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Anosov A, Koplak O, Smirnova E, Borisova E, Korepanova E, Derunets A. Effect of Cobalt Ferrite Nanoparticles in a Hydrophilic Shell on the Conductance of Bilayer Lipid Membrane. MEMBRANES 2022; 12:1106. [PMID: 36363661 PMCID: PMC9692745 DOI: 10.3390/membranes12111106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
We measured the conductance of bilayer lipid membranes of diphytanoylphosphatidylcholine induced by interaction with cubic magnetic nanoparticles (MNPs) of cobalt ferrite 12 and 27 nm in size and coated with a hydrophilic shell. The MNP coating is human serum albumin (HSA) or polyethylene glycol (PEG). The interaction of nanoparticles added to the bulk solution with the lipid bilayer causes the formation of metastable conductive pores, which, in turn, increases the integral conductance of the membranes. The increase in conductance with increasing MNP concentration was practically independent of the particle size. The dependence of the bilayer conductance on the concentration of PEG-coated MNPs was much weaker than that on the concentration with a shell of HSA. Analyzing the current traces, we believe that the conductive pores formed as a result of the interaction of nanoparticles with the membrane can change their size, remaining metastable. The form of multilevel current traces allows us to assume that there are several metastable pore states close in energy. The average radius of the putative cylindrical pores is in the range of 0.4-1.3 nm.
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Affiliation(s)
- Andrey Anosov
- The Department of Medical and Biological Physics, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
- Kotelnikov Institute of Radioengineering and Electronics of RAS, 125009 Moscow, Russia
| | - Oksana Koplak
- The Department of Medical and Biological Physics, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
- Federal Research Center of Problem of Chemical Physics and Medicinal Chemistry RAS, 142432 Chernogolovka, Russia
| | - Elena Smirnova
- The Department of Medical and Biological Physics, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Elizaveta Borisova
- The Department of Medical and Biological Physics, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Eugenia Korepanova
- The Department of General and Medical Biophysics, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Alice Derunets
- National Research Center Kurchatov Institute, Kurchatov Genomic Center, Academician Kurchatov Square 1, 123098 Moscow, Russia
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2
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Adrien V, Rayan G, Astafyeva K, Broutin I, Picard M, Fuchs P, Urbach W, Taulier N. How to best estimate the viscosity of lipid bilayers. Biophys Chem 2021; 281:106732. [PMID: 34844029 DOI: 10.1016/j.bpc.2021.106732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/19/2021] [Indexed: 11/02/2022]
Abstract
The viscosity of lipid bilayers is a property relevant to biological function, as it affects the diffusion of membrane macromolecules. To determine its value, and hence portray the membrane, various literature-reported techniques lead to significantly different results. Herein we compare the results issuing from two widely used techniques to determine the viscosity of membranes: the Fluorescence Lifetime Imaging Microscopy (FLIM), and Fluorescence Recovery After Photobleaching (FRAP). FLIM relates the time of rotation of a molecular rotor inserted into the membrane to the macroscopic viscosity of a fluid. Whereas FRAP measures molecular diffusion coefficients. This approach is based on a hydrodynamic model connecting the mobility of a membrane inclusion to the viscosity of the membrane. We show that: This article emphasizes the pitfalls to be avoided and the rules to be observed in order to obtain a value of the bilayer viscosity that characterizes the bilayer instead of interactions between the bilayer and the embedded probe.
