1
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Woubshete M, Cioccolo S, Byrne B. Advances in Membrane Mimetic Systems for Manipulation and Analysis of Membrane Proteins: Detergents, Polymers, Lipids and Scaffolds. Chempluschem 2024; 89:e202300678. [PMID: 38315323 DOI: 10.1002/cplu.202300678] [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: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/07/2024]
Abstract
Extracting membrane proteins from the hydrophobic environment of the biological membrane, in a physiologically relevant and stable state, suitable for downstream analysis remains a challenge. The traditional route to membrane protein extraction has been to use detergents and the last 15 years or so have seen a veritable explosion in the development of novel detergents with improved properties, making them more suitable for individual proteins and specific applications. There have also been significant advances in the development of encapsulation of membrane proteins in lipid based nanodiscs, either directly from the native membrane using polymers allowing effective capture of the protein and protein-associated membrane lipids, or via reconstitution of detergent extracted and purified protein into nanodiscs of defined lipid composition. All of these advances have been successfully applied to the study of membrane proteins via a range of techniques and there have been some spectacular membrane protein structures solved. In addition, the first detailed structural and biophysical analyses of membrane proteins retained within a biological membrane have been reported. Here we summarise and review the recent advances with respect to these new agents and systems for membrane protein extraction, reconstitution and analysis.
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Affiliation(s)
- Menebere Woubshete
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
| | - Sara Cioccolo
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
- Department of Chemistry, Imperial College London, White City, London, W12 0BZ, United Kingdom
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, United Kingdom
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2
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Workman CE, Bag P, Cawthon B, Ali FH, Brady NG, Bruce BD, Long BK. Alternatives to Styrene- and Diisobutylene-Based Copolymers for Membrane Protein Solubilization via Nanodisc Formation. Angew Chem Int Ed Engl 2023; 62:e202306572. [PMID: 37682083 PMCID: PMC10591821 DOI: 10.1002/anie.202306572] [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: 05/10/2023] [Revised: 09/05/2023] [Accepted: 09/08/2023] [Indexed: 09/09/2023]
Abstract
Styrene-maleic acid copolymers (SMAs), and related amphiphilic copolymers, are promising tools for isolating and studying integral membrane proteins in a native-like state. However, they do not exhibit this ability universally, as several reports have found that SMAs and related amphiphilic copolymers show little to no efficiency when extracting specific membrane proteins. Recently, it was discovered that esterified SMAs could enhance the selective extraction of trimeric Photosystem I from the thylakoid membranes of thermophilic cyanobacteria; however, these polymers are susceptible to saponification that can result from harsh preparation or storage conditions. To address this concern, we herein describe the development of α-olefin-maleic acid copolymers (αMAs) that can extract trimeric PSI from cyanobacterial membranes with the highest extraction efficiencies observed when using any amphiphilic copolymers, including diisobutylene-co-maleic acid (DIBMA) and functionalized SMA samples. Furthermore, we will show that αMAs facilitate the formation of photosystem I-containing nanodiscs that retain an annulus of native lipids and a native-like activity. We also highlight how αMAs provide an agile, tailorable synthetic platform that enables fine-tuning hydrophobicity, controllable molar mass, and consistent monomer incorporation while overcoming shortcomings of prior amphiphilic copolymers.
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Affiliation(s)
| | - Pushan Bag
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Bridgie Cawthon
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Fidaa H Ali
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Nathan G Brady
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
| | - Barry D Bruce
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, USA
| | - Brian K Long
- Department of Chemistry, University of Tennessee, Knoxville, USA
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3
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Kamilar E, Bariwal J, Zheng W, Ma H, Liang H. SMALPs Are Not Simply Nanodiscs: The Polymer-to-Lipid Ratios of Fractionated SMALPs Underline Their Heterogeneous Nature. Biomacromolecules 2023; 24:1819-1838. [PMID: 36947865 DOI: 10.1021/acs.biomac.3c00034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Amphipathic styrene-maleic acid (SMA) copolymers directly solubilize biomembranes into SMA-lipid particles, or SMALPs, that are often regarded as nanodiscs and hailed as a native membrane platform. The promising outlook of SMALPs inspires the discovery of many SMA-like copolymers that also solubilize biomembranes into putative nanodiscs, but a fundamental question remains on how much the SMALPs or SMALP analogues truly resemble the bilayer structure of nanodiscs. This unfortunate ambiguity undermines the utility of SMA or SMA-like copolymers in membrane biology because the structure and function of many membrane proteins depend critically on their surrounding matrices. Here, we report the structural heterogeneity of SMALPs revealed through fractionating SMALPs comprised of lipids and well-defined SMAs via size-exclusion chromatography followed by quantitative determination of the polymer-to-lipid (P/L) stoichiometric ratios in individual fractions. Through the lens of P/L stoichiometric ratios, different self-assembled polymer-lipid nanostructures are inferred, such as polymer-remodeled liposomes, polymer-encased nanodiscs, polymer-lipid mixed micelles, and lipid-doped polymer micellar aggregates. We attribute the structural heterogeneity of SMALPs to the microstructure variations amongst individual polymer chains that give rise to their polydisperse detergency. As an example, we demonstrate that SMAs with a similar S/MA ratio but different chain sizes participate preferentially in different polymer-lipid nanostructures. We further demonstrate that proteorhodopsin, a light-driven proton pump solubilized within the same SMALPs is distributed amongst different self-assembled nanostructures to display different photocycle kinetics. Our discovery challenges the native nanodisc notion of SMALPs or SMALP analogues and highlights the necessity to separate and identify the structurally dissimilar polymer-lipid particles in membrane biology studies.
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Affiliation(s)
- Elizabeth Kamilar
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Jitender Bariwal
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Wan Zheng
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hairong Ma
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
| | - Hongjun Liang
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, United States
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4
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Jayapurna I, Ruan Z, Eres M, Jalagam P, Jenkins S, Xu T. Sequence Design of Random Heteropolymers as Protein Mimics. Biomacromolecules 2023; 24:652-660. [PMID: 36638823 PMCID: PMC9930114 DOI: 10.1021/acs.biomac.2c01036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Random heteropolymers (RHPs) have been computationally designed and experimentally shown to recapitulate protein-like phase behavior and function. However, unlike proteins, RHP sequences are only statistically defined and cannot be sequenced. Recent developments in reversible-deactivation radical polymerization allowed simulated polymer sequences based on the well-established Mayo-Lewis equation to more accurately reflect ground-truth sequences that are experimentally synthesized. This led to opportunities to perform bioinformatics-inspired analysis on simulated sequences to guide the design, synthesis, and interpretation of RHPs. We compared batches on the order of 10000 simulated RHP sequences that vary by synthetically controllable and measurable RHP characteristics such as chemical heterogeneity and average degree of polymerization. Our analysis spans across 3 levels: segments along a single chain, sequences within a batch, and batch-averaged statistics. We discuss simulator fidelity and highlight the importance of robust segment definition. Examples are presented that demonstrate the use of simulated sequence analysis for in-silico iterative design to mimic protein hydrophobic/hydrophilic segment distributions in RHPs and compare RHP and protein sequence segments to explain experimental results of RHPs that mimic protein function. To facilitate the community use of this workflow, the simulator and analysis modules have been made available through an open source toolkit, the RHPapp.
