201
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From Gene to Function: Cell-Free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J 2017; 113:1331-1341. [PMID: 28450130 DOI: 10.1016/j.bpj.2017.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization. However, transport assays in nanodiscs have not been conducted so far, due to limitations of the two-dimensional nature of nanodisc membranes that offers no compartmentalization. Here, we study Krokinobacter eikastus rhodopsin-2 (KR2), a microbial light-driven sodium or proton pump, with noncovalent mass-spectrometric, electrophysiological, and flash photolysis measurements after its cotranslational insertion into nanodiscs. We demonstrate the feasibility of adsorbing nanodiscs containing KR2 to an artificial bilayer. This allows us to record light-induced capacitive currents that reflect KR2's ion transport activity. The solid-supported membrane assay with nanodisc samples provides reliable control over the ionic condition and information of the relative ion activity of this promiscuous pump. Our strategy is complemented with flash photolysis data, where the lifetimes of different photointermediates were determined at different ionic conditions. The advantage of using identical samples to three complementary approaches allows for a comprehensive comparability. The cell-free synthesis in combination with nanodiscs provides a defined hydrophobic lipid environment minimizing the detergent dependence often seen in assays with membrane proteins. KR2 is a promising tool for optogenetics, thus directed engineering to modify ion selectivity can be highly beneficial. Our approach, using the fast generation of functional ion pumps incorporated into nanodiscs and their subsequent analysis by several biophysical techniques, can serve as a versatile screening and engineering platform. This may open new avenues for the study of ion pumps and similar electrogenic targets.
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202
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Cuevas Arenas R, Danielczak B, Martel A, Porcar L, Breyton C, Ebel C, Keller S. Fast Collisional Lipid Transfer Among Polymer-Bounded Nanodiscs. Sci Rep 2017; 7:45875. [PMID: 28378790 PMCID: PMC5381093 DOI: 10.1038/srep45875] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/03/2017] [Indexed: 01/08/2023] Open
Abstract
Some styrene/maleic acid (SMA) copolymers solubilise membrane lipids and proteins to form polymer-bounded nanodiscs termed SMA/lipid particles (SMALPs). Although SMALPs preserve a lipid-bilayer core, they appear to be more dynamic than other membrane mimics. We used time-resolved Förster resonance energy transfer and small-angle neutron scattering to determine the kinetics and the mechanisms of phospholipid transfer among SMALPs. In contrast with vesicles or protein-bounded nanodiscs, SMALPs exchange lipids not only by monomer diffusion but also by fast collisional transfer. Under typical experimental conditions, lipid exchange occurs within seconds in the case of SMALPs but takes minutes to days in the other bilayer particles. The diffusional and second-order collisional exchange rate constants for SMALPs at 30 °C are kdif = 0.287 s-1 and kcol = 222 M-1s-1, respectively. Together with the fast kinetics, the observed invariability of the rate constants with probe hydrophobicity and the moderate activation enthalpy of ~70 kJ mol-1 imply that lipids exchange through a "hydrocarbon continuum" enabled by the flexible nature of the SMA belt surrounding the lipid-bilayer core. Owing to their fast lipid-exchange kinetics, SMALPs represent highly dynamic equilibrium rather than kinetically trapped membrane mimics, which has important implications for studying protein/lipid interactions in polymer-bounded nanodiscs.
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Affiliation(s)
- Rodrigo Cuevas Arenas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Bartholomäus Danielczak
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
| | - Anne Martel
- Institut Max von Laue Paul Langevin, Grenoble, 38042, France
| | - Lionel Porcar
- Institut Max von Laue Paul Langevin, Grenoble, 38042, France
| | - Cécile Breyton
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France
| | - Christine Ebel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, Grenoble, 38044, France
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany
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203
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Zhang R, Sahu ID, Bali AP, Dabney-Smith C, Lorigan GA. Characterization of the structure of lipodisq nanoparticles in the presence of KCNE1 by dynamic light scattering and transmission electron microscopy. Chem Phys Lipids 2017; 203:19-23. [PMID: 27956132 PMCID: PMC5303554 DOI: 10.1016/j.chemphyslip.2016.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/17/2022]
Abstract
A recently developed membrane mimetic system called styrene maleic acid lipid particles (SMALPs) or lipodisq nanoparticles has shown to possess significant potential for biophysical studies of membrane proteins. This new nanoparticle system is composed of lipids encircled by SMA copolymers. Previous studies showed that SMA copolymers are capable of extracting membrane proteins directly from their native environments without the assistance of detergents. However, a full structural characterization of this promising membrane mimetic system is still lacking. In this study, the formation of lipodisq nanoparticles was characterized upon addition of the membrane protein KCNE1. Initially, multi-lamellar vesicles (MLVs) containing KCNE1 (KCNE1-MLVs) at a lipid to protein molar ratio of 500/1 were prepared using a standard dialysis method. SMA copolymers were then added to KCNE1-MLVs at a series of lipid to SMA weight ratios to observe the solubilizing property of SMA in the presence of the KCNE1 membrane protein. The solubilizing process of KCNE1-MLVs by SMA copolymers undergoes a transition phase at low SMA concentrations (samples with weight ratios of 1/0.25, 1/0.5, and 1/0.75). More lipodisq nanoparticles were formed at higher SMA concentrations (Samples with weight ratios of 1/1, 1/1.25, and 1/1.5) were directly observed in the corresponding TEM images. A single sharp DLS peak was observed from the sample at the weight ratio of 1/1.5, which indicated the complete solubilization of KCNE1-MLVs. Interestingly, the critical weight ratio for empty MLVs was found to be 1/1.25 previously, which suggested that the presence of KCNE1 makes it more difficult for the solubilizing process of the SMA copolymers. Also, a TEM image of the 1/1.5 sample showed the presence of silky aggregates of excess copolymers. Overall, this study demonstrated the ability of SMA copolymers to form lipodisq nanoparticles in the presence of the membrane protein KCNE1.
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Affiliation(s)
- Rongfu Zhang
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH 45056, United States; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Indra D Sahu
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Avnika P Bali
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Carole Dabney-Smith
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH 45056, United States; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States
| | - Gary A Lorigan
- Cell, Molecular, and Structural Biology Graduate Program, Miami University, Oxford, OH 45056, United States; Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, United States.
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204
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Oluwole AO, Danielczak B, Meister A, Babalola JO, Vargas C, Keller S. Solubilization of Membrane Proteins into Functional Lipid-Bilayer Nanodiscs Using a Diisobutylene/Maleic Acid Copolymer. Angew Chem Int Ed Engl 2017; 56:1919-1924. [PMID: 28079955 PMCID: PMC5299484 DOI: 10.1002/anie.201610778] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 11/24/2016] [Indexed: 12/22/2022]
Abstract
Once removed from their natural environment, membrane proteins depend on membrane-mimetic systems to retain their native structures and functions. To this end, lipid-bilayer nanodiscs that are bounded by scaffold proteins or amphiphilic polymers such as styrene/maleic acid (SMA) copolymers have been introduced as alternatives to detergent micelles and liposomes for in vitro membrane-protein research. Herein, we show that an alternating diisobutylene/maleic acid (DIBMA) copolymer shows equal performance to SMA in solubilizing phospholipids, stabilizes an integral membrane enzyme in functional bilayer nanodiscs, and extracts proteins of various sizes directly from cellular membranes. Unlike aromatic SMA, aliphatic DIBMA has only a mild effect on lipid acyl-chain order, does not interfere with optical spectroscopy in the far-UV range, and does not precipitate in the presence of low millimolar concentrations of divalent cations.