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Affiliation(s)
- Vladimir Adrien
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France; Sorbonne Université, AP-HP Department of Psychiatry, Hôpital Saint-Antoine, Paris, France
| | - Gamal Rayan
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France.
| | - Ksenia Astafyeva
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - Isabelle Broutin
- Université de Paris, CNRS, Laboratoire CiTCoM, 75006 Paris, France
| | - Martin Picard
- Université de Paris, Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS UMR 7099, F-75005 Paris, France; Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le développement de la recherche Scientifique, F-75005 Paris, France
| | - Patrick Fuchs
- Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France; Université de Paris, UFR Sciences du Vivant, 75013 Paris, France
| | - Wladimir Urbach
- Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France; Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
| | - Nicolas Taulier
- Sorbonne Université, CNRS, INSERM, Laboratoire d'Imagerie Biomédicale, LIB, F-75006 Paris, France
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Liu W, Nestorovich EM. Anthrax toxin channel: What we know based on over 30 years of research. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183715. [PMID: 34332985 DOI: 10.1016/j.bbamem.2021.183715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 07/21/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
Protective antigen channel is the central component of the deadly anthrax exotoxin responsible for binding and delivery of the toxin's enzymatic lethal and edema factor components into the cytosol. The channel, which is more than three times longer than the lipid bilayer membrane thickness and has a 6-Å limiting diameter, is believed to provide a sophisticated unfoldase and translocase machinery for the foreign protein transport into the host cell cytosol. The tripartite toxin can be reengineered, one component at a time or collectively, to adapt it for the targeted cancer therapeutic treatments. In this review, we focus on the biophysical studies of the protective antigen channel-forming activity, small ion transport properties, enzymatic factor translocation, and blockage comparing it with the related clostridial binary toxin channels. We address issues linked to the anthrax toxin channel structural dynamics and lipid dependence, which are yet to become generally recognized as parts of the toxin translocation machinery.
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Affiliation(s)
- Wenxing Liu
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC 20064, USA
| | - Ekaterina M Nestorovich
- Department of Biology, The Catholic University of America, 620 Michigan Ave, Washington, DC 20064, USA.
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4
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Modelling of an autonomous Nav1.5 channel system as a part of in silico pharmacology study. J Mol Model 2021; 27:182. [PMID: 34031769 DOI: 10.1007/s00894-021-04799-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 05/17/2021] [Indexed: 12/22/2022]
Abstract
A homology model of Nav1.5, based mainly on the crystal structures of Nav1.2/1.5 was built, optimized and successfully inserted into the membrane bilayer. We applied steered and free MD simulation protocols for the visualization of the mechanism of Nav1.5 activation. We constrained dihedrals of S4 trigger to introduce a structural tension with further rearrangement and movement of secondary structure elements. From these, we observed an intracellular gate opening and movement of the Lys1419 residue caused by a gradual displacement of the distal S6 α-helix with the extended S4 3-10 helix of voltage-sensing domains (VSD). A construction containing the Lys1419 residue in P-loop also changed its position due to the extension of this helix and subsequent induction of the pore-forming helixes motion. From this point, a double membrane system was generated, implying a free of ligand Nav1.5 protein and on the opposite side its copy containing a docked bupivacaine molecule inside the pore channel. The system can be used for the design of selective inhibitors against the Nav1.7 channel, instead of mixed effect on both channels.
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Heo P, Ramakrishnan S, Coleman J, Rothman JE, Fleury JB, Pincet F. Highly Reproducible Physiological Asymmetric Membrane with Freely Diffusing Embedded Proteins in a 3D-Printed Microfluidic Setup. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900725. [PMID: 30977975 DOI: 10.1002/smll.201900725] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/28/2019] [Indexed: 06/09/2023]
Abstract
Experimental setups to produce and to monitor model membranes have been successfully used for decades and brought invaluable insights into many areas of biology. However, they all have limitations that prevent the full in vitro mimicking and monitoring of most biological processes. Here, a suspended physiological bilayer-forming chip is designed from 3D-printing techniques. This chip can be simultaneously integrated to a confocal microscope and a path-clamp amplifier. It is composed of poly(dimethylsiloxane) and consists of a ≈100 µm hole, where the horizontal planar bilayer is formed, connecting two open crossed-channels, which allows for altering of each lipid monolayer separately. The bilayer, formed by the zipping of two lipid leaflets, is free-standing, horizontal, stable, fluid, solvent-free, and flat with the 14 types of physiologically relevant lipids, and the bilayer formation process is highly reproducible. Because of the two channels, asymmetric bilayers can be formed by making the two lipid leaflets of different composition. Furthermore, proteins, such as transmembrane, peripheral, and pore-forming proteins, can be added to the bilayer in controlled orientation and keep their native mobility and activity. These features allow in vitro recapitulation of membrane process close to physiological conditions.