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Affiliation(s)
- Ivan Jayapurna
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zhiyuan Ruan
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Marco Eres
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Prajna Jalagam
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - Spencer Jenkins
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Ting Xu
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, California 94720, United States.,Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States.,Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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5
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Lakey JH, Paracini N, Clifton LA. Exploiting neutron scattering contrast variation in biological membrane studies. BIOPHYSICS REVIEWS 2022; 3:021307. [PMID: 38505417 PMCID: PMC10903484 DOI: 10.1063/5.0091372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 05/03/2022] [Indexed: 03/21/2024]
Abstract
Biological membranes composed of lipids and proteins are central for the function of all cells and individual components, such as proteins, that are readily studied by a range of structural approaches, including x-ray crystallography and cryo-electron microscopy. However, the study of complex molecular mixtures within the biological membrane structure and dynamics requires techniques that can study nanometer thick molecular bilayers in an aqueous environment at ambient temperature and pressure. Neutron methods, including scattering and spectroscopic approaches, are useful since they can measure structure and dynamics while also being able to penetrate sample holders and cuvettes. The structural approaches, such as small angle neutron scattering and neutron reflectometry, detect scattering caused by the difference in neutron contrast (scattering length) between different molecular components such as lipids or proteins. Usually, the bigger the contrast, the clearer the structural data, and this review uses examples from our research to illustrate how contrast can be increased to allow the structures of individual membrane components to be resolved. Most often this relies upon the use of deuterium in place of hydrogen, but we also discuss the use of magnetic contrast and other elements with useful scattering length values.
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Affiliation(s)
- Jeremy H. Lakey
- Institute for Cell and Molecular Bioscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolò Paracini
- Biofilms Research Center for Biointerfaces, Malmö University, Per Albin Hanssons väg 35, 21432 Malmö, Sweden
| | - Luke A. Clifton
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, United Kingdom
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6
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Daniels GC, Hinnant KM, Brown LC, Weise NK, Aukerman MC, Giordano BC. Copolymer Reversible Addition-Fragmentation Chain Transfer Synthesis of Polyethylene Glycol (PEG) Functionalized with Hydrophobic Acrylates: A Study of Surface and Foam Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4547-4554. [PMID: 35384673 DOI: 10.1021/acs.langmuir.1c02759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A series of amphiphilic statistical copolymers involving poly(ethylene glycol) monomethacrylate (PEGMA, -OH terminated, average Mn 200 molecular weight) and various hydrophobic acrylates were synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization. The gradient copolymers were characterized by gel-permeation chromatography (GPC), 1H nuclear magnetic resonance (NMR), and attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR). Solution properties of the copolymers were investigated utilizing surface tension measurement, dynamic light-scattering (DLS), as well as foam analysis using a dynamic foam analyzer (DFA). The PEG-functionalized copolymers showed a systematic trend depending on the hydrophobic moiety in properties including surface tension, critical micelle concentration (CMC), foam lifetime, and liquid drainage from the foam. Copolymers with alkyl-acrylates exhibited the best foam lifetime, demonstrating that the choice of hydrophobic moiety is crucial for foam stability. The PEG-functionalized materials described are considered promising additives for foam-stability purposes.
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Affiliation(s)
- Grant C Daniels
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Katherine M Hinnant
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Loren C Brown
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
- ASEE Post-Doctoral Fellow, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Nickolaus K Weise
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Mark C Aukerman
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Braden C Giordano
- Chemistry Division, United States Naval Research Laboratory, Washington, D.C. 20375, United States
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7
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Clénet D, Clavier L, Strobbe B, Le Bon C, Zoonens M, Saulnier A. Full-length G glycoprotein directly extracted from rabies virus with detergent and then stabilized by amphipols in liquid and freeze-dried forms. Biotechnol Bioeng 2021; 118:4317-4330. [PMID: 34297405 PMCID: PMC9291542 DOI: 10.1002/bit.27900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 06/22/2021] [Accepted: 07/09/2021] [Indexed: 11/11/2022]
Abstract
Pathogen surface antigens are at the forefront of the viral strategy when invading host organisms. These antigens, including membrane proteins (MPs), are broadly targeted by the host immune response. Obtaining these MPs in a soluble and stable form constitutes a real challenge, regardless of the application purposes (e.g. quantification/characterization assays, diagnosis, and preventive and curative strategies). A rapid process to obtain a native-like antigen by solubilization of a full-length MP directly from a pathogen is reported herein. Rabies virus (RABV) was used as a model for this demonstration and its full-length G glycoprotein (RABV-G) was stabilized with amphipathic polymers, named amphipols (APols). The stability of RABV-G trapped in APol A8-35 (RABV-G/A8-35) was evaluated under different stress conditions (temperature, agitation, and light exposure). RABV-G/A8-35 in liquid form exhibited higher unfolding temperature (+6°C) than in detergent and was demonstrated to be antigenically stable over 1 month at 5°C and 25°C. Kinetic modeling of antigenicity data predicted antigenic stability of RABV-G/A8-35 in a solution of up to 1 year at 5°C. The RABV-G/A8-35 complex formulated in an optimized buffer composition and subsequently freeze-dried displayed long-term stability for 2-years at 5, 25, and 37°C. This study reports for the first time that a natural full-length MP extracted from a virus, complexed to APols and subsequently freeze-dried, displayed long-term antigenic stability, without requiring storage under refrigerated conditions.
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Affiliation(s)
- Didier Clénet
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Léna Clavier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Benoît Strobbe
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France
| | - Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Manuela Zoonens
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS, Institut de Biologie Physico-Chimique, Université de Paris, Paris, France
| | - Aure Saulnier
- Bioprocess R&D Department, Sanofi Pasteur, Marcy l'Etoile, France.,Department of Analytical Sciences, Sanofi Pasteur, Marcy l'Etoile, France
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8
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Hutchison JM, Capone R, Luu DD, Shah KH, Hadziselimovic A, Van Horn WD, Sanders CR. Recombinant SARS-CoV-2 envelope protein traffics to the trans-Golgi network following amphipol-mediated delivery into human cells. J Biol Chem 2021; 297:100940. [PMID: 34237302 PMCID: PMC8256659 DOI: 10.1016/j.jbc.2021.100940] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 11/16/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 envelope protein (S2-E) is a conserved membrane protein that is important for coronavirus (CoV) assembly and budding. Here, we describe the recombinant expression and purification of S2-E in amphipol-class amphipathic polymer solutions, which solubilize and stabilize membrane proteins, but do not disrupt membranes. We found that amphipol delivery of S2-E to preformed planar bilayers results in spontaneous membrane integration and formation of viroporin cation channels. Amphipol delivery of the S2-E protein to human cells results in plasma membrane integration, followed by retrograde trafficking to the trans-Golgi network and accumulation in swollen perinuclear lysosomal-associated membrane protein 1-positive vesicles, likely lysosomes. CoV envelope proteins have previously been proposed to manipulate the luminal pH of the trans-Golgi network, which serves as an accumulation station for progeny CoV particles prior to cellular egress via lysosomes. Delivery of S2-E to cells will enable chemical biological approaches for future studies of severe acute respiratory syndrome coronavirus 2 pathogenesis and possibly even development of "Trojan horse" antiviral therapies. Finally, this work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.
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Affiliation(s)
- James M Hutchison
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, Tennessee, USA; Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - Ricardo Capone
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Dustin D Luu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Karan H Shah
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Arina Hadziselimovic
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA
| | - Wade D Van Horn
- School of Molecular Sciences, Arizona State University, Tempe, Arizona, USA; The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA.
| | - Charles R Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA; Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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9
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Therapeutic Antibodies Targeting Potassium Ion Channels. Handb Exp Pharmacol 2021; 267:507-545. [PMID: 33963460 DOI: 10.1007/164_2021_464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Monoclonal antibodies combine specificity and high affinity binding with excellent pharmacokinetic properties and are rapidly being developed for a wide range of drug targets including clinically important potassium ion channels. Nonetheless, while therapeutic antibodies come with great promise, K+ channels represent particularly difficult targets for biologics development for a variety of reasons that include their dynamic structures and relatively small extracellular loops, their high degree of sequence conservation (leading to immune tolerance), and their generally low-level expression in vivo. The process is made all the more difficult when large numbers of antibody candidates must be screened for a given target, or when lead candidates fail to cross-react with orthologous channels in animal disease models due to their highly selective binding properties. While the number of antibodies targeting potassium channels in preclinical or clinical development is still modest, significant advances in the areas of protein expression and antibody screening are converging to open the field to an avalanche of new drugs. Here, the opportunities and constraints associated with the discovery of antibodies against K+ channels are discussed, with an emphasis on novel technologies that are opening the field to exciting new possibilities for biologics development.
