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Liu T, He X, Zhao J, Shi L, Zhou T, Wen L. Ion transport properties in the pH-dependent bipolar nanochannels. Electrophoresis 2023; 44:1847-1858. [PMID: 37401641 DOI: 10.1002/elps.202300073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/05/2023] [Accepted: 06/20/2023] [Indexed: 07/05/2023]
Abstract
In recent years, researchers have made significant strides in understanding the ion transport characteristics of nanochannels, resulting in the development of various materials, modifications, and shapes of nano ion channel membranes. The aim is to create a nanochannel membrane with optimal ion transport properties and high stability by adjusting factors, such as channel size, surface charge, and wettability. However, during the nanochannel film fabrication process, controlling the geometric structures of nanochannels can be challenging. Therefore, exploring the stability of nanochannel performance under different geometric structures has become an essential aspect of nanochannel design. This article focuses on the study of cylindrical nanochannel structures, which are categorized based on the different methods for generating bipolar surface charges on the channel's inner surface, either through pH gradient effects or different material types. Through these two approaches, the study designed and analyzed the stability of ion transport characteristics in two nanochannel models under varying geometric structures. Our findings indicate that nanochannels with bipolar properties generated through pH gradients demonstrate more stable ion selection, whereas nanochannels with bipolar properties generated through different materials show stronger stability in ion rectification. This conclusion provides a theoretical foundation for future nanochannel designs.
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Affiliation(s)
- Tao Liu
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Xiaohan He
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Juncheng Zhao
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Liuyong Shi
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Teng Zhou
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
| | - Liping Wen
- Mechanical and Electrical Engineering College, Hainan University, Haikou, Hainan, P. R. China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, P. R. China
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2
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Mayse LA, Movileanu L. Gating of β-Barrel Protein Pores, Porins, and Channels: An Old Problem with New Facets. Int J Mol Sci 2023; 24:12095. [PMID: 37569469 PMCID: PMC10418385 DOI: 10.3390/ijms241512095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
β barrels are ubiquitous proteins in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These transmembrane proteins (TMPs) execute a wide variety of tasks. For example, they can serve as transporters, receptors, membrane-bound enzymes, as well as adhesion, structural, and signaling elements. In addition, multimeric β barrels are common structural scaffolds among many pore-forming toxins. Significant progress has been made in understanding the functional, structural, biochemical, and biophysical features of these robust and versatile proteins. One frequently encountered fundamental trait of all β barrels is their voltage-dependent gating. This process consists of reversible or permanent conformational transitions between a large-conductance, highly permeable open state and a low-conductance, solute-restrictive closed state. Several intrinsic molecular mechanisms and environmental factors modulate this universal property of β barrels. This review article outlines the typical signatures of voltage-dependent gating. Moreover, we discuss recent developments leading to a better qualitative understanding of the closure dynamics of these TMPs.
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Affiliation(s)
- Lauren A. Mayse
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244, USA;
- Department of Biomedical and Chemical Engineering, Syracuse University, 223 Link Hall, Syracuse, NY 13244, USA
- The BioInspired Institute, Syracuse University, Syracuse, NY 13244, USA
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3
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Acharya A, Ghai I, Piselli C, Prajapati JD, Benz R, Winterhalter M, Kleinekathöfer U. Conformational Dynamics of Loop L3 in OmpF: Implications toward Antibiotic Translocation and Voltage Gating. J Chem Inf Model 2023; 63:910-927. [PMID: 36525563 DOI: 10.1021/acs.jcim.2c01108] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating through a bacterial channel and uncover the role of conformational dynamics of the constriction loop in this process. Using the temperature accelerated sliced sampling approach, we shed light onto the dynamics of the L3 loop, in particular the F118 to S125 segment, at the constriction regions of the OmpF porin. We complement the findings with single channel electrophysiology experiments and applied-field simulations, and we demonstrate the role of hydrogen-bond stabilization in the conformational dynamics of the L3 loop. A molecular mechanism of permeation is put forward wherein charged antibiotics perturb the network of stabilizing hydrogen-bond interactions and induce conformational changes in the L3 segment, thereby aiding the accommodation and permeation of bulky antibiotic molecules across the constriction region. We complement the findings with single channel electrophysiology experiments and demonstrate the importance of the hydrogen-bond stabilization in the conformational dynamics of the L3 loop. The generality of the present observations and experimental results regarding the L3 dynamics enables us to identify this L3 segment as the source of gating. We propose a mechanism of OmpF gating that is in agreement with previous experimental data that showed the noninfluence of cysteine double mutants that tethered the L3 tip to the barrel wall on the OmpF gating behavior. The presence of similar loop stabilization networks in porins of other clinically relevant pathogens suggests that the conformational dynamics of the constriction loop is possibly of general importance in the context of antibiotic permeation through porins.