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Affiliation(s)
- Paul Heo
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Université Sorbonne Paris Cité, Paris, 75005, France
| | - Sathish Ramakrishnan
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Université Sorbonne Paris Cité, Paris, 75005, France
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - Jeff Coleman
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, 06510, USA
| | - James E Rothman
- Ecole Normale Supérieure, PSL University, Paris, 75005, France
| | - Jean-Baptiste Fleury
- Department of Experimental Physics and Center for Biophysics, Saarland University, Saarbruecken, D-66123, Germany
| | - Frederic Pincet
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL Research University, CNRS, Sorbonne Université, Université Sorbonne Paris Cité, Paris, 75005, France
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6
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Oroskar PA, Jameson CJ, Murad S. Molecular-Level "Observations" of the Behavior of Gold Nanoparticles in Aqueous Solution and Interacting with a Lipid Bilayer Membrane. Methods Mol Biol 2019; 2000:303-359. [PMID: 31148024 DOI: 10.1007/978-1-4939-9516-5_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We use coarse-grained molecular dynamics simulations to "observe" details of interactions between ligand-covered gold nanoparticles and a lipid bilayer model membrane. In molecular dynamics simulations, one puts the individual atoms and groups of atoms of the physical system to be "observed" into a simulation box, specifies the forms of the potential energies of interactions between them (ultimately quantum based), and lets them individually move classically according to Newton's equations of motion, based on the forces arising from the assumed potential energy forms. The atoms that are chemically bonded to each other stay chemically bonded, following known potentials (force fields) that permit internal degrees of freedom (internal rotation, torsion, vibrations), and the interactions between nonbonded atoms are simplified to Lennard-Jones forms (in our case) and coulombic (where electrical charges are present) in which the parameters are previously optimized to reproduce thermodynamic properties or are based on quantum electronic calculations. The system is started out at a reasonable set of coordinates for all atoms or groups of atoms, and then permitted to develop according to the equations of motion, one small step (usually 10 fs time step) at a time, for millions of steps until the system is at a quasi-equilibrium (usually reached after hundreds of nanoseconds). We then let the system play out its motions further for many nanoseconds to observe the behavior, periodically taking snapshots (saving all positions and energies), and post-processing the snapshots to obtain various average descriptions of the system. Alkanethiols of various lengths serve as examples of hydrophobic ligands and methyl-terminated PEG with various numbers of monomer units serve as examples of hydrophilic ligands. Spherical gold particles of various diameters as well as gold nanorods form the core to which ligands are attached. The nanoparticles are characterized at the molecular level, especially the distributions of ligand configurations and their dependence on ligand length, and surface coverage. Self-assembly of the bilayer from an isotropic solution and observation of membrane properties that correspond well to experimental values validate the simulations. The mechanism of permeation of a gold NP coated with either a hydrophobic or a hydrophilic ligand, and its dependence on surface coverage, ligand length, core diameter, and core shape, is investigated. Lipid response such as lipid flip-flops, lipid extraction, and changes in order parameter of the lipid tails are examined in detail. The mechanism of permeation of a PEGylated nanorod is shown to occur by tilting, lying down, rotating, and straightening up. The nature of the information provided by molecular dynamics simulations permits understanding of the detailed behavior of gold nanoparticles interacting with lipid membranes which in turn helps to understand why some known systems work better than others and aids the design of new particles and improvement of methods for preparing existing ones.
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Affiliation(s)
- Priyanka A Oroskar
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Cynthia J Jameson
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Sohail Murad
- Department of Chemical Engineering, University of Illinois at Chicago, Chicago, IL, USA.
- Department of Chemical Engineering, Illinois Institute of Technology, Chicago, IL, USA.