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10
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Shukla MK, Watanabe A, Wilson S, Giovagnetti V, Moustafa EI, Minagawa J, Ruban AV. A novel method produces native light-harvesting complex II aggregates from the photosynthetic membrane revealing their role in nonphotochemical quenching. J Biol Chem 2021; 295:17816-17826. [PMID: 33454016 DOI: 10.1074/jbc.ra120.016181] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/15/2020] [Indexed: 01/31/2023] Open
Abstract
Nonphotochemical quenching (NPQ) is a mechanism of regulating light harvesting that protects the photosynthetic apparatus from photodamage by dissipating excess absorbed excitation energy as heat. In higher plants, the major light-harvesting antenna complex (LHCII) of photosystem (PS) II is directly involved in NPQ. The aggregation of LHCII is proposed to be involved in quenching. However, the lack of success in isolating native LHCII aggregates has limited the direct interrogation of this process. The isolation of LHCII in its native state from thylakoid membranes has been problematic because of the use of detergent, which tends to dissociate loosely bound proteins, and the abundance of pigment-protein complexes (e.g. PSI and PSII) embedded in the photosynthetic membrane, which hinders the preparation of aggregated LHCII. Here, we used a novel purification method employing detergent and amphipols to entrap LHCII in its natural states. To enrich the photosynthetic membrane with the major LHCII, we used Arabidopsis thaliana plants lacking the PSII minor antenna complexes (NoM), treated with lincomycin to inhibit the synthesis of PSI and PSII core proteins. Using sucrose density gradients, we succeeded in isolating the trimeric and aggregated forms of LHCII antenna. Violaxanthin- and zeaxanthin-enriched complexes were investigated in dark-adapted, NPQ, and dark recovery states. Zeaxanthin-enriched antenna complexes showed the greatest amount of aggregated LHCII. Notably, the amount of aggregated LHCII decreased upon relaxation of NPQ. Employing this novel preparative method, we obtained a direct evidence for the role of in vivo LHCII aggregation in NPQ.
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Affiliation(s)
- Mahendra K Shukla
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Akimasa Watanabe
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Sam Wilson
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Vasco Giovagnetti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Ece Imam Moustafa
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, The Graduate University for Advanced Studies, Okazaki, Japan.
| | - Alexander V Ruban
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
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11
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Hutchison JM, Capone R, Luu DD, Hadziselimovic A, Van Horn WD, Sanders CR. Delivery of recombinant SARS-CoV-2 envelope protein into human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.18.431684. [PMID: 33619482 PMCID: PMC7899446 DOI: 10.1101/2021.02.18.431684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 envelope protein (S2-E) is a conserved membrane protein that is essential to coronavirus assembly and budding. Here, we describe the recombinant expression and purification of S2-E into amphipol-class amphipathic polymer solutions. The physical properties of amphipols underpin their ability to solubilize and stabilize membrane proteins without disrupting membranes. Amphipol delivery of S2-E to pre-formed planar bilayers results in spontaneous membrane integration and formation of viroporin ion channels. Amphipol delivery of the S2-E protein to human cells results in membrane integration followed by retrograde trafficking to a location adjacent to the endoplasmic reticulum-to-Golgi intermediate compartment (ERGIC) and the Golgi, which are the sites of coronavirus replication. Delivery of S2-E to cells enables both chemical biological approaches for future studies of SARS-CoV-2 pathogenesis and development of "Trojan Horse" anti-viral therapies. This work also establishes a paradigm for amphipol-mediated delivery of membrane proteins to cells.
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Affiliation(s)
- James M. Hutchison
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, 37240 USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
| | - Ricardo Capone
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
| | - Dustin D. Luu
- School of Molecular Sciences, Arizona State University,Tempe, AZ 85287 USA
- The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Arina Hadziselimovic
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
| | - Wade D. Van Horn
- School of Molecular Sciences, Arizona State University,Tempe, AZ 85287 USA
- The Biodesign Institute Centers for Personalized Diagnostics and Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281 USA
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37240 USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232 USA
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12
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Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
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Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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13
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Han S, Choi S, Kim NH, Kang S, Yu YG. Use of a Poly‐γ‐Glutamic Acid‐Derived Amphipathic Polypeptide for the Reconstitution of Membrane Proteins. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.12038] [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)
- Seong‐Gu Han
- Department of ChemistryKookmin University 861‐1 Jeongneung‐dong Seongbuk‐gu, Seoul 136‐702 Republic of Korea
| | - Saet‐Byeol Choi
- Department of ChemistryKookmin University 861‐1 Jeongneung‐dong Seongbuk‐gu, Seoul 136‐702 Republic of Korea
| | - Nam Hyuk Kim
- Department of ChemistryKookmin University 861‐1 Jeongneung‐dong Seongbuk‐gu, Seoul 136‐702 Republic of Korea
| | - Sumin Kang
- Department of ChemistryKookmin University 861‐1 Jeongneung‐dong Seongbuk‐gu, Seoul 136‐702 Republic of Korea
| | - Yeon Gyu Yu
- Department of ChemistryKookmin University 861‐1 Jeongneung‐dong Seongbuk‐gu, Seoul 136‐702 Republic of Korea
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14
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Kehlenbeck DM, Josts I, Nitsche J, Busch S, Forsyth VT, Tidow H. Comparison of lipidic carrier systems for integral membrane proteins - MsbA as case study. Biol Chem 2020; 400:1509-1518. [PMID: 31141477 DOI: 10.1515/hsz-2019-0171] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/15/2019] [Indexed: 01/13/2023]
Abstract
Membrane protein research suffers from the drawback that detergents, which are commonly used to solubilize integral membrane proteins (IMPs), often lead to protein instability and reduced activity. Recently, lipid nanodiscs (NDs) and saposin-lipoprotein particles (Salipro) have emerged as alternative carrier systems that keep membrane proteins in a native-like lipidic solution environment and are suitable for biophysical and structural studies. Here, we systematically compare nanodiscs and Salipros with respect to long-term stability as well as activity and stability of the incorporated membrane protein using the ABC transporter MsbA as model system. Our results show that both systems are suitable for activity measurements as well as structural studies in solution. Based on our results we suggest screening of different lipids with respect to activity and stability of the incorporated IMP before performing structural studies.
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Affiliation(s)
- Dominique-Maurice Kehlenbeck
- The Hamburg Centre for Ultrafast Imaging and Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Inokentijs Josts
- The Hamburg Centre for Ultrafast Imaging and Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Julius Nitsche
- The Hamburg Centre for Ultrafast Imaging and Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht, Lichtenbergstr. 1, 85747 Garching bei München, Germany
| | - V Trevor Forsyth
- Life Sciences Group, Institut Laue-Langevin, 6 Rue Jules Horowitz, 38042 Grenoble, France.,School of Life Sciences, Keele University, Staffordshire ST5 5BG, England
| | - Henning Tidow
- The Hamburg Centre for Ultrafast Imaging and Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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15
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Wiseman DN, Otchere A, Patel JH, Uddin R, Pollock NL, Routledge SJ, Rothnie AJ, Slack C, Poyner DR, Bill RM, Goddard AD. Expression and purification of recombinant G protein-coupled receptors: A review. Protein Expr Purif 2020; 167:105524. [PMID: 31678667 PMCID: PMC6983937 DOI: 10.1016/j.pep.2019.105524] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 01/15/2023]
Abstract
Given their extensive role in cell signalling, GPCRs are significant drug targets; despite this, many of these receptors have limited or no available prophylaxis. Novel drug design and discovery significantly rely on structure determination, of which GPCRs are typically elusive. Progress has been made thus far to produce sufficient quantity and quality of protein for downstream analysis. As such, this review highlights the systems available for recombinant GPCR expression, with consideration of their advantages and disadvantages, as well as examples of receptors successfully expressed in these systems. Additionally, an overview is given on the use of detergents and the styrene maleic acid (SMA) co-polymer for membrane solubilisation, as well as purification techniques.