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Affiliation(s)
- Abhishek Acharya
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
| | - Ishan Ghai
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Claudio Piselli
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | | | - Roland Benz
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Mathias Winterhalter
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Bremen 28759, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Bremen 28759, Germany
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4
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Ngo VA, Queralt-Martín M, Khan F, Bergdoll L, Abramson J, Bezrukov SM, Rostovtseva TK, Hoogerheide DP, Noskov SY. The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating. J Am Chem Soc 2022; 144:14564-14577. [PMID: 35925797 DOI: 10.1021/jacs.2c03316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The voltage-dependent anion channel (VDAC) is a β-barrel channel of the mitochondrial outer membrane (MOM) that passively transports ions, metabolites, polypeptides, and single-stranded DNA. VDAC responds to a transmembrane potential by "gating," i.e. transitioning to one of a variety of low-conducting states of unknown structure. The gated state results in nearly complete suppression of multivalent mitochondrial metabolite (such as ATP and ADP) transport, while enhancing calcium transport. Voltage gating is a universal property of β-barrel channels, but VDAC gating is anomalously sensitive to transmembrane potential. Here, we show that a single residue in the pore interior, K12, is responsible for most of VDAC's voltage sensitivity. Using the analysis of over 40 μs of atomistic molecular dynamics (MD) simulations, we explore correlations between motions of charged residues inside the VDAC pore and geometric deformations of the β-barrel. Residue K12 is bistable; its motions between two widely separated positions along the pore axis enhance the fluctuations of the β-barrel and augment the likelihood of gating. Single channel electrophysiology of various K12 mutants reveals a dramatic reduction of the voltage-induced gating transitions. The crystal structure of the K12E mutant at a resolution of 2.6 Å indicates a similar architecture of the K12E mutant to the wild type; however, 60 μs of atomistic MD simulations using the K12E mutant show restricted motion of residue 12, due to enhanced connectivity with neighboring residues, and diminished amplitude of barrel motions. We conclude that β-barrel fluctuations, governed particularly by residue K12, drive VDAC gating transitions.