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7
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Kalu N, Atsmon-Raz Y, Momben Abolfath S, Lucas L, Kenney C, Leppla SH, Tieleman DP, Nestorovich EM. Effect of late endosomal DOBMP lipid and traditional model lipids of electrophysiology on the anthrax toxin channel activity. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:2192-2203. [PMID: 30409515 DOI: 10.1016/j.bbamem.2018.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 08/19/2018] [Indexed: 01/26/2023]
Abstract
Anthrax toxin action requires triggering of natural endocytic transport mechanisms whereby the binding component of the toxin forms channels (PA63) within endosomal limiting and intraluminal vesicle membranes to deliver the toxin's enzymatic components into the cytosol. Membrane lipid composition varies at different stages of anthrax toxin internalization, with intraluminal vesicle membranes containing ~70% of anionic bis(monoacylglycero)phosphate lipid. Using model bilayer measurements, we show that membrane lipids can have a strong effect on the anthrax toxin channel properties, including the channel-forming activity, voltage-gating, conductance, selectivity, and enzymatic factor binding. Interestingly, the highest PA63 insertion rate was observed in bis(monoacylglycero)phosphate membranes. The molecular dynamics simulation data show that the conformational properties of the channel are different in bis(monoacylglycero)phosphate compared to PC, PE, and PS lipids. The anthrax toxin protein/lipid bilayer system can be advanced as a novel robust model to directly investigate lipid influence on membrane protein properties and protein/protein interactions.
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Affiliation(s)
- Nnanya Kalu
- Department of Biology, The Catholic University of America, 620 Michigan Ave NE, Washington 20064, DC, USA
| | - Yoav Atsmon-Raz
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Alberta, Canada.
| | - Sanaz Momben Abolfath
- Department of Biology, The Catholic University of America, 620 Michigan Ave NE, Washington 20064, DC, USA
| | - Laura Lucas
- Department of Biology, The Catholic University of America, 620 Michigan Ave NE, Washington 20064, DC, USA
| | - Clare Kenney
- Department of Biology, The Catholic University of America, 620 Michigan Ave NE, Washington 20064, DC, USA
| | - Stephen H Leppla
- Microbial Pathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda 20892, MD, USA
| | - D Peter Tieleman
- Department of Biological Sciences, Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary T2N 1N4, Alberta, Canada
| | - Ekaterina M Nestorovich
- Department of Biology, The Catholic University of America, 620 Michigan Ave NE, Washington 20064, DC, USA.
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8
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Startek JB, Talavera K, Voets T, Alpizar YA. Differential interactions of bacterial lipopolysaccharides with lipid membranes: implications for TRPA1-mediated chemosensation. Sci Rep 2018; 8:12010. [PMID: 30104600 PMCID: PMC6089920 DOI: 10.1038/s41598-018-30534-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
Bacterial lipopolysaccharides (LPS) activate the TRPA1 cation channels in sensory neurons, leading to acute pain and inflammation in mice and to aversive behaviors in fruit flies. However, the precise mechanisms underlying this effect remain elusive. Here we assessed the hypothesis that TRPA1 is activated by mechanical perturbations induced upon LPS insertion in the plasma membrane. We asked whether the effects of different LPS on TRPA1 relate to their ability to induce mechanical alterations in artificial and cellular membranes. We found that LPS from E. coli, but not from S. minnesota, activates TRPA1. We then assessed the effects of these LPS on lipid membranes using dyes whose fluorescence properties change upon alteration of the local lipid environment. E. coli LPS was more effective than S. minnesota LPS in shifting Laurdan’s emission spectrum towards lower wavelengths, increasing the fluorescence anisotropy of diphenylhexatriene and reducing the fluorescence intensity of merocyanine 540. These data indicate that E. coli LPS induces stronger changes in the local lipid environment than S. minnesota LPS, paralleling its distinct ability to activate TRPA1. Our findings indicate that LPS activate TRPA1 by producing mechanical perturbations in the plasma membrane and suggest that TRPA1-mediated chemosensation may result from primary mechanosensory mechanisms.
