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Harb F, Tinland B. Toward Electrophoretic Separation of Membrane Proteins in Supported n-Bilayers. ACS OMEGA 2020; 5:27741-27748. [PMID: 33163756 PMCID: PMC7643068 DOI: 10.1021/acsomega.0c01196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
Membrane proteins are key constituents of the proteome of cells but are poorly characterized, mainly because they are difficult to solubilize. Proteome analysis involves separating proteins as a preliminary step toward their characterization. Currently, the most common method is "solubilizing" them with sophisticated detergent and lipid mixtures for later separation via, for instance, sodium dodecyl sulfate polyacrylamide gel electrophoresis. However, this later step induces loss of 3D structure (denaturation). Migration in a medium that mimics the cell membrane should therefore be more appropriate. Here, we present a successful electrophoretic separation of a mixture first of two and then of three different membrane objects in supported n-bilayers. These "objects" are composed of membrane proteins sulfide quinone reductase and α-hemolysin. Sulfide quinone reductase forms an object from three monomers together and self-inserts into the upper leaflet. α-Hemolysin inserts as a spanning heptamer into a bilayer or can build stable dimers of α-hemolysin heptamers under certain conditions. By appropriately adjusting the pH, it proved possible to move them in different ways. This work holds promise for separating membrane proteins without losing their 3D structure, thus their bioactivity, within a lipidic environment that is closer to physiological conditions and for building drug/diagnostic platforms.
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Affiliation(s)
- Frédéric
F. Harb
- Department
of Biology; Faculty of Sciences − Section II, Lebanese University, Beirut 90656, Lebanon
| | - Bernard Tinland
- Aix-Marseille
Université, CNRS, CINaM UMR 7325, Marseille 13288, France
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Sarkis J, Vié V. Biomimetic Models to Investigate Membrane Biophysics Affecting Lipid-Protein Interaction. Front Bioeng Biotechnol 2020; 8:270. [PMID: 32373596 PMCID: PMC7179690 DOI: 10.3389/fbioe.2020.00270] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 03/16/2020] [Indexed: 12/16/2022] Open
Abstract
Biological membranes are highly dynamic in their ability to orchestrate vital mechanisms including cellular protection, organelle compartmentalization, cellular biomechanics, nutrient transport, molecular/enzymatic recognition, and membrane fusion. Controlling lipid composition of different membranes allows cells to regulate their membrane characteristics, thus modifying their physical properties to permit specific protein interactions and drive structural function (membrane deformation facilitates vesicle budding and fusion) and signal transduction. Yet, how lipids control protein structure and function is still poorly understood and needs systematic investigation. In this review, we explore different in vitro membrane models and summarize our current understanding of the interplay between membrane biophysical properties and lipid-protein interaction, taken as example few proteins involved in muscular activity (dystrophin), digestion and Legionella pneumophila effector protein DrrA. The monolayer model with its movable barriers aims to mimic any membrane deformation while surface pressure modulation imitates lipid packing and membrane curvature changes. It is frequently used to investigate peripheral protein binding to the lipid headgroups. Examples of how lipid lateral pressure modifies protein interaction and organization within the membrane are presented using various biophysical techniques. Interestingly, the shear elasticity and surface viscosity of the monolayer will increase upon specific protein(s) binding, supporting the importance of such mechanical link for membrane stability. The lipid bilayer models such as vesicles are not only used to investigate direct protein binding based on the lipid nature, but more importantly to assess how local membrane curvature (vesicles with different size) influence the binding properties of a protein. Also, supported lipid bilayer model has been used widely to characterize diffusion law of lipids within the bilayer and/or protein/biomolecule binding and diffusion on the membrane. These membrane models continue to elucidate important advances regarding the dynamic properties harmonizing lipid-protein interaction.
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Affiliation(s)
- Joe Sarkis
- Department of Cell Biology, Harvard Medical School and Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA, United States
- Univ Rennes, CNRS, IPR-UMR 6251, Rennes, France
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Bao P, Cartron ML, Sheikh KH, Johnson BRG, Hunter CN, Evans SD. Controlling transmembrane protein concentration and orientation in supported lipid bilayers. Chem Commun (Camb) 2018; 53:4250-4253. [PMID: 28361139 DOI: 10.1039/c7cc01023k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The trans-membrane protein - proteorhodopsin (pR) has been incorporated into supported lipid bilayers (SLB). In-plane electric fields have been used to manipulate the orientation and concentration of these proteins, within the SLB, through electrophoresis leading to a 25-fold increase concentration of pR.