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Affiliation(s)
- Abraham Olusegun Oluwole
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
- Department of ChemistryUniversity of Ibadan200284IbadanNigeria
| | - Bartholomäus Danielczak
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
| | - Annette Meister
- Institute of Chemistry and Institute of Biochemistry and BiotechnologyMartin Luther University Halle-WittenbergVon-Danckelmann-Platz 406120HalleGermany
| | | | - Carolyn Vargas
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
| | - Sandro Keller
- Molecular BiophysicsUniversity of KaiserslauternErwin-Schrödinger-Str. 1367663KaiserslauternGermany
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205
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Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure 2017; 25:384-392. [DOI: 10.1016/j.str.2016.12.004] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/20/2016] [Accepted: 12/12/2016] [Indexed: 11/20/2022]
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206
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Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Protonendetektierte Festkörper-NMR-Spektroskopie an einem Zinktransporter-Membranprotein in nativen Nanoscheiben. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610441] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Beate Bersch
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
| | - Jonas M. Dörr
- Membrane Biochemistry and Biophysics; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht Niederlande
| | - Audrey Hessel
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
| | - J. Antoinette Killian
- Membrane Biochemistry and Biophysics; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584 CH Utrecht Niederlande
| | - Paul Schanda
- CEA, CNRS; Université Grenoble Alpes; Institut de Biologie Structurale; 71, avenue des martyrs 38044 Grenoble Frankreich
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207
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Bersch B, Dörr JM, Hessel A, Killian JA, Schanda P. Proton-Detected Solid-State NMR Spectroscopy of a Zinc Diffusion Facilitator Protein in Native Nanodiscs. Angew Chem Int Ed Engl 2017; 56:2508-2512. [PMID: 28128538 DOI: 10.1002/anie.201610441] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 12/13/2016] [Indexed: 12/30/2022]
Abstract
The structure, dynamics, and function of membrane proteins are intimately linked to the properties of the membrane environment in which the proteins are embedded. For structural and biophysical characterization, membrane proteins generally need to be extracted from the membrane and reconstituted in a suitable membrane-mimicking environment. Ensuring functional and structural integrity in these environments is often a major concern. The styrene/maleic acid co-polymer has recently been shown to be able to extract lipid/membrane protein patches directly from native membranes to form nanosize discoidal proteolipid particles, also referred to as native nanodiscs. In this work, we show that high-resolution solid-state NMR spectra can be obtained from an integral membrane protein in native nanodiscs, as exemplified by the 2×34 kDa bacterial cation diffusion facilitator CzcD.
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Affiliation(s)
- Beate Bersch
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Audrey Hessel
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Paul Schanda
- CEA, CNRS, Univ. Grenoble Alpes, Institut de Biologie Structurale, 71, avenue des martyrs, 38044, Grenoble, France
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208
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Oluwole AO, Danielczak B, Meister A, Babalola JO, Vargas C, Keller S. Solubilisierung von Membranproteinen in funktionelle Lipiddoppelschicht-Nanodiscs mithilfe eines Diisobutylen/ Maleinsäure-Copolymers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610778] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Abraham Olusegun Oluwole
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
- Department of Chemistry; University of Ibadan; 200284 Ibadan Nigeria
| | - Bartholomäus Danielczak
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
| | - Annette Meister
- Institut für Chemie und Institut für Biochemie und Biotechnologie; Martin-Luther-Universität Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle Deutschland
| | | | - Carolyn Vargas
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
| | - Sandro Keller
- Molekulare Biophysik; Technische Universität Kaiserslautern; Erwin-Schrödinger-Str. 13 67663 Kaiserslautern Deutschland
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209
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Efremov RG, Gatsogiannis C, Raunser S. Lipid Nanodiscs as a Tool for High-Resolution Structure Determination of Membrane Proteins by Single-Particle Cryo-EM. Methods Enzymol 2017; 594:1-30. [DOI: 10.1016/bs.mie.2017.05.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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210
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Voskoboynikova N, Mosslehy W, Colbasevici A, Ismagulova TT, Bagrov DV, Akovantseva AA, Timashev PS, Mulkidjanian AY, Bagratashvili VN, Shaitan KV, Kirpichnikov MP, Steinhoff HJ. Characterization of an archaeal photoreceptor/transducer complex from Natronomonas pharaonis assembled within styrene–maleic acid lipid particles. RSC Adv 2017. [DOI: 10.1039/c7ra10756k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The archaeal receptor/transducer complex NpSRII/NpHtrII retains its integrity upon reconstitution in styrene–maleic acid lipid particles.
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Affiliation(s)
| | - W. Mosslehy
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - A. Colbasevici
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
| | - T. T. Ismagulova
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - D. V. Bagrov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - A. A. Akovantseva
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - P. S. Timashev
- Institute for Regenerative Medicine of I. M. Sechenov First Moscow State Medical University
- Moscow
- Russia
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
| | | | - V. N. Bagratashvili
- Institute of Photonic Technologies of Research Center “Crystallography and Photonics” of RAS
- Moscow
- Russia
| | - K. V. Shaitan
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - M. P. Kirpichnikov
- Department of Bioengineering
- Faculty of Biology
- Lomonosov Moscow State University
- Moscow
- Russia
| | - H.-J. Steinhoff
- Department of Physics
- University of Osnabrück
- Osnabrück
- Germany
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211
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Dominguez Pardo JJ, Dörr JM, Iyer A, Cox RC, Scheidelaar S, Koorengevel MC, Subramaniam V, Killian JA. Solubilization of lipids and lipid phases by the styrene-maleic acid copolymer. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2017; 46:91-101. [PMID: 27815573 PMCID: PMC5209432 DOI: 10.1007/s00249-016-1181-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/11/2016] [Indexed: 10/27/2022]
Abstract
A promising tool in membrane research is the use of the styrene-maleic acid (SMA) copolymer to solubilize membranes in the form of nanodiscs. Since membranes are heterogeneous in composition, it is important to know whether SMA thereby has a preference for solubilization of either specific types of lipids or specific bilayer phases. Here, we investigated this by performing partial solubilization of model membranes and analyzing the lipid composition of the solubilized fraction. We found that SMA displays no significant lipid preference in homogeneous binary lipid mixtures in the fluid phase, even when using lipids that by themselves show very different solubilization kinetics. By contrast, in heterogeneous phase-separated bilayers, SMA was found to have a strong preference for solubilization of lipids in the fluid phase as compared to those in either a gel phase or a liquid-ordered phase. Together the results suggest that (1) SMA is a reliable tool to characterize native interactions between membrane constituents, (2) any solubilization preference of SMA is not due to properties of individual lipids but rather due to properties of the membrane or membrane domains in which these lipids reside and (3) exploiting SMA resistance rather than detergent resistance may be an attractive approach for the isolation of ordered domains from biological membranes.
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Affiliation(s)
- Juan J Dominguez Pardo
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands.
| | - Jonas M Dörr
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Aditya Iyer
- Nanoscale Biophysics Group, FOM Institute AMOLF, Science Park 104, 1098, Amsterdam, The Netherlands
| | - Ruud C Cox
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Stefan Scheidelaar
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands
| | - Vinod Subramaniam
- Nanoscale Biophysics Group, FOM Institute AMOLF, Science Park 104, 1098, Amsterdam, The Netherlands
- Vrije Universiteit Amsterdam, De Boelelaan 1105, 1081, Amsterdam, The Netherlands
| | - J Antoinette Killian
- Department of Chemistry, Faculty of Science, Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research, Padualaan 8, 3584, Utrecht, The Netherlands.