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Affiliation(s)
- Justyna B Startek
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine. KU Leuven; VIB Center for Brain & Disease Research, Leuven, Belgium
| | - Karel Talavera
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine. KU Leuven; VIB Center for Brain & Disease Research, Leuven, Belgium.
| | - Thomas Voets
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine. KU Leuven; VIB Center for Brain & Disease Research, Leuven, Belgium
| | - Yeranddy A Alpizar
- Laboratory of Ion Channel Research, Department of Cellular and Molecular Medicine. KU Leuven; VIB Center for Brain & Disease Research, Leuven, Belgium
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9
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Zhang J, Li D, Yue X, Zhang M, Liu P, Li G. Colorimetric in situ assay of membrane-bound enzyme based on lipid bilayer inhibition of ion transport. Theranostics 2018; 8:3275-3283. [PMID: 29930729 PMCID: PMC6010988 DOI: 10.7150/thno.25123] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/01/2018] [Indexed: 12/19/2022] Open
Abstract
Membrane-bound enzymes (MBEs), which make up a very high proportion of intracellular enzymes, catalyze a variety of activities that are currently analyzed by various techniques after purification. However, due to their amphipathic character, the purification of MBEs is difficult. Therefore, the most productive approach represents in situ analysis of MBEs in the cellular membrane. Methods: In this study, using membrane-bound α-glucosidase (α-Glu) as an example, we have developed a colorimetric in situ assay for MBEs based on the inhibitory effect of lipid bilayer on ion transport. The enzyme substrate could mediate the self-assembly of phospholipid PEG derivative around magnetic nanospheres that were modified with boronic acid. The formation of lipid bilayer could inhibit the leaking of iron ions under acidic conditions. However, the product of the catalytic reaction had no capability for self-assembly of the lipid bilayer, leading to the release of iron ions from the magnetic nanospheres under acidic pH. Results: The colorimetric in situ assay for MBEs could not only analyze the activity of membrane-bound α-Glu located on Caco-2 cells but could also evaluate the α-Glu inhibitors in cell medium. Conclusions: The simple, economic, and efficient method proposed here offers a potential application for high-throughput testing of α-Glu and its inhibitors. Our study also outlines a strategy for exploring the colorimetric method to detect the activities of MBEs in situ.
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Affiliation(s)
- Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Defeng Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- Shanghai Key Laboratory of Bio-Energy Crops, Shanghai University, Shanghai 200444, P. R. China
| | - Xiquan Yue
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Meiling Zhang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Ping Liu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
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10
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Emelyanova KA, Victorov AI. Driving Force for Spontaneous Perforation of Bilayers Formed by Ionic Amphiphiles in Aqueous Salt. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13438-13443. [PMID: 29064715 DOI: 10.1021/acs.langmuir.7b02885] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spontaneous perforation of amphiphilic membranes is important in both living matter and technology because of an impact on functions of biological membranes and shape transitions of self-assembling structures. Nevertheless, no definite molecular mechanism has been established so far even for simple ionic surfactant systems. We show that spontaneous perforation of a bilayer formed by an ionic amphiphile is driven by electrostatics. Creation of large pores with a concave-convex geometry of the rim is promoted by lower electrostatic free energy than that for a flat nonperforated bilayer. The opposite effect comes from the elasticity of the hydrocarbon tails of the amphiphile that prefer flat geometry of a nonperforated bilayer. The balance between electrostatics and tail deformation controls the appearance of pores; this balance is modulated by added salt that screens the electrostatic interactions. We illustrate the proposed mechanism with the aid of classical aggregation model that has been extended by including an analytical description of the electrostatic contribution for the toroidal rim of a pore. Numerical solution of the linearized Poisson-Boltzmann equation confirms the role of electrostatic forces in formation of pores. For the ionic surfactants of CnTAB family, we predict shape transitions including bilayer perforations and formation of branched micellar networks induced by changing salinity or temperature and demonstrate the effect of surfactant's molecular parameters on these transitions.