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Affiliation(s)
- Daniel N Wiseman
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Abigail Otchere
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Jaimin H Patel
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Romez Uddin
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | | | - Sarah J Routledge
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Cathy Slack
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - David R Poyner
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Roslyn M Bill
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Alan D Goddard
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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16
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Chill JH, Qasim A, Sher I, Gross R. NMR Perspectives of the KcsA Potassium Channel in the Membrane Environment. Isr J Chem 2019. [DOI: 10.1002/ijch.201900107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordan H. Chill
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Arwa Qasim
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Inbal Sher
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
| | - Renana Gross
- Department of ChemistryBar Ilan University Ramat Gan 52900 Israel
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17
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Saouros S, Cecchetti C, Jones A, Cameron AD, Byrne B. Strategies for successful isolation of a eukaryotic transporter. Protein Expr Purif 2019; 166:105522. [PMID: 31654736 DOI: 10.1016/j.pep.2019.105522] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/18/2019] [Accepted: 10/20/2019] [Indexed: 11/24/2022]
Abstract
The isolation of integral membrane proteins for structural analysis remains challenging and this is particularly the case for eukaryotic membrane proteins. Here we describe our efforts to isolate OsBOR3, a boron transporter from Oryza sativa. OsBOR3 was expressed as both full length and a C-terminally truncated form lacking residues 643-672 (OsBOR3Δ1-642). While both express well as C-terminal GFP fusion proteins in Saccharomyces cerevisiae, the full length protein isolates poorly in the detergent dodecyl-β-d-maltoside (DDM). The OsBOR3Δ1-642 isolated in DDM in large quantities but was contaminated with GFP tagged protein, indicated incomplete protease removal of the tag. Addition of the reducing agent dithiothreitol (DTT) had no effect on isolation. Detergent screening indicated that the neopentyl glycol detergents, LMNG, UDMNG and DMNG conferred greater stability on the OsBOR3Δ1-642 than DDM. Isolation of OsBOR3Δ1-642 in LMNG both in the presence and absence of DTT produced large quantities of protein but contaminated with GFP tagged protein. Isolation of OsBOR3Δ1-642 in DMNG + DTT resulted in protein sample that does not contain any detectable GFP but elutes at a higher retention volume than that seen for protein isolated in either DDM or LMNG. Mass spectrometry confirmed that the LMNG and DMNG purified protein is OsBOR3Δ1-642 indicating that the DMNG isolated protein is monomer compared to the dimer isolated using LMNG. This was further supported by single particle electron microscopic analysis revealing that the DMNG protein particles are roughly half the size of the LMNG protein particles.
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Affiliation(s)
- Savvas Saouros
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Cristina Cecchetti
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Alex Jones
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Alexander D Cameron
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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18
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Klöpfer K, Hagn F. Beyond detergent micelles: The advantages and applications of non-micellar and lipid-based membrane mimetics for solution-state NMR. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:271-283. [PMID: 31779883 DOI: 10.1016/j.pnmrs.2019.08.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 06/10/2023]
Abstract
Membrane proteins are important players in signal transduction and the exchange of metabolites within or between cells. Thus, this protein class is the target of around 60 % of currently marketed drugs, emphasizing their essential biological role. Besides functional assays, structural and dynamical investigations on this protein class are crucial to fully understanding their functionality. Even though X-ray crystallography and electron microscopy are the main methods to determine structures of membrane proteins and their complexes, NMR spectroscopy can contribute essential information on systems that (a) do not crystallize and (b) are too small for EM. Furthermore, NMR is a versatile tool for monitoring functional dynamics of biomolecules at various time scales. A crucial aspect of such studies is the use of a membrane mimetic that resembles a native environment and thus enables the extraction of functional insights. In recent decades, the membrane protein NMR community has moved from rather harsh detergents to membrane systems having more native-like properties. In particular, most recently phospholipid nanodiscs have been developed and optimized mainly for solution-state NMR but are now also being used for solid-state NMR spectroscopy. Nanodiscs consist of a patch of a planar lipid bilayer that is encircled by different (bio-)polymers to form particles of defined and tunable size. In this review, we provide an overview of available membrane mimetics, including nanodiscs, amphipols and bicelles, that are suitable for high-resolution NMR spectroscopy and describe how these advanced membrane mimetics can facilitate NMR studies on the structure and dynamics of membrane proteins. Since the stability of membrane proteins depends critically on the chosen membrane mimetic, we emphasize the importance of a suitable system that is not necessarily developed for solution-state NMR applications and hence requires optimization for each membrane protein. However, lipid-based membrane mimetics offer the possibility of performing NMR experiments at elevated temperatures and studying ligand and partner protein complexes as well as their functional dynamics in a realistic membrane environment. In order to be able to make an informed decision during the selection of a suitable membrane system, we provide a detailed overview of the available options for various membrane protein classes and thereby facilitate this often-difficult selection process for a broad range of desired NMR applications.
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Affiliation(s)
- Kai Klöpfer
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Str. 2, 85747 Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.
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19
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Zhang Q, Cherezov V. Chemical tools for membrane protein structural biology. Curr Opin Struct Biol 2019; 58:278-285. [PMID: 31285102 DOI: 10.1016/j.sbi.2019.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 01/24/2023]
Abstract
Solving high-resolution structures of membrane proteins has been an important challenge for decades, still lagging far behind that of soluble proteins even with the recent remarkable technological advances in X-ray crystallography and electron microscopy. Central to this challenge is the necessity to isolate and solubilize membrane proteins in a stable, natively folded and functional state, a process influenced by not only the proteins but also their surrounding chemical environment. This review highlights recent community efforts in the development and characterization of novel membrane agents and ligand tools to stabilize individual proteins and protein complexes, which together have accelerated progress in membrane protein structural biology.
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Affiliation(s)
- Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Vadim Cherezov
- Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
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20
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Autzen HE, Julius D, Cheng Y. Membrane mimetic systems in CryoEM: keeping membrane proteins in their native environment. Curr Opin Struct Biol 2019; 58:259-268. [PMID: 31279500 DOI: 10.1016/j.sbi.2019.05.022] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 05/24/2019] [Accepted: 05/27/2019] [Indexed: 01/02/2023]
Abstract
Advances in electron microscopes, detectors and data processing algorithms have greatly facilitated the structural determination of many challenging integral membrane proteins that have been evasive to crystallization. These breakthroughs facilitate the application and development of various membrane protein solubilization approaches for structural studies, including reconstitution into lipid nanoparticles. In this review, we discuss various approaches for preparing transmembrane proteins for structural determination with single-particle electron cryo microscopy (cryoEM).
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Affiliation(s)
- Henriette E Autzen
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - David Julius
- Department of Physiology, University of California, San Francisco, CA 94143, USA.
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, CA 94143, USA.
