1
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Ma C, Gong C. Considerations in production of the prokaryotic ZIP family transporters for structural and functional studies. Methods Enzymol 2023; 687:1-30. [PMID: 37666628 DOI: 10.1016/bs.mie.2023.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Zinc ions play essential roles as components of enzymes and many other important biomolecules, and are associated with numerous diseases. The uptake of Zn2+ and other metal ions require a widely distributed transporter protein family called Zrt/Irt-like Proteins (ZIP family), the majority members of which tend to have eight transmembrane helices with both N- and C- termini located on the extracellular or periplasmic side. Their small sizes and dynamic conformations bring many difficulties in their production for structural studies either by crystallography or Cryo-EM. Here, we summarize the problems that may encounter at the various steps of processing the ZIP proteins from gene to structural and functional studies, and provide some solutions and examples from our and other labs for the cloning, expression, purification, stability screening, metal ion transport assays and structural studies of prokaryotic ZIP family transporters using Escherichia coli as a heterologous host.
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Affiliation(s)
- Cheng Ma
- Protein Facility, Zhejiang University School of Medicine, Hangzhou, P.R. China; The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China.
| | - Caixia Gong
- The First Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, P.R. China; Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, Hangzhou, P.R. China.
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2
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Catania R, Machin J, Rappolt M, Muench SP, Beales PA, Jeuken LJC. Detergent-Free Functionalization of Hybrid Vesicles with Membrane Proteins Using SMALPs. Macromolecules 2022; 55:3415-3422. [PMID: 35571225 PMCID: PMC9097535 DOI: 10.1021/acs.macromol.2c00326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/08/2022] [Indexed: 11/28/2022]
Abstract
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Hybrid
vesicles (HVs) that consist of mixtures of block copolymers
and lipids are robust biomimetics of liposomes, providing a valuable
building block in bionanotechnology, catalysis, and synthetic biology.
However, functionalization of HVs with membrane proteins remains laborious
and expensive, creating a significant current challenge in the field.
Here, using a new approach of extraction with styrene-maleic acid
(SMA), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9
± 13.5% without the requirement of detergent, long incubation
times, or mechanical disruption. Direct transfer of membrane proteins
using this approach was not possible into liposomes, suggesting that
HVs are more amenable than liposomes to membrane protein incorporation
from a SMA lipid particle system. Finally, we show that this transfer
method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
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Affiliation(s)
- Rosa Catania
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Jonathan Machin
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Michael Rappolt
- School of Food Science and Nutrition, University of Leeds, Leeds LS2 9JT, U.K
| | - Stephen P. Muench
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A. Beales
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Lars J. C. Jeuken
- Astbury Centre of Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, U.K
- Leiden Institute of Chemistry, University Leiden, Leiden 2300RA, The Netherlands
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3
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Ma C, Gong C. Expression, Purification and Characterization of a ZIP Family Transporter from Desulfovibrio vulgaris. Protein J 2021; 40:776-785. [PMID: 34101092 DOI: 10.1007/s10930-021-10008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
The ZIP family transport zinc ions from the extracellular medium across the plasma membrane or from the intracellular compartments across endomembranes, which play fundamental roles in metal homeostasis and are broadly involved in physiological and pathological processes. Desulfovibrio is the predominant sulphate-reducing bacteria in human colonic microbiota, but also a potential choice for metal bioremediation. while, there are no published studies describing the zinc transporters from Desulfovibrio up to now. In this study, we obtained for the first time a heterologously expressed ZIP homolog from Desulfovibrio vulgaris, termed dvZip. The purified dvZip was reconstituted into proteoliposomes, and confirmed its zinc transport ability in vitro. By combining topology prediction, homology modeling and phylogenetic approaches, we also noticed that dvZip belongs to the GufA and probably have 8 transmembrane α-helical segments (TM 1-8) in which both termini are located on the extracellular, with TM2, 4, 5 and 7 create an inner bundle. We believe that purification and characterization of zinc (probably also cadmium) transporters from Desulfovibrio vulgaris such as dvZip could shed light on understanding of metal homeostasis of Desulfovibrio and provided protein products for future detailed function and structural studies.
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Affiliation(s)
- Cheng Ma
- Protein Facility, Zhejiang University School of Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Caixia Gong
- Department of Geriatrics, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310058, China
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4
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Membrane protein engineering to the rescue. Biochem Soc Trans 2018; 46:1541-1549. [PMID: 30381335 DOI: 10.1042/bst20180140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 02/07/2023]
Abstract
The inherent hydrophobicity of membrane proteins is a major barrier to membrane protein research and understanding. Their low stability and solubility in aqueous environments coupled with poor expression levels make them a challenging area of research. For many years, the only way of working with membrane proteins was to optimise the environment to suit the protein, through the use of different detergents, solubilising additives, and other adaptations. However, with innovative protein engineering methodologies, the membrane proteins themselves are now being adapted to suit the environment. This mini-review looks at the types of adaptations which are applied to membrane proteins from a variety of different fields, including water solubilising fusion tags, thermostabilising mutation screening, scaffold proteins, stabilising protein chimeras, and isolating water-soluble domains.