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212
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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213
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Membrane protein extraction and purification using styrene–maleic acid (SMA) copolymer: effect of variations in polymer structure. Biochem J 2016; 473:4349-4360. [DOI: 10.1042/bcj20160723] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/27/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The use of styrene–maleic acid (SMA) copolymers to extract and purify transmembrane proteins, while retaining their native bilayer environment, overcomes many of the disadvantages associated with conventional detergent-based procedures. This approach has huge potential for the future of membrane protein structural and functional studies. In this investigation, we have systematically tested a range of commercially available SMA polymers, varying in both the ratio of styrene and maleic acid and in total size, for the ability to extract, purify and stabilise transmembrane proteins. Three different membrane proteins (BmrA, LeuT and ZipA), which vary in size and shape, were used. Our results show that several polymers, can be used to extract membrane proteins, comparably to conventional detergents. A styrene:maleic acid ratio of either 2:1 or 3:1, combined with a relatively small average molecular mass (7.5–10 kDa), is optimal for membrane extraction, and this appears to be independent of the protein size, shape or expression system. A subset of polymers were taken forward for purification, functional and stability tests. Following a one-step affinity purification, SMA 2000 was found to be the best choice for yield, purity and function. However, the other polymers offer subtle differences in size and sensitivity to divalent cations that may be useful for a variety of downstream applications.
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214
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Bagrov DV, Voskoboynikova N, Armeev GA, Mosslehy W, Gluhov GS, Ismagulova TT, Mulkidjanian AY, Kirpichnikov MP, Steinhoff HJ, Shaitan KV. Characterization of lipodisc nanoparticles containing sensory rhodopsin II and its cognate transducer from Natronomonas pharaonis. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916060063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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215
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Scheidelaar S, Koorengevel MC, van Walree CA, Dominguez JJ, Dörr JM, Killian JA. Effect of Polymer Composition and pH on Membrane Solubilization by Styrene-Maleic Acid Copolymers. Biophys J 2016; 111:1974-1986. [PMID: 27806279 PMCID: PMC5103014 DOI: 10.1016/j.bpj.2016.09.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/21/2016] [Accepted: 09/21/2016] [Indexed: 11/28/2022] Open
Abstract
The styrene-maleic acid (SMA) copolymer is rapidly gaining attention as a tool in membrane research, due to its ability to directly solubilize lipid membranes into nanodisk particles without the requirement of conventional detergents. Although many variants of SMA are commercially available, so far only SMA variants with a 2:1 and 3:1 styrene-to-maleic acid ratio have been used in lipid membrane studies. It is not known how SMA composition affects the solubilization behavior of SMA. Here, we systematically investigated the effect of varying the styrene/maleic acid on the properties of SMA in solution and on its interaction with membranes. Also the effect of pH was studied, because the proton concentration in the solution will affect the charge density and thereby may modulate the properties of the polymers. Using model membranes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipids at pH > pHagg, we found that membrane solubilization is promoted by a low charge density and by a relatively high fraction of maleic acid units in the polymer. Furthermore, it was found that a collapsed conformation of the polymer is required to ensure efficient insertion into the lipid membrane and that efficient solubilization may be improved by a more homogenous distribution of the maleic acid monomer units along the polymer chain. Altogether, the results show large differences in behavior between the SMA variants tested in the various steps of solubilization. The main conclusion is that the variant with a 2:1 styrene-to-maleic acid ratio is the most efficient membrane solubilizer in a wide pH range.
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Affiliation(s)
- Stefan Scheidelaar
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
| | - Martijn C Koorengevel
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Cornelius A van Walree
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Juan J Dominguez
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Jonas M Dörr
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry & Biophysics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, the Netherlands.
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216
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Glab JA, Mbogo GW, Puthalakath H. BH3-Only Proteins in Health and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 328:163-196. [PMID: 28069133 DOI: 10.1016/bs.ircmb.2016.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BH3-only proteins are proapoptotic members of the broader Bcl-2 family, which promote cell death by directly or indirectly activating Bax and Bak. The expression of BH3-only proteins is regulated both transcriptionally and posttranscriptionally in a cell type-specific and a tissue-specific manner. Research over the last 20 years has provided significant insights into their roles in tissue homeostasis and various pathologies, which in turn has led to the development of novel therapeutics for numerous diseases. In this review, a snapshot of the progress over this period is given, including our current understanding of their regulation, mode of action, role in mammalian development, and pathology.
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Affiliation(s)
- J A Glab
- Department of Biochemistry, La Trobe Institute of Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, Australia
| | - G W Mbogo
- Department of Biochemistry, La Trobe Institute of Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, Australia
| | - H Puthalakath
- Department of Biochemistry, La Trobe Institute of Molecular Science, La Trobe University, Kingsbury Drive, Melbourne, VIC, Australia.
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217
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From Nanodiscs to Isotropic Bicelles: A Procedure for Solution Nuclear Magnetic Resonance Studies of Detergent-Sensitive Integral Membrane Proteins. Structure 2016; 24:1830-1841. [PMID: 27618661 DOI: 10.1016/j.str.2016.07.017] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/25/2016] [Accepted: 07/25/2016] [Indexed: 01/04/2023]
Abstract
Nanodiscs and isotropic bicelles are promising membrane mimetics in the field of solution nuclear magnetic resonance (NMR) spectroscopy of integral membrane proteins (IMPs). Despite varied challenges to solution NMR studies of IMPs, we attribute the paucity of solution NMR structures in these environments to the inability of diverse IMPs to withstand detergent treatment during standard nanodisc and bicelle preparations. Here, we present a strategy that creates small isotropic bicelles from IMPs co-translationally embedded in large nanodiscs using cell-free expression. Our results demonstrate appreciable gains in NMR spectral quality while preserving lipid-IMP contacts. We validate the approach on the detergent-sensitive LspA, which finally allowed us to perform high-quality triple-resonance NMR experiments for structural studies. Our strategy of producing bicelles from nanodiscs comprehensively avoids detergent during expression and preparation and is suitable for solution NMR spectroscopy of lipid-IMP complexes.
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218
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Smirnova IA, Sjöstrand D, Li F, Björck M, Schäfer J, Östbye H, Högbom M, von Ballmoos C, Lander GC, Ädelroth P, Brzezinski P. Isolation of yeast complex IV in native lipid nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2984-2992. [PMID: 27620332 DOI: 10.1016/j.bbamem.2016.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 12/31/2022]
Abstract
We used the amphipathic styrene maleic acid (SMA) co-polymer to extract cytochrome c oxidase (CytcO) in its native lipid environment from S. cerevisiae mitochondria. Native nanodiscs containing one CytcO per disc were purified using affinity chromatography. The longest cross-sections of the native nanodiscs were 11nm×14nm. Based on this size we estimated that each CytcO was surrounded by ~100 phospholipids. The native nanodiscs contained the same major phospholipids as those found in the mitochondrial inner membrane. Even though CytcO forms a supercomplex with cytochrome bc1 in the mitochondrial membrane, cyt. bc1 was not found in the native nanodiscs. Yet, the loosely-bound Respiratory SuperComplex factors were found to associate with the isolated CytcO. The native nanodiscs displayed an O2-reduction activity of ~130 electrons CytcO-1s-1 and the kinetics of the reaction of the fully reduced CytcO with O2 was essentially the same as that observed with CytcO in mitochondrial membranes. The kinetics of CO-ligand binding to the CytcO catalytic site was similar in the native nanodiscs and the mitochondrial membranes. We also found that excess SMA reversibly inhibited the catalytic activity of the mitochondrial CytcO, presumably by interfering with cyt. c binding. These data point to the importance of removing excess SMA after extraction of the membrane protein. Taken together, our data shows the high potential of using SMA-extracted CytcO for functional and structural studies.