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21
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Chowdhury S, Rakshit A, Acharjee A, Saha B. Novel Amphiphiles and Their Applications for Different Purposes with Special Emphasis on Polymeric Surfactants. ChemistrySelect 2019. [DOI: 10.1002/slct.201901160] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Suman Chowdhury
- Homogeneous Catalysis LaboratoryDepartment Of ChemistryThe University Of Burdwan, Golapbag, Burdwan, Pin - 713104 West Bengal India
| | - Atanu Rakshit
- Homogeneous Catalysis LaboratoryDepartment Of ChemistryThe University Of Burdwan, Golapbag, Burdwan, Pin - 713104 West Bengal India
| | - Animesh Acharjee
- Homogeneous Catalysis LaboratoryDepartment Of ChemistryThe University Of Burdwan, Golapbag, Burdwan, Pin - 713104 West Bengal India
| | - Bidyut Saha
- Homogeneous Catalysis LaboratoryDepartment Of ChemistryThe University Of Burdwan, Golapbag, Burdwan, Pin - 713104 West Bengal India
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22
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Machale J, Majumder SK, Ghosh P, Sen TK. Role of chemical additives and their rheological properties in enhanced oil recovery. REV CHEM ENG 2019. [DOI: 10.1515/revce-2018-0033] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
A significant amount of oil (i.e. 60–70%) remains trapped in reservoirs after the conventional primary and secondary methods of oil recovery. Enhanced oil recovery (EOR) methods are therefore necessary to recover the major fraction of unrecovered trapped oil from reservoirs to meet the present-day energy demands. The chemical EOR method is one of the promising methods where various chemical additives, such as alkalis, surfactants, polymer, and the combination of all alkali–surfactant–polymer (ASP) or surfactant–polymer (SP) solutions, are injected into the reservoir to improve the displacement and sweep efficiency. Every oil field has different conditions, which imposes new challenges toward alternative but more effective EOR techniques. Among such attractive alternative additives are polymeric surfactants, natural surfactants, nanoparticles, and self-assembled polymer systems for EOR. In this paper, water-soluble chemical additives such as alkalis, surfactants, polymer, and ASP or SP solution for chemical EOR are highlighted. This review also discusses the concepts and techniques related to the chemical methods of EOR, and highlights the rheological properties of the chemicals involved in the efficiency of EOR methods.
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Affiliation(s)
- Jinesh Machale
- Department of Chemical Engineering , Indian Institute of Technology Guwahati , Guwahati 781039, Assam , India
| | - Subrata Kumar Majumder
- Department of Chemical Engineering , Indian Institute of Technology Guwahati , Guwahati 781039, Assam , India
| | - Pallab Ghosh
- Department of Chemical Engineering , Indian Institute of Technology Guwahati , Guwahati 781039, Assam , India
| | - Tushar Kanti Sen
- Department of Chemical Engineering , Curtin University , GPO Box U1987 , Perth, WA 6845 , Australia
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23
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Perry TN, Souabni H, Rapisarda C, Fronzes R, Giusti F, Popot JL, Zoonens M, Gubellini F. BAmSA: Visualising transmembrane regions in protein complexes using biotinylated amphipols and electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:466-477. [DOI: 10.1016/j.bbamem.2018.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/06/2018] [Accepted: 11/08/2018] [Indexed: 12/30/2022]
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24
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Arunmanee W, Heenan RK, Lakey JH. Determining the amphipol distribution within membrane-protein fibre samples using small-angle neutron scattering. Acta Crystallogr D Struct Biol 2018; 74:1192-1199. [PMID: 30605133 PMCID: PMC6317593 DOI: 10.1107/s205979831800476x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/22/2018] [Indexed: 11/10/2022] Open
Abstract
Detergent micelles can solubilize membrane proteins, but there is always a need for a pool of free detergent at the critical micellar concentration to maintain the micelle-monomer equilibrium. Amphipol polymeric surfactants (APols) have been developed to replace conventional detergents in membrane-protein studies, but the role of free amphipol is unclear. It has previously been shown that the removal of free APol causes monodisperse outer membrane protein F (OmpF) to form long filaments. However, any remaining APol could not be resolved using electron microscopy. Here, small-angle neutron scattering with isotope contrast matching was used to separately determine the distributions of membrane protein and amphipol in a mixed sample. The data showed that after existing free amphipol had been removed from monodisperse complexes, a new equilibrium was established between protein-amphipol filaments and a pool of newly liberated free amphipol. The filaments consisted of OmpF proteins surrounded by a belt of Apol, whilst free oblate spheroid micelles of Apol were also present. No indications of long-range order were observed, suggesting a lack of defined structure in the filaments.
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Affiliation(s)
- Wanatchaporn Arunmanee
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Richard K Heenan
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, England
| | - Jeremy H Lakey
- Institute for Cell and Molecular Bioscience, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, England
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25
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Successful amphiphiles as the key to crystallization of membrane proteins: Bridging theory and practice. Biochim Biophys Acta Gen Subj 2018; 1863:437-455. [PMID: 30419284 DOI: 10.1016/j.bbagen.2018.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Membrane proteins constitute a major group of proteins and are of great significance as pharmaceutical targets, but underrepresented in the Protein Data Bank. Particular reasons are their low expression yields and the constant need for cautious and diligent handling in a sufficiently stable hydrophobic environment substituting for the native membrane. When it comes to protein crystallization, such an environment is often established by detergents. SCOPE OF REVIEW In this review, 475 unique membrane protein X-ray structures from the online data bank "Membrane proteins of known 3D structure" are presented with a focus on the detergents essential for protein crystallization. By systematic analysis of the most successful compounds, including current trends in amphiphile development, we provide general insights for selection and design of detergents for membrane protein crystallization. MAJOR CONCLUSIONS The most successful detergents share common features, giving rise to favorable protein interactions. The hydrophile-lipophile balance concept of well-balanced hydrophilic and hydrophobic detergent portions is still the key to successful protein crystallization. Although a single detergent compound is sufficient in most cases, sometimes a suitable mixture of detergents has to be found to alter the resulting protein-detergent complex. Protein crystals with a high diffraction limit involve a tight crystal packing generally favored by detergents with shorter alkyl chains. GENERAL SIGNIFICANCE The formation of well-diffracting membrane protein crystals strongly depends on suitable surfactants, usually screened in numerous crystallization trials. The here-presented findings provide basic criteria for the assessment of surfactants within the vast space of potential crystallization conditions for membrane proteins.
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26
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Serra-Batiste M, Tolchard J, Giusti F, Zoonens M, Carulla N. Stabilization of a Membrane-Associated Amyloid-β Oligomer for Its Validation in Alzheimer's Disease. Front Mol Biosci 2018; 5:38. [PMID: 29725595 PMCID: PMC5917194 DOI: 10.3389/fmolb.2018.00038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/28/2018] [Indexed: 11/13/2022] Open
Abstract
We have recently reported on the preparation of a membrane-associated β-barrel Pore-Forming Aβ42 Oligomer (βPFOAβ42). It corresponds to a stable and homogeneous Aβ42 oligomer that inserts into lipid bilayers as a well-defined pore and adopts a specific structure with characteristics of a β-barrel arrangement. As a follow-up of this work, we aim to establish βPFOAβ42's relevance in Alzheimer's disease (AD). However, βPFOAβ42 is formed under dodecyl phosphocholine (DPC) micelle conditions-intended to mimic the hydrophobic environment of membranes-which are dynamic. Consequently, dilution of the βPFOAβ42/DPC complex in a detergent-free buffer leads to dispersion of the DPC molecules from the oligomer surface, leaving the oligomer without the hydrophobic micelle belt that stabilizes it. Since dilution is required for any biological test, transfer of βPFOAβ42 from DPC micelles into another hydrophobic biomimetic membrane environment, that remains associated with βPFOAβ42 even under high dilution conditions, is a requisite for the validation of βPFOAβ42 in AD. Here we describe conditions for exchanging DPC micelles with amphipols (APols), which are amphipathic polymers designed to stabilize membrane proteins in aqueous solutions. APols bind in an irreversible but non-covalent manner to the hydrophobic surface of membrane proteins preserving their structure even under extreme dilution conditions. We tested three types of APols with distinct physical-chemical properties and found that the βPFOAβ42/DPC complex can only be trapped in non-ionic APols (NAPols). The characterization of the resulting βPFOAβ42/NAPol complex by biochemical tools and structural biology techniques allowed us to establish that the oligomer structure is maintained even under high dilution. Based on these findings, this work constitutes a first step towards the in vivo validation of βPFOAβ42 in AD.