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Affiliation(s)
- Ksenia A Emelyanova
- St. Petersburg State University , 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
| | - Alexey I Victorov
- St. Petersburg State University , 7/9 Universitetskaya nab., 199034 St. Petersburg, Russia
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11
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Kara S, Afonin S, Babii O, Tkachenko AN, Komarov IV, Ulrich AS. Diphytanoyl lipids as model systems for studying membrane-active peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1828-1837. [PMID: 28587828 DOI: 10.1016/j.bbamem.2017.06.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 01/28/2023]
Abstract
The branched chains in diphytanoyl lipids provide membranes with unique properties, such as high chemical/physical stability, low water permeability, and no gel-to-fluid phase transition at ambient temperature. Synthetic diphytanoyl phospholipids are often used as model membranes for electrophysiological experiments. To evaluate whether these sturdy lipids are also suitable for solid-state NMR, we have examined their interactions with a typical amphiphilic peptide in comparison with straight-chain lipids. First, their phase properties were monitored using 31P NMR, and the structural behaviour of the antimicrobial peptide PGLa was studied by 19F NMR and circular dichroism in oriented membrane samples. Only lipids with choline headgroups (DPhPC) were found to form stable lipid bilayers in oriented samples, while DPhPG, DPhPE and DPhPS display non-lamellar structures. Hence, the experimental temperature and hydration are crucial factors when using supported diphytanoyl lipids, as both parameters must be maintained in an appropriate range to avoid the formation of non-bilayer structures. For the same reason, a high content of other diphytanoyl lipids besides DPhPC in mixed lipid systems is not favourable. Unlike the situation in straight-chain membranes, we found that the α-helical PGLa was not able to insert into the tightly packed fluid bilayer of DPhPC but remained in a surface-bound state even at very high peptide concentration. This behaviour can be explained by the high cohesivity and the negative spontaneous curvature of the diphytanoyl lipids. These characteristic features must therefore be taken into consideration, both, in electrophysiological studies, and when interpreting the structural behaviour of membrane-active peptides in such lipid environment.
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Affiliation(s)
- Sezgin Kara
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O.B. 3640, 76021 Karlsruhe, Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biology and Medicine (IBM), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Anton N Tkachenko
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biology and Medicine (IBM), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Igor V Komarov
- Enamine Ltd., vul. Chervonotkatska 78, 02094 Kyiv, Ukraine; Institute of High Technologies (IHT), Taras Shevchenko National University of Kyiv, vul. Volodymyrska 60, 01601 Kyiv, Ukraine
| | - Anne S Ulrich
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, P.O.B. 3640, 76021 Karlsruhe, Germany.
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12
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Zhu Z, Sheng N, Fang H, Wan R. Colored spectrum characteristics of thermal noise on the molecular scale. Phys Chem Chem Phys 2016; 18:30189-30195. [PMID: 27779258 DOI: 10.1039/c6cp04433f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Thermal noise is of fundamental importance to many processes. Traditionally, thermal noise has been treated as white noise on the macroscopic scale. Using molecular dynamics simulations and power spectrum analysis, we show that the thermal noise of solute molecules in water is non-white on the molecular scale, which is in contrast to the conventional theory. In the frequency domain from 2 × 1011 Hz to 1013 Hz, the power spectrum of thermal noise for polar solute molecules resembles the spectrum of 1/f noise. The power spectrum of thermal noise for non-polar solute molecules deviates only slightly from the spectrum of white noise. The key to this phenomenon is the existence of hydrogen bonds between polar solute molecules and solvent water molecules. Furthermore, for polar solute molecules, the degree of power spectrum deviation from that of white noise is associated with the average lifetime of the hydrogen bonds between the solute and the solvent molecules.
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Affiliation(s)
- Zhi Zhu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Nan Sheng
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
| | - Rongzheng Wan
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai 201800, China.