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Affiliation(s)
- Irina A Smirnova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; Belozersky Institute, Moscow State University, Leninskie Gory 1, Bldg. 40, 119991 Moscow, Russian Federation
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Fei Li
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Markus Björck
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jacob Schäfer
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Henrik Östbye
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Christoph von Ballmoos
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Pia Ädelroth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden.
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219
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Wang J, Zhang Z, Zhao W, Wang L, Yang J. Heating and temperature gradients of lipid bilayer samples induced by RF irradiation in MAS solid-state NMR experiments. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:753-759. [PMID: 27161041 DOI: 10.1002/mrc.4450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/16/2016] [Accepted: 04/18/2016] [Indexed: 05/15/2023]
Abstract
The MAS solid-state NMR has been a powerful technique for studying membrane proteins within the native-like lipid bilayer environment. In general, RF irradiation in MAS NMR experiments can heat and potentially destroy expensive membrane protein samples. However, under practical MAS NMR experimental conditions, detailed characterization of RF heating effect of lipid bilayer samples is still lacking. Herein, using 1 H chemical shift of water for temperature calibration, we systematically study the dependence of RF heating on hydration levels and salt concentrations of three lipids in MAS NMR experiments. Under practical 1 H decoupling conditions used in biological MAS NMR experiments, three lipids show different dependence of RF heating on hydration levels as well as salt concentrations, which are closely associated with the properties of lipids. The maximum temperature elevation of about 10 °C is similar for the three lipids containing 200% hydration, which is much lower than that in static solid-state NMR experiments. The RF heating due to salt is observed to be less than that due to hydration, with a maximum temperature elevation of less than 4 °C in the hydrated samples containing 120 mmol l-1 of salt. Upon RF irradiation, the temperature gradient across the sample is observed to be greatly increased up to 20 °C, as demonstrated by the remarkable broadening of 1 H signal of water. Based on detailed characterization of RF heating effect, we demonstrate that RF heating and temperature gradient can be significantly reduced by decreasing the hydration levels of lipid bilayer samples from 200% to 30%. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jing Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhengfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Weijing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Liying Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Jun Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
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220
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Schroeder I. How to resolve microsecond current fluctuations in single ion channels: the power of beta distributions. Channels (Austin) 2016; 9:262-80. [PMID: 26368656 DOI: 10.1080/19336950.2015.1083660] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
A main ingredient for the understanding of structure/function correlates of ion channels is the quantitative description of single-channel gating and conductance. However, a wealth of information provided from fast current fluctuations beyond the temporal resolution of the recording system is often ignored, even though it is close to the time window accessible to molecular dynamics simulations. This kind of current fluctuations provide a special technical challenge, because individual opening/closing or blocking/unblocking events cannot be resolved, and the resulting averaging over undetected events decreases the single-channel current. Here, I briefly summarize the history of fast-current fluctuation analysis and focus on the so-called "beta distributions." This tool exploits characteristics of current fluctuation-induced excess noise on the current amplitude histograms to reconstruct the true single-channel current and kinetic parameters. A guideline for the analysis and recent applications demonstrate that a construction of theoretical beta distributions by Markov Model simulations offers maximum flexibility as compared to analytical solutions.
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Affiliation(s)
- Indra Schroeder
- a Plant Membrane Biophysics, Technical University of Darmstadt ; Darmstadt , Germany
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221
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Furse S, Scott DJ. Three-Dimensional Distribution of Phospholipids in Gram Negative Bacteria. Biochemistry 2016; 55:4742-7. [PMID: 27509296 DOI: 10.1021/acs.biochem.6b00541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Exploration of the molecular structure of the bacterial cell envelope informs our understanding of its role in bacterial growth. This is crucial for research into both inhibiting and promoting bacterial growth as well as fundamental studies of cell cycle control. The spatial arrangement of the lipids in the cell envelope of Gram negative bacteria in particular has attracted considerable research attention in recent years. In this mini-review, we explore advances in understanding the spatial distribution of lipids in the model Gram negative prokaryote Escherichia coli. This includes the distribution of lipids in three dimensions, (a) lateral distribution within a monolayer, (b) asymmetry between bilayers and monolayers, and (c) distribution as a function of progress through membrane division (temporal shifts). We conclude that lipid distribution in E. coli and probably all bacteria is dynamic despite a narrow lipid profile and that the biophysical properties of the membrane are inhomogeneous as a result. Finally, we suggest that further work in this field may indicate how lipid distribution is controlled and what this means for bacterial growth and metabolism and even cell cycle control.
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Affiliation(s)
- Samuel Furse
- MBI, Department of Molecular Biology, University of Bergen , Thormøhlensgate 55, 5008 Bergen, Norway
| | - David J Scott
- National Centre for Macromolecular Hydrodynamics, University of Nottingham , College Road, Sutton Bonington, Nottinghamshire LE12 5RD, U.K.,ISIS Spallation Neutron Source, STFC, Rutherford Appleton Laboratory , Harwell Science and Innovation Campus, Harwell, Oxon OX11 0QX, U.K
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222
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Cuevas Arenas R, Klingler J, Vargas C, Keller S. Influence of lipid bilayer properties on nanodisc formation mediated by styrene/maleic acid copolymers. NANOSCALE 2016; 8:15016-26. [PMID: 27471007 DOI: 10.1039/c6nr02089e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Copolymers of styrene and maleic acid (SMA) have gained great attention as alternatives to conventional detergents, as they offer decisive advantages for studying membrane proteins and lipids in vitro. These polymers self-insert into artificial and biological membranes and, at sufficiently high concentrations, solubilise them into disc-shaped nanostructures containing a lipid bilayer core surrounded by a polymer belt. We have used (31)P nuclear magnetic resonance spectroscopy and dynamic light scattering to systematically study the solubilisation of vesicles composed of saturated or unsaturated phospholipids by an SMA copolymer with a 3 : 1 styrene/maleic acid molar ratio at different temperatures. Solubilisation was thermodynamically rationalised in terms of a three-stage model that treats various lipid/polymer aggregates as pseudophases. The solubilising capacity of SMA(3 : 1) towards a saturated lipid is higher in the gel than in the liquid-crystalline state of the membrane even though solubilisation is slower. Although the solubilisation of mixed fluid membranes is non-selective, the presence of a non-bilayer phospholipid lowers the threshold at which the membrane becomes saturated with SMA(3 : 1) but raises the polymer concentration required for complete solubilisation. Both of these trends can be explained by considering the vesicle-to-nanodisc transfer free energies of the lipid and the polymer. On the basis of the phase diagrams thus obtained, re-association of polymer-solubilised lipids with vesicles is possible under mild conditions, which has implications for the reconstitution of proteins and lipids from nanodiscs into vesicular membranes. Finally, the phase diagrams provide evidence for the absence of free SMA(3 : 1) in vesicular lipid suspensions.
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Affiliation(s)
- Rodrigo Cuevas Arenas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Johannes Klingler
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
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223
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Abstract
AbstractIncreasing evidence suggests that most proteins occur and function in complexes rather than as isolated entities when embedded in cellular membranes. Nuclear magnetic resonance (NMR) provides increasing possibilities to study structure, dynamics and assembly of such systems. In our review, we discuss recent methodological progress to study membrane–protein complexes (MPCs) by NMR, starting with expression, isotope-labeling and reconstitution protocols. We review approaches to deal with spectral complexity and limited spectral spectroscopic sensitivity that are usually encountered in NMR-based studies of MPCs. We highlight NMR applications in various classes of MPCs, including G-protein-coupled receptors, ion channels and retinal proteins and extend our discussion to protein–protein complexes that span entire cellular compartments or orchestrate processes such as protein transport across or within membranes. These examples demonstrate the growing potential of NMR-based studies of MPCs to provide critical insight into the energetics of protein–ligand and protein–protein interactions that underlie essential biological functions in cellular membranes.