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Affiliation(s)
- Van A Ngo
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada.,Advanced Computing for Life Sciences and Engineering, Computing and Computational Sciences, National Center for Computational Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
| | - María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States.,Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain
| | - Farha Khan
- Department of Physiology, University of California, Los Angeles, California 90095, United States
| | - Lucie Bergdoll
- LISM UMR 7255, CNRS and Aix-Marseille University, Marseille cedex 20, 13402, France
| | - Jeff Abramson
- Department of Physiology, University of California, Los Angeles, California 90095, United States
| | - Sergey M Bezrukov
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Tatiana K Rostovtseva
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David P Hoogerheide
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sergei Yu Noskov
- Center for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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5
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Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Proc Natl Acad Sci U S A 2022; 119:2117009119. [PMID: 35193963 PMCID: PMC8872756 DOI: 10.1073/pnas.2117009119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2022] [Indexed: 12/26/2022] Open
Abstract
Antibiotic resistance in Gram-negative pathogens has been identified as an urgent threat to human health by the World Health Organization. The major challenge with treating infections by these pathogens is developing antibiotics that can traverse the dense bacterial outer membrane (OM) formed by a mesh of lipopolysaccharides. Effective antibiotics permeate through OM porins, which have evolved for nutrient diffusion; however, the conformational states of these porins regulating permeation are still unclear. Here, we used molecular dynamics simulations, free energy calculations, Markov-state modeling, and whole-cell accumulation assays to provide mechanistic insight on how a porin shifts between open and closed states. We provide a mechanism of how Gram-negative bacteria confer resistance to antibiotics. Gram-negative bacteria pose a serious public health concern due to resistance to many antibiotics, caused by the low permeability of their outer membrane (OM). Effective antibiotics use porins in the OM to reach the interior of the cell; thus, understanding permeation properties of OM porins is instrumental to rationally develop broad-spectrum antibiotics. A functionally important feature of OM porins is undergoing open–closed transitions that modulate their transport properties. To characterize the molecular basis of these transitions, we performed an extensive set of molecular dynamics (MD) simulations of Escherichia coli OM porin OmpF. Markov-state analysis revealed that large-scale motion of an internal loop, L3, underlies the transition between energetically stable open and closed states. The conformation of L3 is controlled by H bonds between highly conserved acidic residues on the loop and basic residues on the OmpF β-barrel. Mutation of key residues important for the loop’s conformation shifts the equilibrium between open and closed states and regulates translocation of permeants (ions and antibiotics), as observed in the simulations and validated by our whole-cell accumulation assay. Notably, one mutant system G119D, which we find to favor the closed state, has been reported in clinically resistant bacterial strains. Overall, our accumulated ∼200 µs of simulation data (the wild type and mutants) along with experimental assays suggest the involvement of internal loop dynamics in permeability of OM porins and antibiotic resistance in Gram-negative bacteria.
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6
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Cao L, Liu X, Shinde DB, Chen C, Chen I, Li Z, Zhou Z, Yang Z, Han Y, Lai Z. Oriented Two‐Dimensional Covalent Organic Framework Membranes with High Ion Flux and Smart Gating Nanofluidic Transport. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Li Cao
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Xiaowei Liu
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Digambar B. Shinde
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Cailing Chen
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - I‐Chun Chen
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Zhen Li
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Zongyao Zhou
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry North Dakota State University Fargo ND 58102 USA
| | - Yu Han
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
| | - Zhiping Lai
- Division of Physical Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal 23955-6900 Saudi Arabia
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7
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Cao L, Liu X, Shinde DB, Chen C, Chen IC, Li Z, Zhou Z, Yang Z, Han Y, Lai Z. Oriented Two-Dimensional Covalent Organic Framework Membranes with High Ion Flux and Smart Gating Nanofluidic Transport. Angew Chem Int Ed Engl 2021; 61:e202113141. [PMID: 34816574 DOI: 10.1002/anie.202113141] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/09/2022]
Abstract
Nanofluidic ion transport holds high promise in bio-sensing and energy conversion applications. However, smart nanofluidic devices with high ion flux and modulable ion transport capabilities remain to be realised. Herein, we demonstrate smart nanofluidic devices based on oriented two-dimensional covalent organic framework (2D COF) membranes with vertically aligned nanochannel arrays that achieved a 2-3 orders of magnitude higher ion flux compared with that of conventional single-channel nanofluidic devices. The surface-charge-governed ion conductance is dominant for electrolyte concentration up to 0.01 M. Moreover, owing to the customisable pH-responsivity of imine and phenol hydroxyl groups, the COF-DT membranes attained an actively modulable ion transport with a high pH-gating on/off ratio of ≈100. The customisable structure and rich chemistry of COF materials will offer a promising platform for manufacturing nanofluidic devices with modifiable ion/molecular transport features.