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Affiliation(s)
- Montserrat Serra-Batiste
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain
| | - James Tolchard
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain.,CBMN (UMR 5248), Centre National de la Recherche Scientifique - IPB, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
| | - Fabrice Giusti
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires (UMR 7099), Université Paris-7 - Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires (UMR 7099), Université Paris-7 - Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Paris, France
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute Science and Technology (BIST), Barcelona, Spain.,CBMN (UMR 5248), Centre National de la Recherche Scientifique - IPB, Institut Européen de Chimie et Biologie, University of Bordeaux, Pessac, France
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27
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Le Bon C, Marconnet A, Masscheleyn S, Popot JL, Zoonens M. Folding and stabilizing membrane proteins in amphipol A8-35. Methods 2018; 147:95-105. [PMID: 29678587 DOI: 10.1016/j.ymeth.2018.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/06/2018] [Accepted: 04/13/2018] [Indexed: 01/07/2023] Open
Abstract
Membrane proteins (MPs) are important pharmacological targets because of their involvement in many essential cellular processes whose dysfunction can lead to a large variety of diseases. A detailed knowledge of the structure of MPs and the molecular mechanisms of their activity is essential to the design of new therapeutic agents. However, studying MPs in vitro is challenging, because it generally implies their overexpression under a functional form, followed by their extraction from membranes and purification. Targeting an overexpressed MP to a membrane is often toxic and expression yields tend to be limited. One alternative is the formation of inclusion bodies (IBs) in the cytosol of the cell, from which MPs need then to be folded to their native conformation before structural and functional analysis can be contemplated. Folding MPs targeted to IBs is a difficult task. Specially designed amphipathic polymers called 'amphipols' (APols), which have been initially developed with the view of improving the stability of MPs in aqueous solutions compared to detergents, can be used to fold both α-helical and β-barrel MPs. APols represent an interesting novel amphipathic medium, in which high folding yields can be achieved. In this review, the properties of APol A8-35 and of the complexes they form with MPs are summarized. An overview of the most important studies reported so far using A8-35 to fold MPs is presented. Finally, from a practical point of view, a detailed description of the folding and trapping methods is given.
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Affiliation(s)
- Christel Le Bon
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Anaïs Marconnet
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Sandrine Masscheleyn
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Jean-Luc Popot
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Manuela Zoonens
- CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France.
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28
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Panganiban B, Qiao B, Jiang T, DelRe C, Obadia MM, Nguyen TD, Smith AAA, Hall A, Sit I, Crosby MG, Dennis PB, Drockenmuller E, Olvera de la Cruz M, Xu T. Random heteropolymers preserve protein function in foreign environments. Science 2018; 359:1239-1243. [DOI: 10.1126/science.aao0335] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 01/25/2018] [Indexed: 12/25/2022]
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29
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Hu Z, Ho JC, Nallani M. Synthetic (polymer) biology (membrane): functionalization of polymer scaffolds for membrane proteins. Curr Opin Biotechnol 2017; 46:51-56. [DOI: 10.1016/j.copbio.2016.10.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 10/24/2016] [Indexed: 12/13/2022]
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30
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Uner A, Doganci E, Tasdelen MA, Yilmaz F, Gürek AG. Synthesis, characterization and surface properties of star-shaped polymeric surfactants with polyhedral oligomeric silsesquioxane core. POLYM INT 2017. [DOI: 10.1002/pi.5420] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ahmet Uner
- Department of Chemistry; Gebze Technical University, Gebze; Kocaeli Turkey
| | - Erdinc Doganci
- Department of Chemistry and Chemical Processing Technology; Kocaeli University; Kocaeli Turkey
| | | | | | - Ayşe Gül Gürek
- Department of Chemistry; Gebze Technical University, Gebze; Kocaeli Turkey
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31
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Xu X, Kanduč M, Wu J, Dzubiella J. Potential of mean force and transient states in polyelectrolyte pair complexation. J Chem Phys 2017; 145:034901. [PMID: 27448900 DOI: 10.1063/1.4958675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The pair association between two polyelectrolytes (PEs) of the same size but opposite charge is systematically studied in terms of the potential of mean force (PMF) along their center-of-mass reaction coordinate via coarse-grained, implicit-solvent, explicit-salt computer simulations. The focus is set on the onset and the intermediate transient stages of complexation. At conditions above the counterion-condensation threshold, the PE association process exhibits a distinct sliding-rod-like behavior where the polymer chains approach each other by first stretching out at a critical distance close to their contour length, then "shaking hand" and sliding along each other in a parallel fashion, before eventually folding into a neutral complex. The essential part of the PMF for highly charged PEs can be very well described by a simple theory based on sliding charged "Debye-Hückel" rods with renormalized charges in addition to an explicit entropy contribution owing to the release of condensed counterions. Interestingly, at the onset of complex formation, the mean force between the PE chains is found to be discontinuous, reflecting a bimodal structural behavior that arises from the coexistence of interconnected-rod and isolated-coil states. These two microstates of the PE complex are balanced by subtle counterion release effects and separated by a free-energy barrier due to unfavorable stretching entropy.
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Affiliation(s)
- Xiao Xu
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany
| | - Matej Kanduč
- Institut für Weiche Materie und Funktionale Materialien, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - Jianzhong Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstr. 15, 12489 Berlin, Germany
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32
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Watkinson TG, Calabrese AN, Ault JR, Radford SE, Ashcroft AE. FPOP-LC-MS/MS Suggests Differences in Interaction Sites of Amphipols and Detergents with Outer Membrane Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:50-55. [PMID: 27343183 PMCID: PMC5174144 DOI: 10.1007/s13361-016-1421-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/10/2016] [Accepted: 05/11/2016] [Indexed: 05/24/2023]
Abstract
Amphipols are a class of novel surfactants that are capable of stabilizing the native state of membrane proteins. They have been shown to be highly effective, in some cases more so than detergent micelles, at maintaining the structural integrity of membrane proteins in solution, and have shown promise as vehicles for delivering native membrane proteins into the gas phase for structural interrogation. Here, we use fast photochemical oxidation of proteins (FPOP), which irreversibly labels the side chains of solvent-accessible residues with hydroxyl radicals generated by laser photolysis of hydrogen peroxide, to compare the solvent accessibility of the outer membrane protein OmpT when solubilized with the amphipol A8-35 or with n-dodecyl-β-maltoside (DDM) detergent micelles. Using quantitative mass spectrometry analyses, we show that fast photochemical oxidation reveals differences in the extent of solvent accessibility of residues between the A8-35 and DDM solubilized states, providing a rationale for the increased stability of membrane proteins solubilized with amphipol compared with detergent micelles, as a result of additional intermolecular contacts. Graphical Abstract ᅟ.
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Affiliation(s)
- Thomas G Watkinson
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - James R Ault
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Alison E Ashcroft
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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33
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Artificial membranes for membrane protein purification, functionality and structure studies. Biochem Soc Trans 2016; 44:877-82. [DOI: 10.1042/bst20160054] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Indexed: 11/17/2022]
Abstract
Membrane proteins represent one of the most important targets for pharmaceutical companies. Unfortunately, technical limitations have long been a major hindrance in our understanding of the function and structure of such proteins. Recent years have seen the refinement of classical approaches and the emergence of new technologies that have resulted in a significant step forward in the field of membrane protein research. This review summarizes some of the current techniques used for studying membrane proteins, with overall advantages and drawbacks for each method.