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224
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Mineev KS, Nadezhdin KD, Goncharuk SA, Arseniev AS. Characterization of Small Isotropic Bicelles with Various Compositions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6624-6637. [PMID: 27285636 DOI: 10.1021/acs.langmuir.6b00867] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Structural studies of membrane proteins are of great importance and interest, with solution and solid state NMR spectroscopy being very promising tools for that task. However, such investigations are hindered by a number of obstacles, and in the first place by the fact that membrane proteins need an adequate environment that models the cell membrane. One of the most widely used and prospective membrane mimetics is isotropic bicelles. While large anisotropic bicelles are well-studied, the field of small bicelles contains a lot of "white spots". The present work reports the radii of particles and concentration of the detergents in the monomeric state in solutions of isotropic bicelles, formed by 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate (CHAPSO), and sodium cholate, as a function of lipid/detergent ratio and temperature. These parameters were measured using (1)H NMR diffusion spectroscopy for the bicelles composed of lipids with saturated fatty chains of different length and lipids, containing unsaturated fatty acid residue. The influence of a model transmembrane protein (membrane domain of rat TrkA) on the properties of bicelles and the effect of the bicelle size and composition on the properties of the transmembrane protein were investigated with heteronuclear NMR and nuclear Overhauser effect spectroscopy. We show that isotropic bicelles that are applicable for solution NMR spectroscopy behave as predicted by the theoretical models and are likely to be bicelles rather than mixed micelles. Using the obtained data, we propose a simple approach to control the size of bicelles at low concentrations. On the basis of our results, we compared different rim-forming agents and selected CHAPS as a detergent of choice for structural studies in bicelles, if the deuteration of the detergent is not required.
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Affiliation(s)
- K S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
| | - K D Nadezhdin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
| | - S A Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Lomonosov Moscow State University , Leninskiye Gory, 1, Moscow, 119991, Russian Federation
| | - A S Arseniev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences RAS , str. Miklukho-Maklaya 16/10, Moscow, 117997 Russian Federation
- Moscow Institute of Physics and Technology , Institutsky per., 9, 141700, Dolgoprudnyi, Russian Federation
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225
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Kondo H, Ikeda K, Nakano M. Formation of size-controlled, denaturation-resistant lipid nanodiscs by an amphiphilic self-polymerizing peptide. Colloids Surf B Biointerfaces 2016; 146:423-30. [PMID: 27393815 DOI: 10.1016/j.colsurfb.2016.06.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/22/2016] [Accepted: 06/22/2016] [Indexed: 11/28/2022]
Abstract
Nanodiscs are discoidal particles with a planar phospholipid bilayer enwrapped by proteins such as apolipoprotein A-I. Nanodiscs have been widely used for analyzing structures and functions of membrane proteins by dispersing them in solution. They are expected to be used as drug carriers and therapeutic agents. Amphiphilic peptides are known to form nanodiscs. However, the lipid-peptide nanodiscs are relatively unstable in solution, making them unsuitable for many applications. Here, we report the synthesis of an amphiphilic self-polymerizing peptide termed ASPP1, which polymerizes by intermolecular native chemical ligation reactions. ASPP1 spontaneously formed nanodiscs when added to phospholipid vesicles without using detergents. The diameter of the planar lipid bilayer in the nanodiscs was controlled by the lipid:peptide molar ratio. ASPP1-nanodiscs exhibited greater stability at high temperatures or in the presence of urea than nanodiscs formed by the non-polymerizing amphiphilic peptide or apolipoprotein A-I. Average and maximal degrees of ASPP1 polymerization were 2.4 and 12, respectively. Self-polymerization of the peptide appears to be responsible for stabilization of the nanodiscs. Our results open a new avenue for the development of nanodisc technology.
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Affiliation(s)
- Hiroaki Kondo
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Minoru Nakano
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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226
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Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics. Biochem Soc Trans 2016; 44:905-15. [DOI: 10.1042/bst20160024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Indexed: 12/19/2022]
Abstract
During their mechanistic cycles membrane transporters often undergo extensive conformational changes, sampling a range of orientations, in order to complete their function. Such membrane transporters present somewhat of a challenge to conventional structural studies; indeed, crystallization of membrane-associated proteins sometimes require conditions that vary vastly from their native environments. Moreover, this technique currently only allows for visualization of single selected conformations during any one experiment. EPR spectroscopy is a magnetic resonance technique that offers a unique opportunity to study structural, environmental and dynamic properties of such proteins in their native membrane environments, as well as readily sampling their substrate-binding-induced dynamic conformational changes especially through complementary computational analyses. Here we present a review of recent studies that utilize a variety of EPR techniques in order to investigate both the structure and dynamics of a range of membrane transporters and associated proteins, focusing on both primary (ABC-type transporters) and secondary active transporters which were key interest areas of the late Professor Stephen Baldwin to whom this review is dedicated.
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227
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Rashid R, Veleba M, Kline KA. Focal Targeting of the Bacterial Envelope by Antimicrobial Peptides. Front Cell Dev Biol 2016; 4:55. [PMID: 27376064 PMCID: PMC4894902 DOI: 10.3389/fcell.2016.00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/23/2016] [Indexed: 01/15/2023] Open
Abstract
Antimicrobial peptides (AMPs) are utilized by both eukaryotic and prokaryotic organisms. AMPs such as the human beta defensins, human neutrophil peptides, human cathelicidin, and many bacterial bacteriocins are cationic and capable of binding to anionic regions of the bacterial surface. Cationic AMPs (CAMPs) target anionic lipids [e.g., phosphatidylglycerol (PG) and cardiolipins (CL)] in the cell membrane and anionic components [e.g., lipopolysaccharide (LPS) and lipoteichoic acid (LTA)] of the cell envelope. Bacteria have evolved mechanisms to modify these same targets in order to resist CAMP killing, e.g., lysinylation of PG to yield cationic lysyl-PG and alanylation of LTA. Since CAMPs offer a promising therapeutic alternative to conventional antibiotics, which are becoming less effective due to rapidly emerging antibiotic resistance, there is a strong need to improve our understanding about the AMP mechanism of action. Recent literature suggests that AMPs often interact with the bacterial cell envelope at discrete foci. Here we review recent AMP literature, with an emphasis on focal interactions with bacteria, including (1) CAMP disruption mechanisms, (2) delocalization of membrane proteins and lipids by CAMPs, and (3) CAMP sensing systems and resistance mechanisms. We conclude with new approaches for studying the bacterial membrane, e.g., lipidomics, high resolution imaging, and non-detergent-based membrane domain extraction.