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Affiliation(s)
- P Bao
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
| | - M L Cartron
- Department of Molecular Biology & Biotechnology, University of Sheffield, S10 2TH, UK
| | - K H Sheikh
- School of Biomedical Science, University of Leeds, LS2 9JT, UK
| | - B R G Johnson
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
| | - C N Hunter
- Department of Molecular Biology & Biotechnology, University of Sheffield, S10 2TH, UK
| | - S D Evans
- School of Physics & Astronomy, University of Leeds, LS2 9JT, UK.
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Javanainen M, Martinez-Seara H, Metzler R, Vattulainen I. Diffusion of Integral Membrane Proteins in Protein-Rich Membranes. J Phys Chem Lett 2017; 8:4308-4313. [PMID: 28823153 DOI: 10.1021/acs.jpclett.7b01758] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes-like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different from protein-poor conditions and plays a significant role in formation of functional multiprotein complexes.
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Affiliation(s)
- Matti Javanainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Department of Physics, University of Helsinki , 00014 Helsinki, Finland
| | - Hector Martinez-Seara
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , 166 10 Prague, Czech Republic
| | - Ralf Metzler
- Institute for Physics and Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany
| | - Ilpo Vattulainen
- Laboratory of Physics, Tampere University of Technology , 33101 Tampere, Finland
- Department of Physics, University of Helsinki , 00014 Helsinki, Finland
- MEMPHYS - Centre for Biomembrane Physics, University of Southern Denmark , 5230 Odense, Denmark
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Klaus CJS, Raghunathan K, DiBenedetto E, Kenworthy AK. Analysis of diffusion in curved surfaces and its application to tubular membranes. Mol Biol Cell 2016; 27:3937-3946. [PMID: 27733625 PMCID: PMC5170615 DOI: 10.1091/mbc.e16-06-0445] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/08/2016] [Accepted: 10/04/2016] [Indexed: 11/11/2022] Open
Abstract
Diffusion of particles in curved surfaces is inherently complex compared with diffusion in a flat membrane, owing to the nonplanarity of the surface. The consequence of such nonplanar geometry on diffusion is poorly understood but is highly relevant in the case of cell membranes, which often adopt complex geometries. To address this question, we developed a new finite element approach to model diffusion on curved membrane surfaces based on solutions to Fick's law of diffusion and used this to study the effects of geometry on the entry of surface-bound particles into tubules by diffusion. We show that variations in tubule radius and length can distinctly alter diffusion gradients in tubules over biologically relevant timescales. In addition, we show that tubular structures tend to retain concentration gradients for a longer time compared with a comparable flat surface. These findings indicate that sorting of particles along the surfaces of tubules can arise simply as a geometric consequence of the curvature without any specific contribution from the membrane environment. Our studies provide a framework for modeling diffusion in curved surfaces and suggest that biological regulation can emerge purely from membrane geometry.
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Affiliation(s)
| | - Krishnan Raghunathan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232
| | | | - Anne K Kenworthy
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 .,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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Harb F, Prunetti L, Giudici-Orticoni MT, Guiral M, Tinland B. Insertion and self-diffusion of a monotopic protein, the Aquifex aeolicus sulfide quinone reductase, in supported lipid bilayers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2015; 38:110. [PMID: 26490251 DOI: 10.1140/epje/i2015-15110-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
Monotopic proteins constitute a class of membrane proteins that bind tightly to cell membranes, but do not span them. We present a FRAPP (Fluorescence Recovery After Patterned Photobleaching) study of the dynamics of a bacterial monotopic protein, SQR (sulfide quinone oxidoreductase) from the thermophilic bacteria Aquifex aeolicus, inserted into two different types of lipid bilayers (EggPC: L-α-phosphatidylcholine (Egg, Chicken) and DMPC: 1,2-dimyristoyl-sn-glycero-3-phosphocholine) supported on two different types of support (mica or glass). It sheds light on the behavior of a monotopic protein inside the bilayer. The insertion of SQR is more efficient when the bilayer is in the fluid phase than in the gel phase. We observed diffusion of the protein, with no immobile fraction, and deduced from the diffusion coefficient measurements that the resulting inserted object is the same whatever the incubation conditions, i.e. homogeneous in terms of oligomerization state. As expected, the diffusion coefficient of the SQR is smaller in the gel phase than in the fluid phase. In the supported lipid bilayer, the diffusion coefficient of the SQR is smaller than the diffusion coefficient of phospholipids in both gel and fluid phase. SQR shows a diffusion behavior different from the transmembrane protein α-hemolysin, and consistent with its monotopic character. Preliminary experiments in the presence of the substrate of SQR, DecylUbiquinone, an analogue of quinone, component of transmembrane electrons transport systems of eukaryotic and prokaryotic organisms, have been carried out. Finally, we studied the behavior of SQR, in terms of insertion and diffusion, in bilayers formed with lipids from Aquifex aeolicus. All the conclusions that we have found in the biomimetic systems applied to the biological system.