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34
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Yigit C, Heyda J, Ballauff M, Dzubiella J. Like-charged protein-polyelectrolyte complexation driven by charge patches. J Chem Phys 2016; 143:064905. [PMID: 26277164 DOI: 10.1063/1.4928078] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the pair complexation of a single, highly charged polyelectrolyte (PE) chain (of 25 or 50 monomers) with like-charged patchy protein models (CPPMs) by means of implicit-solvent, explicit-salt Langevin dynamics computer simulations. Our previously introduced set of CPPMs embraces well-defined zero-, one-, and two-patched spherical globules each of the same net charge and (nanometer) size with mono- and multipole moments comparable to those of globular proteins with similar size. We observe large binding affinities between the CPPM and the like-charged PE in the tens of the thermal energy, kBT, that are favored by decreasing salt concentration and increasing charge of the patch(es). Our systematic analysis shows a clear correlation between the distance-resolved potentials of mean force, the number of ions released from the PE, and CPPM orientation effects. In particular, we find a novel two-site binding behavior for PEs in the case of two-patched CPPMs, where intermediate metastable complex structures are formed. In order to describe the salt-dependence of the binding affinity for mainly dipolar (one-patched) CPPMs, we introduce a combined counterion-release/Debye-Hückel model that quantitatively captures the essential physics of electrostatic complexation in our systems.
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Affiliation(s)
- Cemil Yigit
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, 166 28 Praha 6, Czech Republic
| | - Matthias Ballauff
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany
| | - Joachim Dzubiella
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin, 14109 Berlin, Germany
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35
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Abstract
Which properties of the membrane environment are essential for the folding and oligomerization of transmembrane proteins? Because the lipids that surround membrane proteins in situ spontaneously organize into bilayers, it may seem intuitive that interactions with the bilayer provide both hydrophobic and topological constraints that help the protein to achieve a stable and functional three-dimensional structure. However, one may wonder whether folding is actually driven by the membrane environment or whether the folded state just reflects an adaptation of integral proteins to the medium in which they function. Also, apart from the overall transmembrane orientation, might the asymmetry inherent in biosynthesis processes cause proteins to fold to out-of-equilibrium, metastable topologies? Which of the features of a bilayer are essential for membrane protein folding, and which are not? To which extent do translocons dictate transmembrane topologies? Recent data show that many membrane proteins fold and oligomerize very efficiently in media that bear little similarity to a membrane, casting doubt on the essentiality of many bilayer constraints. In the following discussion, we argue that some of the features of bilayers may contribute to protein folding, stability and regulation, but they are not required for the basic three-dimensional structure to be achieved. This idea, if correct, would imply that evolution has steered membrane proteins toward an accommodation to biosynthetic pathways and a good fit into their environment, but that their folding is not driven by the latter or dictated by insertion apparatuses. In other words, the three-dimensional structure of membrane proteins is essentially determined by intramolecular interactions and not by bilayer constraints and insertion pathways. Implications are discussed.
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Affiliation(s)
- Jean-Luc Popot
- Centre National de la Recherche Scientifique/Université Paris-7 UMR 7099 , Institut de Biologie Physico-Chimique (FRC 550), 13, rue Pierre-et-Marie-Curie, F-75005 Paris, France
| | - Donald M Engelman
- Department of Molecular Biophysics and Biochemistry, Yale University , Box 208114, New Haven, Connecticut 06520-8114, United States
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36
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Tu Y, Peng F, Adawy A, Men Y, Abdelmohsen LKEA, Wilson DA. Mimicking the Cell: Bio-Inspired Functions of Supramolecular Assemblies. Chem Rev 2015; 116:2023-78. [DOI: 10.1021/acs.chemrev.5b00344] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yingfeng Tu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Fei Peng
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Alaa Adawy
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yongjun Men
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Loai K. E. A. Abdelmohsen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Daniela A. Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
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37
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Giusti F, Kessler P, Hansen RW, Della Pia EA, Le Bon C, Mourier G, Popot JL, Martinez KL, Zoonens M. Synthesis of a Polyhistidine-bearing Amphipol and its Use for Immobilizing Membrane Proteins. Biomacromolecules 2015; 16:3751-61. [DOI: 10.1021/acs.biomac.5b01010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fabrice Giusti
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Pascal Kessler
- CEA, Institut
de Biologie et de Technologies de Saclay, Service d’Ingénierie
Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Randi Westh Hansen
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Eduardo A. Della Pia
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Christel Le Bon
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Gilles Mourier
- CEA, Institut
de Biologie et de Technologies de Saclay, Service d’Ingénierie
Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Jean-Luc Popot
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
| | - Karen L. Martinez
- Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Manuela Zoonens
- Laboratoire de
Biologie Physico-Chimique des Protéines Membranaires, UMR 7099,
CNRS/Université Paris 7, Institut de Biologie Physico-Chimique
(FRC 550), 13 rue Pierre et Marie Curie, F−75005 Paris, France
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38
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Raffa P, Wever DAZ, Picchioni F, Broekhuis AA. Polymeric Surfactants: Synthesis, Properties, and Links to Applications. Chem Rev 2015; 115:8504-63. [PMID: 26182291 DOI: 10.1021/cr500129h] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Patrizio Raffa
- Department of Chemical Engineering-Product Technology, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Dutch Polymer Institute DPI , P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Diego Armando Zakarias Wever
- Department of Chemical Engineering-Product Technology, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.,Dutch Polymer Institute DPI , P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Francesco Picchioni
- Department of Chemical Engineering-Product Technology, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Antonius A Broekhuis
- Department of Chemical Engineering-Product Technology, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands
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39
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Mehmood S, Allison TM, Robinson CV. Mass Spectrometry of Protein Complexes: From Origins to Applications. Annu Rev Phys Chem 2015; 66:453-74. [DOI: 10.1146/annurev-physchem-040214-121732] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Timothy M. Allison
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
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40
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Abstract
Membrane proteins play an essential role in several biological processes like ion transport, signal transduction, and electron transfer to name a few. For structural and functional studies of integral membrane proteins, it is critically important to isolate proteins from the membrane using biological detergents. Detergents disrupt the native lipid components of the native membrane and encase the membrane protein in an unnatural environment in aqueous solution. However, a particular membrane protein is best solubilized in a specific detergent; therefore, screening for the optimal detergent is essential. Apart from keeping the membrane protein monodispered in solution, the detergent has to be compatible with downstream processes to isolate and characterize a membrane protein. Over the past several years, a number of membrane proteins have been successfully isolated for structural and functional studies that allowed an outline of general strategies for isolating a novel membrane protein of interest.
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Affiliation(s)
- Ankita Roy
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
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41
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Baker MR, Fan G, Serysheva II. Single-Particle Cryo-EM of the Ryanodine Receptor Channel in an Aqueous Environment. Eur J Transl Myol 2015; 25:4803. [PMID: 26913144 PMCID: PMC4748972 DOI: 10.4081/ejtm.2015.4803] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/22/2014] [Accepted: 12/31/2014] [Indexed: 12/31/2022] Open
Abstract
Ryanodine receptors (RyRs) are tetrameric ligand-gated Ca2+ release channels that are responsible for the increase of cytosolic Ca2+ concentration leading to muscle contraction. Our current understanding of RyR channel gating and regulation is greatly limited due to the lack of a high-resolution structure of the channel protein. The enormous size and unwieldy shape of Ca2+ release channels make X-ray or NMR methods difficult to apply for high-resolution structural analysis of the full-length functional channel. Single-particle electron cryo-microscopy (cryo-EM) is one of the only effective techniques for the study of such a large integral membrane protein and its molecular interactions. Despite recent developments in cryo-EM technologies and break-through single-particle cryo-EM studies of ion channels, cryospecimen preparation, particularly the presence of detergent in the buffer, remains the main impediment to obtaining atomic-resolution structures of ion channels and a multitude of other integral membrane protein complexes. In this review we will discuss properties of several detergents that have been successfully utilized in cryo-EM studies of ion channels and the emergence of the detergent alternative amphipol to stabilize ion channels for structure-function characterization. Future structural studies of challenging specimen like ion channels are likely to be facilitated by cryo-EM amenable detergents or alternative surfactants.
