Parsons
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
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43
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Gurnev PA, Rostovtseva TK, Bezrukov SM. Tubulin-blocked state of VDAC studied by polymer and ATP partitioning. FEBS Lett 2011; 585:2363-6. [PMID: 21722638 DOI: 10.1016/j.febslet.2011.06.008] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 11/26/2022]
Abstract
Recently reported functional interaction between voltage-dependent anion channel of the outer mitochondrial membrane, VDAC, and dimeric tubulin is observed as a reversible channel blockage. Using partitioning of poly-(ethylene glycol)s of different molecular weights and reversal potential measurements, we probe the size and ion selectivity of the fully open and tubulin-blocked states of VDAC reconstituted into planar lipid bilayers. While the effective radius of the channel decreases by only a factor of 1.34±0.15, the selectivity reverses from initially anionic to cationic. Directly measuring ATP partitioning we demonstrate that these changes prohibit ATP from entering the channel in its tubulin-blocked state.
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Affiliation(s)
- Philip A Gurnev
- Program in Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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44
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Queralt-Martín M, García-Giménez E, Mafé S, Alcaraz A. Divalent cations reduce the pH sensitivity of OmpF channel inducing the pKashift of key acidic residues. Phys Chem Chem Phys 2011; 13:563-9. [DOI: 10.1039/c0cp01325k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Faraudo J, Calero C, Aguilella-Arzo M. Ionic partition and transport in multi-ionic channels: a molecular dynamics simulation study of the OmpF bacterial porin. Biophys J 2010; 99:2107-15. [PMID: 20923644 PMCID: PMC3042589 DOI: 10.1016/j.bpj.2010.07.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/29/2010] [Accepted: 07/30/2010] [Indexed: 11/15/2022] Open
Abstract
We performed all-atom molecular dynamics simulations studying the partition of ions and the ionic current through the bacterial porin OmpF and two selected mutants. The study is motivated by new, interesting experimental findings concerning their selectivity and conductance behavior at neutral pH. The mutations considered here are designed to study the effect of removal of negative charges present in the constriction zone of the wild-type OmpF channel (which contains, on one side, a cluster with three positive residues, and on the other side, two negatively charged residues). Our results show that these mutations induce an exclusion of cations from the constriction zone of the channel, substantially reducing the flow of cations. In fact, the partition of ions inside the mutant channels is strongly inhomogeneous, with regions containing an excess of cations and regions containing an excess of anions. Interestingly, the overall number of cations inside the channel is larger than the number of anions, this excess being different for each protein channel. We found that the differences in ionic charge inside these channels are justified by the differences in electric charge between the wild-type OmpF and the mutants, following an electroneutral balance.
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Affiliation(s)
- Jordi Faraudo
- Institut de Ciència de Materials de Barcelona, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Carles Calero
- Institut de Ciència de Materials de Barcelona, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
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