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Affiliation(s)
- Rafi Rashid
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| | - Mark Veleba
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University Singapore, Singapore
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228
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Lee SC, Knowles TJ, Postis VLG, Jamshad M, Parslow RA, Lin YP, Goldman A, Sridhar P, Overduin M, Muench SP, Dafforn TR. A method for detergent-free isolation of membrane proteins in their local lipid environment. Nat Protoc 2016; 11:1149-62. [PMID: 27254461 DOI: 10.1038/nprot.2016.070] [Citation(s) in RCA: 269] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite the great importance of membrane proteins, structural and functional studies of these proteins present major challenges. A significant hurdle is the extraction of the functional protein from its natural lipid membrane. Traditionally achieved with detergents, purification procedures can be costly and time consuming. A critical flaw with detergent approaches is the removal of the protein from the native lipid environment required to maintain functionally stable protein. This protocol describes the preparation of styrene maleic acid (SMA) co-polymer to extract membrane proteins from prokaryotic and eukaryotic expression systems. Successful isolation of membrane proteins into SMA lipid particles (SMALPs) allows the proteins to remain with native lipid, surrounded by SMA. We detail procedures for obtaining 25 g of SMA (4 d); explain the preparation of protein-containing SMALPs using membranes isolated from Escherichia coli (2 d) and control protein-free SMALPS using E. coli polar lipid extract (1-2 h); investigate SMALP protein purity by SDS-PAGE analysis and estimate protein concentration (4 h); and detail biophysical methods such as circular dichroism (CD) spectroscopy and sedimentation velocity analytical ultracentrifugation (svAUC) to undertake initial structural studies to characterize SMALPs (∼2 d). Together, these methods provide a practical tool kit for those wanting to use SMALPs to study membrane proteins.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Tim J Knowles
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Vincent L G Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, Leeds, UK
| | | | | | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK.,Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Pooja Sridhar
- School of Cancer Sciences, University of Birmingham, Birmingham, UK.,Present address: Department of Biosciences, University of Birmingham, Birmingham, UK
| | - Michael Overduin
- School of Biosciences, University of Birmingham, Birmingham, UK.,Department of Biochemistry, Faculty of Medicine &Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, UK
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229
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Shirzad-Wasei N, DeGrip WJ. Heterologous expression of melanopsin: Present, problems and prospects. Prog Retin Eye Res 2016; 52:1-21. [DOI: 10.1016/j.preteyeres.2016.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/25/2016] [Accepted: 02/01/2016] [Indexed: 12/12/2022]
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230
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Lindhoud S, Carvalho V, Pronk JW, Aubin-Tam ME. SMA-SH: Modified Styrene–Maleic Acid Copolymer for Functionalization of Lipid Nanodiscs. Biomacromolecules 2016; 17:1516-22. [DOI: 10.1021/acs.biomac.6b00140] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Simon Lindhoud
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology. Lorentzweg
1, Delft 2628 CJ, The Netherlands
| | - Vanessa Carvalho
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology. Lorentzweg
1, Delft 2628 CJ, The Netherlands
| | - Joachim W. Pronk
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology. Lorentzweg
1, Delft 2628 CJ, The Netherlands
| | - Marie-Eve Aubin-Tam
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology. Lorentzweg
1, Delft 2628 CJ, The Netherlands
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231
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Lee SC, Khalid S, Pollock NL, Knowles TJ, Edler K, Rothnie AJ, R T Thomas O, Dafforn TR. Encapsulated membrane proteins: A simplified system for molecular simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2549-2557. [PMID: 26946242 DOI: 10.1016/j.bbamem.2016.02.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 12/19/2022]
Abstract
Over the past 50years there has been considerable progress in our understanding of biomolecular interactions at an atomic level. This in turn has allowed molecular simulation methods employing full atomistic modelling at ever larger scales to develop. However, some challenging areas still remain where there is either a lack of atomic resolution structures or where the simulation system is inherently complex. An area where both challenges are present is that of membranes containing membrane proteins. In this review we analyse a new practical approach to membrane protein study that offers a potential new route to high resolution structures and the possibility to simplify simulations. These new approaches collectively recognise that preservation of the interaction between the membrane protein and the lipid bilayer is often essential to maintain structure and function. The new methods preserve these interactions by producing nano-scale disc shaped particles that include bilayer and the chosen protein. Currently two approaches lead in this area: the MSP system that relies on peptides to stabilise the discs, and SMALPs where an amphipathic styrene maleic acid copolymer is used. Both methods greatly enable protein production and hence have the potential to accelerate atomic resolution structure determination as well as providing a simplified format for simulations of membrane protein dynamics. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Tim J Knowles
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Karen Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Owen R T Thomas
- School of Chemical Engineering, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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232
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Constantine M, Liew CK, Lo V, Macmillan A, Cranfield CG, Sunde M, Whan R, Graham RM, Martinac B. Heterologously-expressed and Liposome-reconstituted Human Transient Receptor Potential Melastatin 4 Channel (TRPM4) is a Functional Tetramer. Sci Rep 2016; 6:19352. [PMID: 26785754 PMCID: PMC4726259 DOI: 10.1038/srep19352] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/11/2015] [Indexed: 11/24/2022] Open
Abstract
Mutation, irregular expression and sustained activation of the Transient Receptor Potential Channel, type Melastatin 4 (TRPM4), have been linked to various cardiovascular diseases. However, much remains unknown about the structure of this important ion channel. Here, we have purified a heterologously expressed TRPM4-eGFP fusion protein and investigated the oligomeric state of TRPM4-eGFP in detergent micelles using crosslinking, native gel electrophoresis, multi-angle laser light scattering and electron microscopy. Our data indicate that TRPM4 is tetrameric, like other TRP channels studied to date. Furthermore, the functionality of liposome reconstituted TRPM4-eGFP was examined using electrophysiology. Single-channel recordings from TRPM4-eGFP proteoliposomes showed inhibition of the channel using Flufenamic acid, a well-established inhibitor of TRPM4, suggesting that the channels are functional upon reconstitution. Our characterisation of the oligomeric structure of TRPM4 and the ability to reconstitute functional channels in liposomes should facilitate future studies into the structure, function and pharmacology of this therapeutically relevant channel.
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Affiliation(s)
- Maryrose Constantine
- Victor Chang Cardiac Research Institute, Lowy Packer Building, NSW 2010
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Chu Kong Liew
- Victor Chang Cardiac Research Institute, Lowy Packer Building, NSW 2010
| | - Victor Lo
- School of Medical Sciences, The Bosch Institute, The University of Sydney, NSW 2006
| | - Alex Macmillan
- Biomedical Imaging Facility, Lowy Cancer Research Centre, The University of New South Wales, Kensington, NSW 2052, Australia
| | | | - Margaret Sunde
- School of Medical Sciences, The Bosch Institute, The University of Sydney, NSW 2006
| | - Renee Whan
- Biomedical Imaging Facility, Lowy Cancer Research Centre, The University of New South Wales, Kensington, NSW 2052, Australia
| | - Robert M. Graham
- Victor Chang Cardiac Research Institute, Lowy Packer Building, NSW 2010
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Boris Martinac
- Victor Chang Cardiac Research Institute, Lowy Packer Building, NSW 2010
- St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
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233
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Dörr JM, Scheidelaar S, Koorengevel MC, Dominguez JJ, Schäfer M, van Walree CA, Killian JA. The styrene-maleic acid copolymer: a versatile tool in membrane research. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2016; 45:3-21. [PMID: 26639665 PMCID: PMC4698303 DOI: 10.1007/s00249-015-1093-y] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 10/28/2022]
Abstract
A new and promising tool in membrane research is the detergent-free solubilization of membrane proteins by styrene-maleic acid copolymers (SMAs). These amphipathic molecules are able to solubilize lipid bilayers in the form of nanodiscs that are bounded by the polymer. Thus, membrane proteins can be directly extracted from cells in a water-soluble form while conserving a patch of native membrane around them. In this review article, we briefly discuss current methods of membrane protein solubilization and stabilization. We then zoom in on SMAs, describe their physico-chemical properties, and discuss their membrane-solubilizing effect. This is followed by an overview of studies in which SMA has been used to isolate and investigate membrane proteins. Finally, potential future applications of the methodology are discussed for structural and functional studies on membrane proteins in a near-native environment and for characterizing protein-lipid and protein-protein interactions.