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13
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Singh MK, Shweta H, Khan MF, Sen S. New insight into probe-location dependent polarity and hydration at lipid/water interfaces: comparison between gel- and fluid-phases of lipid bilayers. Phys Chem Chem Phys 2016; 18:24185-97. [DOI: 10.1039/c6cp01201a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Location dependent polarity and hydration probed by a new series of 4-aminophthalimide-based fluorescent molecules (4AP-Cn;n= 2–10, 12) show different behaviour at gel- and fluid-phase lipid/water interfaces.
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Affiliation(s)
- Moirangthem Kiran Singh
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Him Shweta
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Mohammad Firoz Khan
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
| | - Sobhan Sen
- Spectroscopy Laboratory
- School of Physical Sciences
- Jawaharlal Nehru University
- New Delhi 110067
- India
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14
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Kirsch SA, Böckmann RA. Membrane pore formation in atomistic and coarse-grained simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1858:2266-2277. [PMID: 26748016 DOI: 10.1016/j.bbamem.2015.12.031] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022]
Abstract
Biological cells and their organelles are protected by ultra thin membranes. These membranes accomplish a broad variety of important tasks like separating the cell content from the outer environment, they are the site for cell-cell interactions and many enzymatic reactions, and control the in- and efflux of metabolites. For certain physiological functions e.g. in the fusion of membranes and also in a number of biotechnological applications like gene transfection the membrane integrity needs to be compromised to allow for instance for the exchange of polar molecules across the membrane barrier. Mechanisms enabling the transport of molecules across the membrane involve membrane proteins that form specific pores or act as transporters, but also so-called lipid pores induced by external fields, stress, or peptides. Recent progress in the simulation field enabled to closely mimic pore formation as supposed to occur in vivo or in vitro. Here, we review different simulation-based approaches in the study of membrane pores with a focus on lipid pore properties such as their size and energetics, poration mechanisms based on the application of external fields, charge imbalances, or surface tension, and on pores that are induced by small molecules, peptides, and lipids. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sonja A Kirsch
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany.
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15
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Allolio C, Baxova K, Vazdar M, Jungwirth P. Guanidinium Pairing Facilitates Membrane Translocation. J Phys Chem B 2015; 120:143-53. [DOI: 10.1021/acs.jpcb.5b10404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christoph Allolio
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Institut
für Physikalische and Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany
| | - Katarina Baxova
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
| | - Mario Vazdar
- Institut
Rudjer
Bošković, Bijenička
cesta 54, 10000 Zagreb, Croatia
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-166 10 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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16
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Milianta PJ, Muzzio M, Denver J, Cawley G, Lee S. Water Permeability across Symmetric and Asymmetric Droplet Interface Bilayers: Interaction of Cholesterol Sulfate with DPhPC. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:12187-12196. [PMID: 26492572 DOI: 10.1021/acs.langmuir.5b02748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cellular membranes employ a variety of strategies for controlling the flow of small molecules into the cytoplasmic space, including incorporation of sterols for modulation of permeability and maintenance of lipid asymmetry to provide both sides of the membrane with differing biophysical properties. The specific case of cholesterol asymmetry, especially, is known to have profound effects in neurological cellular systems. Synthetic membrane models that can readily determine valuable physical parameters, such as water transport rates, for sterol-containing membranes of defined lipid composition remain in demand. We report the use of the droplet interface bilayer (DIB), composed of adherent aqueous droplets surrounded by a lipid monolayer and immersed in a hydrophobic medium, for measurement of water permeability across the membrane, with rapid visualization and ease of experimental setup. We studied droplet bilayer membranes composed of the prototypical synthetic membrane lipid (i.e., the archaeal lipid DPhPC) as well as of symmetric and asymmetric DIBs formed by DPhPC and sodium cholesterol sulfate (S-Chol). The presence of S-Chol in DPhPC in symmetric DIB reduced the passive water permeability rate (P(f)) at all concentrations and increased the activation energy (E(a)) to 17-18 kcal/mol. When only one side of the DIB contains S-Chol (asymmetric DIB), an E(a) of 14-15 kcal/mol was obtained, a value intermediate that of pure lipid and symmetrical DIB containing lipid and S-Chol. Our data are consistent with a capability for regulation of water transport by one leaflet independent of the other. The engineering of our various systems is believed to have implications for garnering detailed knowledge regarding the transport of small moieties across bilayers in a wide variety of lipid systems.