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Affiliation(s)
- Frédéric Harb
- Department of Biology, Faculty of Sciences - Section II, Lebanese University, Beirut, Lebanon
- CINaM-CNRS, Aix-Marseille Université, UMR7325, 13288, Marseille, France
| | - Laurence Prunetti
- CNRS, BIP UMR 7281, Aix Marseille Université, 13402, Marseille, France
| | | | - Marianne Guiral
- CNRS, BIP UMR 7281, Aix Marseille Université, 13402, Marseille, France
| | - Bernard Tinland
- CINaM-CNRS, Aix-Marseille Université, UMR7325, 13288, Marseille, France.
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Wang CY, Hill RJ. Transmembrane protein diffusion in gel-supported dual-leaflet membranes. Biophys J 2014; 107:2296-304. [PMID: 25418298 DOI: 10.1016/j.bpj.2014.10.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/09/2014] [Accepted: 10/15/2014] [Indexed: 10/24/2022] Open
Abstract
Tools to measure transmembrane-protein diffusion in lipid bilayer membranes have advanced in recent decades, providing a need for predictive theoretical models that account for interleaflet leaflet friction on tracer mobility. Here we address the fully three-dimensional flows driven by a (nonprotruding) transmembrane protein embedded in a dual-leaflet membrane that is supported above and below by soft porous supports (e.g., hydrogel or extracellular matrix), each of which has a prescribed permeability and solvent viscosity. For asymmetric configurations, i.e., supports with contrasting permeability, as realized for cells in contact with hydrogel scaffolds or culture media, the diffusion coefficient can reflect interleaflet friction. Reasonable approximations, for sufficiently large tracers on low-permeability supports, are furnished by a recent phenomenological theory from the literature. Interpreting literature data, albeit for hard-supported membranes, provides a theoretical basis for the phenomenological Stokes drag law as well as strengthening assertions that nonhydrodynamic interactions are important in supported bilayer systems, possibly leading to overestimates of the membrane/leaflet viscosity. Our theory provides a theoretical foundation for future experimental studies of tracer diffusion in gel-supported membranes.
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Affiliation(s)
- Chih-Ying Wang
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada
| | - Reghan J Hill
- Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada.
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Seki K, Mogre S, Komura S. Diffusion coefficients in leaflets of bilayer membranes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:022713. [PMID: 25353515 DOI: 10.1103/physreve.89.022713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Indexed: 06/04/2023]
Abstract
We study diffusion coefficients of liquid domains by explicitly taking into account the two-layered structure called leaflets of the bilayer membrane. In general, the velocity fields associated with each leaflet are different and the layers sliding past each other cause frictional coupling. We obtain analytical results of diffusion coefficients for a circular liquid domain in a leaflet, and quantitatively study their dependence on the interleaflet friction. We also show that the diffusion coefficients diverge in the absence of coupling between the bilayer and solvents, even when the interleaflet friction is taken into account. In order to corroborate our theory, the effect of the interleaflet friction on the correlated diffusion is examined.
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Affiliation(s)
- Kazuhiko Seki
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), AIST Central 5, Higashi 1-1-1, Tsukuba, Ibaraki 305-8565, Japan
| | - Saurabh Mogre
- Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra 400 076, India
| | - Shigeyuki Komura
- Department of Chemistry, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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Harb F, Tinland B. Electric migration of α-hemolysin in supported n-bilayers: a model for transmembrane protein microelectrophoresis. Electrophoresis 2013; 34:3054-63. [PMID: 23925931 DOI: 10.1002/elps.201300202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 06/26/2013] [Accepted: 07/12/2013] [Indexed: 11/06/2022]
Abstract
Proteome analysis involves separating proteins as a preliminary step toward their characterization. This paper reports on the translational migration of a model transmembrane protein (α-hemolysin) in supported n-bilayers (n, the number of bilayers, varies from 1 to around 500 bilayers) when an electric field parallel to the membrane plane is applied. The migration changes in direction as the charge on the protein changes its sign. Its electrophoretic mobility is shown to depend on size and charge. The electrophoretic mobility varies as 1/R(2), with R the equivalent geometric radius of the embedded part of the protein. Measuring mobilities at differing pH in our system enables us to determine the pI and the charge of the protein. Establishing all these variations points to the feasibility of electrophoretic transport of a charged object in this medium and is a first step toward electrophoretic separation of membrane proteins in n-bilayer systems.
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Affiliation(s)
- Frédéric Harb
- Aix-Marseille Université, CINaM, CNRS, Marseille, France
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