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Affiliation(s)
- Jonas M Dörr
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Stefan Scheidelaar
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Martijn C Koorengevel
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Juan J Dominguez
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Marre Schäfer
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Cornelis A van Walree
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- School of Chemical and Physical Sciences, Flinders University, GPO Box 2100, Adelaide, 5001, Australia
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Bijvoet Center for Biomolecular Research and Institute of Biomembranes, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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234
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Abstract
Membrane proteins are localized within a lipid bilayer; in order to purify them for functional and structural studies the first step must involve solubilizing or extracting the protein from these lipids. To date this has been achieved using detergents which disrupt the bilayer and bind to the protein in the transmembrane region. However finding conditions for optimal extraction, without destabilizing protein structure, is time consuming and expensive. Here we present a recently-developed method using a styrene-maleic acid (SMA) co-polymer instead of detergents. The SMA co-polymer extracts membrane proteins in a small disc of lipid bilayer which can be used for affinity chromatography purification, thus enabling the purification of membrane proteins while maintaining their native lipid bilayer environment.
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Affiliation(s)
- Alice J Rothnie
- Life & Health Sciences, Aston University, Birmingham, B4 7ET, UK.
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235
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Polidori A, Raynal S, Barret LA, Dahani M, Barrot-Ivolot C, Jungas C, Frotscher E, Keller S, Ebel C, Breyton C, Bonneté F. Sparingly fluorinated maltoside-based surfactants for membrane-protein stabilization. NEW J CHEM 2016. [DOI: 10.1039/c5nj03502c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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236
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Abstract
Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.
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Affiliation(s)
- A. J. Miles
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
| | - B. A. Wallace
- Institute of Structural and Molecular Biology
- Birkbeck College
- University of London
- London
- UK
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237
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Vargas C, Arenas RC, Frotscher E, Keller S. Nanoparticle self-assembly in mixtures of phospholipids with styrene/maleic acid copolymers or fluorinated surfactants. NANOSCALE 2015; 7:20685-96. [PMID: 26599076 DOI: 10.1039/c5nr06353a] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Self-assembling nanostructures in aqueous mixtures of bilayer-forming lipids and micelle-forming surfactants are relevant to in vitro studies on biological and synthetic membranes and membrane proteins. Considerable efforts are currently underway to replace conventional detergents by milder alternatives such as styrene/maleic acid (SMA) copolymers and fluorinated surfactants. However, these compounds and their nanosized assemblies remain poorly understood as regards their interactions with lipid membranes, particularly, the thermodynamics of membrane partitioning and solubilisation. Using (19)F and (31)P nuclear magnetic resonance spectroscopy, static and dynamic light scattering, and isothermal titration calorimetry, we have systematically investigated the aggregational state of a zwitterionic bilayer-forming phospholipid upon exposure to an SMA polymer with a styrene/maleic acid ratio of 3 : 1 or to a fluorinated octyl phosphocholine derivative called F(6)OPC. The lipid interactions of SMA(3 : 1) and F(6)OPC can be thermodynamically conceptualised within the framework of a three-stage model that treats bilayer vesicles, discoidal or micellar nanostructures, and the aqueous solution as distinct pseudophases. The exceptional solubilising power of SMA(3 : 1) is reflected in very low membrane-saturating and solubilising polymer/lipid molar ratios of 0.10 and 0.15, respectively. Although F(6)OPC saturates bilayers at an even lower molar ratio of 0.031, this nondetergent does not solubilise lipids even at >1000-fold molar excess, thus highlighting fundamental differences between these two types of mild membrane-mimetic systems. We rationalise these findings in terms of a new classification of surfactants based on bilayer-to-micelle transfer free energies and discuss practical implications for membrane-protein research.
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Affiliation(s)
- Carolyn Vargas
- Molecular Biophysics, University of Kaiserslautern, Erwin-Schrödinger-Str. 13, 67663 Kaiserslautern, Germany.
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238
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Logez C, Damian M, Legros C, Dupré C, Guéry M, Mary S, Wagner R, M’Kadmi C, Nosjean O, Fould B, Marie J, Fehrentz JA, Martinez J, Ferry G, Boutin JA, Banères JL. Detergent-free Isolation of Functional G Protein-Coupled Receptors into Nanometric Lipid Particles. Biochemistry 2015; 55:38-48. [DOI: 10.1021/acs.biochem.5b01040] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christel Logez
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Marjorie Damian
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Céline Legros
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Clémence Dupré
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Mélody Guéry
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Sophie Mary
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Renaud Wagner
- CNRS
UMR7242, Institut de Recherche de l’ESBS, Biotechnologie et
Signalisation Cellulaire, Université de Strasbourg, 300 Boulevard
Sébastien Brant, 67412 Ilkirch cedex, France
| | - Céline M’Kadmi
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Olivier Nosjean
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Benjamin Fould
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jacky Marie
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean-Alain Fehrentz
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Jean Martinez
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
| | - Gilles Ferry
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean A. Boutin
- Pole
d’expertise Biotechnologie, Chimie, Biologie, Institut de Recherches Servier, 125, chemin de Ronde, F-78290 Croissy-sur-Seine, France
| | - Jean-Louis Banères
- Faculté
de Pharmacie, Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Université Montpellier-ENSCM, 15 Avenue C. Flahault, F-34093 Montpellier, France
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239
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Prabudiansyah I, Kusters I, Caforio A, Driessen AJ. Characterization of the annular lipid shell of the Sec translocon. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2050-6. [DOI: 10.1016/j.bbamem.2015.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/24/2015] [Accepted: 06/26/2015] [Indexed: 11/16/2022]
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240
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Characterization of the direct interaction between KcsA-Kv1.3 and its inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1974-80. [DOI: 10.1016/j.bbamem.2015.06.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 05/28/2015] [Accepted: 06/08/2015] [Indexed: 11/19/2022]
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241
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Routledge SJ, Mikaliunaite L, Patel A, Clare M, Cartwright SP, Bawa Z, Wilks MDB, Low F, Hardy D, Rothnie AJ, Bill RM. The synthesis of recombinant membrane proteins in yeast for structural studies. Methods 2015; 95:26-37. [PMID: 26431670 DOI: 10.1016/j.ymeth.2015.09.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/28/2015] [Accepted: 09/29/2015] [Indexed: 12/22/2022] Open
Abstract
Historically, recombinant membrane protein production has been a major challenge meaning that many fewer membrane protein structures have been published than those of soluble proteins. However, there has been a recent, almost exponential increase in the number of membrane protein structures being deposited in the Protein Data Bank. This suggests that empirical methods are now available that can ensure the required protein supply for these difficult targets. This review focuses on methods that are available for protein production in yeast, which is an important source of recombinant eukaryotic membrane proteins. We provide an overview of approaches to optimize the expression plasmid, host cell and culture conditions, as well as the extraction and purification of functional protein for crystallization trials in preparation for structural studies.
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Affiliation(s)
- Sarah J Routledge
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Lina Mikaliunaite
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Anjana Patel
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Michelle Clare
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Stephanie P Cartwright
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Zharain Bawa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Martin D B Wilks
- Smallpeice Enterprises Ltd, 27 Newbold Terrace East, Leamington Spa, Warwickshire CV32 4ES, UK
| | - Floren Low
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - David Hardy
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Alice J Rothnie
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Roslyn M Bill
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK.