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Affiliation(s)
- Mariah R Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Guizhen Fan
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Irina I Serysheva
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School at Houston, 6431 Fannin Street, Houston, TX 77030, USA
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42
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43
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Folding and stability of integral membrane proteins in amphipols. Arch Biochem Biophys 2014; 564:327-43. [PMID: 25449655 DOI: 10.1016/j.abb.2014.10.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 10/11/2014] [Accepted: 10/22/2014] [Indexed: 11/23/2022]
Abstract
Amphipols (APols) are a family of amphipathic polymers designed to keep transmembrane proteins (TMPs) soluble in aqueous solutions in the absence of detergent. APols have proven remarkably efficient at (i) stabilizing TMPs, as compared to detergent solutions, and (ii) folding them from a denatured state to a native, functional one. The underlying physical-chemical mechanisms are discussed.
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44
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Stangl M, Unger S, Keller S, Schneider D. Sequence-specific dimerization of a transmembrane helix in amphipol A8-35. PLoS One 2014; 9:e110970. [PMID: 25347769 PMCID: PMC4210147 DOI: 10.1371/journal.pone.0110970] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
As traditional detergents might destabilize or even denature membrane proteins, amphiphilic polymers have moved into the focus of membrane-protein research in recent years. Thus far, Amphipols are the best studied amphiphilic copolymers, having a hydrophilic backbone with short hydrophobic chains. However, since stabilizing as well as destabilizing effects of the Amphipol belt on the structure of membrane proteins have been described, we systematically analyze the impact of the most commonly used Amphipol A8-35 on the structure and stability of a well-defined transmembrane protein model, the glycophorin A transmembrane helix dimer. Amphipols are not able to directly extract proteins from their native membranes, and detergents are typically replaced by Amphipols only after protein extraction from membranes. As Amphipols form mixed micelles with detergents, a better understanding of Amphipol-detergent interactions is required. Therefore, we analyze the interaction of A8-35 with the anionic detergent sodium dodecyl sulfate and describe the impact of the mixed-micelle-like system on the stability of a transmembrane helix dimer. As A8-35 may highly stabilize and thereby rigidify a transmembrane protein structure, modest destabilization by controlled addition of detergents and formation of mixed micellar systems might be helpful to preserve the function of a membrane protein in Amphipol environments.
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Affiliation(s)
- Michael Stangl
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University, Mainz, Germany
| | - Sebastian Unger
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Dirk Schneider
- Department of Pharmacy and Biochemistry, Johannes-Gutenberg-University, Mainz, Germany
- * E-mail:
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45
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Han SG, Na JH, Lee WK, Park D, Oh J, Yoon SH, Lee CK, Sung MH, Shin YK, Yu YG. An amphipathic polypeptide derived from poly-γ-glutamic acid for the stabilization of membrane proteins. Protein Sci 2014; 23:1800-7. [PMID: 25283538 DOI: 10.1002/pro.2575] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 09/14/2014] [Accepted: 09/30/2014] [Indexed: 11/11/2022]
Abstract
Difficulties in the extraction of membrane proteins from cell membrane and their solubilization in native conformations have hindered their structural and biochemical analysis. To overcome these difficulties, an amphipathic polypeptide was synthesized by the conjugation of octyl and glucosyl groups to the carboxyl groups of poly-γ-glutamic acid (PGA). This polymer, called amphipathic PGA (APG), self-assembles as mono-disperse oligomers consisted of 4-5 monomers. APG shows significantly low value of critical micelle concentration and stabilization activity toward membrane proteins. Most of the sodium dodecyl sulfate (SDS)-solubilized membrane proteins from Escherichia coli remain soluble state in the presence of APG even after the removal of SDS. In addition, APG stabilizes purified 7 transmembrane proteins such as bacteriorhodopsin and human endothelin receptor Type A (ETA ) in their active conformations. Furthermore, ETA in complex with APG is readily inserted into liposomes without disrupting the integrity of liposomes. These properties of APG can be applied to overcome the difficulties in the stabilization and reconstitution of membrane proteins.
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Affiliation(s)
- Seong-Gu Han
- Department of Chemistry, Kookmin University, Seongbuk-gu, Seoul, 136-702, Republic of Korea
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46
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Le Bon C, Popot JL, Giusti F. Labeling and functionalizing amphipols for biological applications. J Membr Biol 2014; 247:797-814. [PMID: 24696186 PMCID: PMC4185061 DOI: 10.1007/s00232-014-9655-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/07/2014] [Indexed: 12/19/2022]
Abstract
Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively for biochemical and biophysical studies of MPs. One of the attractive characteristics of APols is that it is relatively easy to label them, isotopically or otherwise, without affecting their physical-chemical properties. Furthermore, several variously modified APols can be mixed, achieving multiple functionalization of MP/APol complexes in the easiest possible manner. Labeled or tagged APols are being used to study the solution properties of APols, their miscibility, their biodistribution upon injection into living organisms, their association with MPs and the composition, structure and dynamics of MP/APol complexes, examining the exchange of surfactants at the surface of MPs, labeling MPs to follow their distribution in fractionation experiments or to immobilize them, increasing the contrast between APols and solvent or MPs in biophysical experiments, improving NMR spectra, etc. Labeling or functionalization of APols can take various courses, each of which has its specific constraints and advantages regarding both synthesis and purification. The present review offers an overview of the various derivatives of A8-35 and its congeners that have been developed in our laboratory and discusses the pros and cons of various synthetic routes.
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Affiliation(s)
- Christel Le Bon
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), CNRS/Université Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France
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47
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Abstract
Amphipols (APols) are short amphipathic polymers that can substitute for detergents at the transmembrane surface of membrane proteins (MPs) and, thereby, keep them soluble in detergent free aqueous solutions. APol-trapped MPs are, as a rule, more stable biochemically than their detergent-solubilized counterparts. APols have proven useful to produce MPs, most noticeably by assisting their folding from the denatured state obtained after solubilizing MP inclusion bodies in either SDS or urea. They facilitate the handling in aqueous solution of fragile MPs for the purpose of proteomics, structural and functional studies, and therapeutics. Because APols can be chemically labeled or functionalized, and they form very stable complexes with MPs, they can also be used to functionalize those indirectly, which opens onto many novel applications. Following a brief recall of the properties of APols and MP/APol complexes, an update is provided of recent progress in these various fields.
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Affiliation(s)
- Manuela Zoonens
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
| | - Jean-Luc Popot
- Laboratoire de Physico-Chimie Moléculaire des Protéines Membranaires, UMR 7099, Institut de Biologie Physico-Chimique (FRC 550), Centre National de la Recherche Scientifique/Université Paris-7, 13, rue Pierre-et-Marie-Curie, 75005 Paris, France
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48
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Polovinkin V, Balandin T, Volkov O, Round E, Borshchevskiy V, Utrobin P, von Stetten D, Royant A, Willbold D, Arzumanyan G, Chupin V, Popot JL, Gordeliy V. Nanoparticle Surface-Enhanced Raman Scattering of Bacteriorhodopsin Stabilized by Amphipol A8-35. J Membr Biol 2014; 247:971-80. [DOI: 10.1007/s00232-014-9701-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/16/2014] [Indexed: 11/28/2022]
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49
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High-Resolution Structure of a Membrane Protein Transferred from Amphipol to a Lipidic Mesophase. J Membr Biol 2014; 247:997-1004. [DOI: 10.1007/s00232-014-9700-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/16/2014] [Indexed: 11/25/2022]
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50
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Thermal Fluctuations in Amphipol A8-35 Particles: A Neutron Scattering and Molecular Dynamics Study. J Membr Biol 2014; 247:897-908. [DOI: 10.1007/s00232-014-9725-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 08/26/2014] [Indexed: 01/03/2023]
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