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Affiliation(s)
- Li Cao
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Xiaowei Liu
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Digambar B Shinde
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Cailing Chen
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - I-Chun Chen
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhen Li
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zongyao Zhou
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
| | - Yu Han
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhiping Lai
- Division of Physical Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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8
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Perini DA, Alcaraz A, Queralt-Martín M. Lipid Headgroup Charge and Acyl Chain Composition Modulate Closure of Bacterial β-Barrel Channels. Int J Mol Sci 2019; 20:ijms20030674. [PMID: 30764475 PMCID: PMC6386941 DOI: 10.3390/ijms20030674] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/14/2022] Open
Abstract
The outer membrane of Gram-negative bacteria contains β-barrel proteins that form high-conducting ion channels providing a path for hydrophilic molecules, including antibiotics. Traditionally, these proteins have been considered to exist only in an open state so that regulation of outer membrane permeability was accomplished via protein expression. However, electrophysiological recordings show that β-barrel channels respond to transmembrane voltages by characteristically switching from a high-conducting, open state, to a so-called 'closed' state, with reduced permeability and possibly exclusion of large metabolites. Here, we use the bacterial porin OmpF from E. coli as a model system to gain insight on the control of outer membrane permeability by bacterial porins through the modulation of their open state. Using planar bilayer electrophysiology, we perform an extensive study of the role of membrane lipids in the OmpF channel closure by voltage. We pay attention not only to the effects of charges in the hydrophilic lipid heads but also to the contribution of the hydrophobic tails in the lipid-protein interactions. Our results show that gating kinetics is governed by lipid characteristics so that each stage of a sequential closure is different from the previous one, probably because of intra- or intermonomeric rearrangements.
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Affiliation(s)
- D Aurora Perini
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - Antonio Alcaraz
- Laboratory of Molecular Biophysics, Department of Physics, Universitat Jaume I, 12071 Castellón, Spain.
| | - María Queralt-Martín
- Section on Molecular Transport, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Mimicking the cell membrane: bio-inspired simultaneous functions with monovalent anion selectivity and antifouling properties of anion exchange membrane. Sci Rep 2016; 6:37285. [PMID: 27853255 PMCID: PMC5112527 DOI: 10.1038/srep37285] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/26/2016] [Indexed: 01/01/2023] Open
Abstract
A new bio-inspired method was applied in this study to simultaneously improve the monovalent anion selectivity and antifouling properties of anion exchange membranes (AEMs). Three-layer architecture was developed by deposition of polydopamine (PDA) and electro-deposition of N-O-sulfonic acid benzyl chitosan (NSBC). The innermost and outermost layers were PDA with different deposition time. The middle layer was prepared by NSBC. Fourier transform infrared spectroscopy and scanning electron microscopy confirmed that PDA and NSBC were successfully modified on the surfaces of AEMs. The contact angle of the membranes indicated an improved hydrophilicity of the modified membranes. A series of electrodialysis experiments in which Cl−/SO42− separation was studied, demonstrating the monovalent anion selectivity of the samples. The Cl−/SO42− permselectivity of the modified membranes can reach up to 2.20, higher than that of the commercial membrane (only 0.78) during 90 minutes in electrodialysis (ED). The increase value of the resistance of the membranes was also measured to evaluate the antifouling properties. Sodium dodecyl benzene sulfonate (SDBS) was used as the fouling material in the ED process and the membrane area resistance of modified membrane increase value of was only 0.08 Ωcm2 30 minutes later.
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10
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Zhang Z, Kong XY, Xiao K, Xie G, Liu Q, Tian Y, Zhang H, Ma J, Wen L, Jiang L. A Bioinspired Multifunctional Heterogeneous Membrane with Ultrahigh Ionic Rectification and Highly Efficient Selective Ionic Gating. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:144-150. [PMID: 26551055 DOI: 10.1002/adma.201503668] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 08/27/2015] [Indexed: 06/05/2023]
Abstract
A bioinspired multifunctional heterogeneous membrane composed of a block copolymer (PS-b-P4VP) membrane and a porous anodic alumina membrane is fabricated. The ionic rectification is so strong that the maximum ratio is ≈489, and the chemical actuation of the anion or cation gate from the "OFF" to the "ON" state promotes a 98.5% increase in the channel conductance.