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242
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Nakatani-Webster E, Hu SL, Atkins WM, Catalano CE. Assembly and characterization of gp160-nanodiscs: A new platform for biochemical characterization of HIV envelope spikes. J Virol Methods 2015; 226:15-24. [PMID: 26424619 DOI: 10.1016/j.jviromet.2015.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 09/21/2015] [Accepted: 09/25/2015] [Indexed: 01/12/2023]
Abstract
The human immunodeficiency virus (HIV) is the causative agent of acquired immune deficiency syndrome (AIDS) and is thus responsible for significant morbidity and mortality worldwide. Despite considerable effort, preparation of an effective vaccine for AIDS has been elusive and it has become clear that a fundamental understanding of the relevant antigenic targets on HIV is essential. The Env trimer spike is the only viral antigen present on the surface of the viral particle and it is the target of all broadly neutralizing antibodies isolated to date. Thus, a soluble, homogeneous, and well-defined preparation of Env trimers is an important first step toward biochemical and structural characterization of the antigenic spike. Phospholipid bilayer nanodiscs represent a relatively new technology that can serve as a platform for the assembly of membrane proteins into a native membrane-like environment. Here we describe the preparation and characterization of unprocessed full-length, natively glycoslyated gp160 Env proteins incorporated into nanodiscs (gp160-ND). The particles are soluble and well defined in the absence of detergent, and possess a morphology anticipated of Env incorporated into a lipid ND. Importantly, the gp160-NDs retain CD4 and Env antibody binding characteristics expected of a functional trimer spike and their incorporation into a lipid membrane allows interrogation of epitopes associated with the membrane-proximal ectodomain region of gp41. These studies provide the groundwork for the use of gp160-ND in more detailed biochemical and structural studies that may set the stage for their use in vaccine development.
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Affiliation(s)
- Eri Nakatani-Webster
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, H-172 Health Sciences Building, Box 357610, Seattle, WA 98195, United States
| | - Shiu-Lok Hu
- Department of Pharmaceutics, School of Pharmacy, University of Washington, H272 Health Sciences Building, Box 357610, Seattle, WA 98195, United States
| | - William M Atkins
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, H-172 Health Sciences Building, Box 357610, Seattle, WA 98195, United States
| | - Carlos Enrique Catalano
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, H-172 Health Sciences Building, Box 357610, Seattle, WA 98195, United States.
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243
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Skaar K, Korza HJ, Tarry M, Sekyrova P, Högbom M. Expression and Subcellular Distribution of GFP-Tagged Human Tetraspanin Proteins in Saccharomyces cerevisiae. PLoS One 2015. [PMID: 26218426 PMCID: PMC4517926 DOI: 10.1371/journal.pone.0134041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Tetraspanins are integral membrane proteins that function as organizers of multimolecular complexes and modulate function of associated proteins. Mammalian genomes encode approximately 30 different members of this family and remotely related eukaryotic species also contain conserved tetraspanin homologs. Tetraspanins are involved in a number of fundamental processes such as regulation of cell migration, fusion, immunity and signaling. Moreover, they are implied in numerous pathological states including mental disorders, infectious diseases or cancer. Despite the great interest in tetraspanins, the structural and biochemical basis of their activity is still largely unknown. A major bottleneck lies in the difficulty of obtaining stable and homogeneous protein samples in large quantities. Here we report expression screening of 15 members of the human tetraspanin superfamily and successful protocols for the production in S. cerevisiae of a subset of tetraspanins involved in human cancer development. We have demonstrated the subcellular localization of overexpressed tetraspanin-green fluorescent protein fusion proteins in S. cerevisiae and found that despite being mislocalized, the fusion proteins are not degraded. The recombinantly produced tetraspanins are dispersed within the endoplasmic reticulum membranes or localized in granule-like structures in yeast cells. The recombinantly produced tetraspanins can be extracted from the membrane fraction and purified with detergents or the poly (styrene-co-maleic acid) polymer technique for use in further biochemical or biophysical studies.
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Affiliation(s)
- Karin Skaar
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Henryk J. Korza
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Michael Tarry
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Petra Sekyrova
- Department of Pharmacology and Physiology, Karolinska Institutet, Stockholm, Sweden
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
- * E-mail:
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244
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Affiliation(s)
- Samuel Furse
- Membrane Biochemistry & Biophysics, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands
| | - Maarten R. Egmond
- Membrane Biochemistry & Biophysics, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands
| | - J. Antoinette Killian
- Membrane Biochemistry & Biophysics, Universiteit Utrecht, Padualaan 8, Utrecht, The Netherlands
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245
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Bae HE, Gotfryd K, Thomas J, Hussain H, Ehsan M, Go J, Loland CJ, Byrne B, Chae PS. Deoxycholate-Based Glycosides (DCGs) for Membrane Protein Stabilisation. Chembiochem 2015; 16:1454-9. [PMID: 25953685 DOI: 10.1002/cbic.201500151] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Indexed: 12/16/2022]
Abstract
Detergents are an absolute requirement for studying the structure of membrane proteins. However, many conventional detergents fail to stabilise denaturation-sensitive membrane proteins, such as eukaryotic proteins and membrane protein complexes. New amphipathic agents with enhanced efficacy in stabilising membrane proteins will be helpful in overcoming the barriers to studying membrane protein structures. We have prepared a number of deoxycholate-based amphiphiles with carbohydrate head groups, designated deoxycholate-based glycosides (DCGs). These DCGs are the hydrophilic variants of previously reported deoxycholate-based N-oxides (DCAOs). Membrane proteins in these agents, particularly the branched diglucoside-bearing amphiphiles DCG-1 and DCG-2, displayed favourable behaviour compared to previously reported parent compounds (DCAOs) and conventional detergents (LDAO and DDM). Given their excellent properties, these agents should have significant potential for membrane protein studies.
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Affiliation(s)
- Hyoung Eun Bae
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Kamil Gotfryd
- Department of Neuroscience and Pharmacology, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark).,Present address: Department of Biomedical Sciences, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark)
| | - Jennifer Thomas
- Present address: MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 OQH (UK).,Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ (UK)
| | - Hazrat Hussain
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Muhammad Ehsan
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Juyeon Go
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea)
| | - Claus J Loland
- Department of Neuroscience and Pharmacology, University of Copenhagen, Nørre Alle 20, 2200 Copenhagen (Denmark)
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ (UK)
| | - Pil Seok Chae
- Department of Bionanotechnology, Hanyang University, Hanyangdaehak-ro, Ansan, 426-791 (Korea).
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246
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Bechara C, Robinson CV. Different Modes of Lipid Binding to Membrane Proteins Probed by Mass Spectrometry. J Am Chem Soc 2015; 137:5240-7. [DOI: 10.1021/jacs.5b00420] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chérine Bechara
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - Carol V. Robinson
- Department of Chemistry,
Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, United Kingdom
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247
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Hirano-Iwata A, Ishinari Y, Yamamoto H, Niwano M. Micro- and Nano-Technologies for Lipid Bilayer-Based Ion-Channel Functional Assays. Chem Asian J 2015; 10:1266-74. [DOI: 10.1002/asia.201403391] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Indexed: 11/06/2022]
Affiliation(s)
- Ayumi Hirano-Iwata
- CREST (Japan) Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
| | - Yutaka Ishinari
- CREST (Japan) Science and Technology Agency (JST); 4-1-8 Honcho Kawaguchi Saitama 332-0012 Japan
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
| | - Hideaki Yamamoto
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
- Frontier Research Institute for Interdisciplinary Sciences; Tohoku University; 6-3 Aoba Aramaki, Aoba-ku Sendai 980-8578 Japan
| | - Michio Niwano
- Graduate School of Biomedical Engineering; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
- Laboratory for Nanoelectronics and Spintronics; Research Institute of Electrical Communication; Tohoku University; 6-6 Aoba Aramaki, Aoba-ku Sendai 980-8579 Japan
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