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Affiliation(s)
- Peter J Milianta
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Michelle Muzzio
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Jacqueline Denver
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Geoffrey Cawley
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
| | - Sunghee Lee
- Department of Chemistry, Iona College , 715 North Avenue, New Rochelle, New York 10801, United States
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17
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Carr M, MacPhee CE. Membrainy: a 'smart', unified membrane analysis tool. SOURCE CODE FOR BIOLOGY AND MEDICINE 2015; 10:3. [PMID: 26060507 PMCID: PMC4460882 DOI: 10.1186/s13029-015-0033-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/19/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND The study of biological membranes using Molecular Dynamics has become an increasingly popular means by which to investigate the interactions of proteins, peptides and potentials with lipid bilayers. These interactions often result in changes to the properties of the lipids which can modify the behaviour of the membrane. Membrainy is a unified membrane analysis tool that contains a broad spectrum of analytical techniques to enable: measurement of acyl chain order parameters; presentation of 2D surface and thickness maps; determination of lateral and axial headgroup orientations; measurement of bilayer and leaflet thickness; analysis of the annular shell surrounding membrane-embedded objects; quantification of gel percentage; time evolution of the transmembrane voltage; area per lipid calculations; and quantification of lipid mixing/demixing entropy. RESULTS Each analytical component within Membrainy has been tested on a variety of lipid bilayer systems and was found to be either comparable to or an improvement upon existing software. For the analytical techniques that have no direct comparable software, our results were confirmed with experimental data. CONCLUSIONS Membrainy is a user-friendly, intelligent membrane analysis tool that automatically interprets a variety of input formats and force fields, is compatible with both single and double bilayers, and capable of handling asymmetric bilayers and lipid flip-flopping. Membrainy has been designed for ease of use, requiring no installation or configuration and minimal user-input to operate.
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Affiliation(s)
- Matthew Carr
- Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, UK
| | - Cait E MacPhee
- Institute for Condensed Matter and Complex Systems, School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh, UK
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18
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Garten M, Prévost C, Cadart C, Gautier R, Bousset L, Melki R, Bassereau P, Vanni S. Methyl-branched lipids promote the membrane adsorption of α-synuclein by enhancing shallow lipid-packing defects. Phys Chem Chem Phys 2015; 17:15589-97. [DOI: 10.1039/c5cp00244c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reconstitution experiments on Giant Unilamellar Vesicles and Molecular Dynamics Simulations indicate that alpha-synuclein binds to neutral flat membranes in the presence of methyl-branched lipids.
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Affiliation(s)
| | | | | | - Romain Gautier
- Institut de Pharmacologie Moléculaire et Cellulaire
- Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique
- UMR 7275
- 06560 Valbonne
- France
| | - Luc Bousset
- CNRS
- Paris Saclay Institute of Neuroscience
- Gif-sur-Yvette
- France
| | - Ronald Melki
- CNRS
- Paris Saclay Institute of Neuroscience
- Gif-sur-Yvette
- France
| | | | - Stefano Vanni
- Institut de Pharmacologie Moléculaire et Cellulaire
- Université de Nice Sophia-Antipolis and Centre National de la Recherche Scientifique
- UMR 7275
- 06560 Valbonne
- France
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19
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Poger D, Caron B, Mark AE. Effect of Methyl-Branched Fatty Acids on the Structure of Lipid Bilayers. J Phys Chem B 2014; 118:13838-48. [DOI: 10.1021/jp503910r] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- David Poger
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Bertrand Caron
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular
Biosciences and ‡Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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