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Affiliation(s)
- Zhen Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Xiang-Yu Kong
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Kai Xiao
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Ganhua Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Qian Liu
- Beijing Key Laboratory of Energy Conversion and Storage Materials, College of Chemistry, Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ye Tian
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Huacheng Zhang
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Jie Ma
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Liping Wen
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Lei Jiang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
- Laboratory of Bioinspired Smart Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
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11
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Abstract
Bacteria secrete and harbor in their membranes a number of pore-forming proteins. Some of these are bona fide ion channels that may respond to changes in membrane tension, voltage, or pH. Others may be large translocons used for the secretion of folded or unfolded polypeptide substrates. Additionally, many secreted toxins insert into target cell membranes and form pores that either collapse membrane electrochemical gradients or provide conduits for the delivery of virulence factors. In all cases, electrophysiological approaches have yielded much progress in past decades in understanding the functional mechanisms of these pores. By monitoring the changes in current due to ion flow through the pores, these techniques are used as high-resolution tools to gather detailed information on the kinetic and permeation properties of these proteins, including those whose physiological role is not ion flux. This review highlights some of the electrophysiological studies that have advanced the field of transport by pore-forming proteins of bacterial origin.
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Affiliation(s)
- Anne H Delcour
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001;
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12
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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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13
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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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14
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Cheneke BR, Indic M, van den Berg B, Movileanu L. An outer membrane protein undergoes enthalpy- and entropy-driven transitions. Biochemistry 2012; 51:5348-58. [PMID: 22680931 DOI: 10.1021/bi300332z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
β-Barrel membrane proteins often fluctuate among various open substates, yet the nature of these transitions is not fully understood. Using temperature-dependent, single-molecule electrophysiology analysis, along with rational protein design, we show that OccK1, a member of the outer membrane carboxylate channel from Pseudomonas aeruginosa, features a discrete gating dynamics comprising both enthalpy-driven and entropy-driven current transitions. OccK1 was chosen for the analysis of these transitions, because it is a monomeric transmembrane β-barrel of a known high-resolution crystal structure and displays three distinguishable, time-resolvable open substates. Native and loop-deletion OccK1 proteins showed substantial changes in the activation enthalpies and entropies of the channel transitions, but modest alterations in the equilibrium free energies, confirming that the system never departs from equilibrium. Moreover, some current fluctuations of OccK1 indicated a counterintuitive, negative activation enthalpy, which was compensated by a significant decrease in the activation entropy. Temperature scanning of the single-channel properties of OccK1 exhibited a thermally induced switch of the energetically most favorable open substate at the lowest examined temperature of 4 °C. Therefore, such a semiquantitative assessment of the current fluctuation dynamics not only demonstrates the complexity of channel gating but also reveals distinct functional traits of a β-barrel outer membrane protein under different temperature circumstances.
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Affiliation(s)
- Belete R Cheneke
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, NY 13244-1130, USA
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Cheneke BR, van den Berg B, Movileanu L. Analysis of gating transitions among the three major open states of the OpdK channel. Biochemistry 2011; 50:4987-97. [PMID: 21548584 PMCID: PMC3107985 DOI: 10.1021/bi200454j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
OpdK is an outer membrane protein of the pathogenic bacterium Pseudomonas aeruginosa. The recent crystal structure of this protein revealed a monomeric, 18-stranded β-barrel with a kidney-shaped pore, whose constriction features a diameter of 8 Å. Using systematic single-channel electrical recordings of this protein pore reconstituted into planar lipid bilayers under a broad range of ion concentrations, we were able to probe its discrete gating kinetics involving three major and functionally distinct conformations, in which a dominant open substate O(2) is accompanied by less thermodynamically stable substates O(1) and O(3). Single-channel electrical data enabled us to determine the alterations in the energetics and kinetics of the OpdK protein when experimental conditions were changed. In the future, such a semiquantitative analysis might provide a better understanding on the dynamics of current fluctuations of other β-barrel membrane protein channels.
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Affiliation(s)
- Belete R. Cheneke
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
| | - Bert van den Berg
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Syracuse Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, New York 13244, USA
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