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5
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Parmar M, Rawson S, Scarff CA, Goldman A, Dafforn TR, Muench SP, Postis VLG. Using a SMALP platform to determine a sub-nm single particle cryo-EM membrane protein structure. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2018; 1860:378-383. [PMID: 28993151 PMCID: PMC5780298 DOI: 10.1016/j.bbamem.2017.10.005] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/10/2023]
Abstract
The field of membrane protein structural biology has been revolutionized over the last few years with a number of high profile structures being solved using cryo-EM including Piezo, Ryanodine receptor, TRPV1 and the Glutamate receptor. Further developments in the EM field hold the promise of even greater progress in terms of greater resolution, which for membrane proteins is still typically within the 4-7Å range. One advantage of a cryo-EM approach is the ability to study membrane proteins in more "native" like environments for example proteoliposomes, amphipols and nanodiscs. Recently, styrene maleic acid co-polymers (SMA) have been used to extract membrane proteins surrounded by native lipids (SMALPs) maintaining a more natural environment. We report here the structure of the Escherichia coli multidrug efflux transporter AcrB in a SMALP scaffold to sub-nm resolution, with the resulting map being consistent with high resolution crystal structures and other EM derived maps. However, both the C-terminal helix (TM12) and TM7 are poorly defined in the map. These helices are at the exterior of the helical bundle and form the greater interaction with the native lipids and SMA polymer and may represent a more dynamic region of the protein. This work shows the promise of using an SMA approach for single particle cryo-EM studies to provide sub-nm structures.
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Affiliation(s)
- Mayuriben Parmar
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Charlotte A Scarff
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK
| | - Adrian Goldman
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK; Department of Biosciences, Division of Biochemistry, University of Helsinki, Helsinki, Finland
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.
| | - Vincent L G Postis
- Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK; School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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6
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Membrane proteins structures: A review on computational modeling tools. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2021-2039. [DOI: 10.1016/j.bbamem.2017.07.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/04/2017] [Accepted: 07/13/2017] [Indexed: 01/02/2023]
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7
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Pollock NL, Lee SC, Patel JH, Gulamhussein AA, Rothnie AJ. Structure and function of membrane proteins encapsulated in a polymer-bound lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:809-817. [PMID: 28865797 DOI: 10.1016/j.bbamem.2017.08.012] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022]
Abstract
New technologies for the purification of stable membrane proteins have emerged in recent years, in particular methods that allow the preparation of membrane proteins with their native lipid environment. Here, we look at the progress achieved with the use of styrene-maleic acid copolymers (SMA) which are able to insert into biological membranes forming nanoparticles containing membrane proteins and lipids. This technology can be applied to membrane proteins from any host source, and, uniquely, allows purification without the protein ever being removed from a lipid bilayer. Not only do these SMA lipid particles (SMALPs) stabilise membrane proteins, allowing structural and functional studies, but they also offer opportunities to understand the local lipid environment of the host membrane. With any new or different method, questions inevitably arise about the integrity of the protein purified: does it retain its activity; its native structure; and ability to perform its function? How do membrane proteins within SMALPS perform in existing assays and lend themselves to analysis by established methods? We outline here recent work on the structure and function of membrane proteins that have been encapsulated like this in a polymer-bound lipid bilayer, and the potential for the future with this approach. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.
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Affiliation(s)
- Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jaimin H Patel
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Alice J Rothnie
- School of Life and Health Sciences, Aston University, Birmingham B4 7ET, UK.
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8
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Abstract
Membrane proteins play crucial roles in cellular processes and are often important pharmacological drug targets. The hydrophobic properties of these proteins make full structural and functional characterization challenging because of the need to use detergents or other solubilizing agents when extracting them from their native lipid membranes. To aid membrane protein research, new methodologies are required to allow these proteins to be expressed and purified cheaply, easily, in high yield and to provide water soluble proteins for subsequent study. This mini review focuses on the relatively new area of water soluble membrane proteins and in particular two innovative approaches: the redesign of membrane proteins to yield water soluble variants and how adding solubilizing fusion proteins can help to overcome these challenges. This review also looks at naturally occurring membrane proteins, which are able to exist as stable, functional, water soluble assemblies with no alteration to their native sequence.
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9
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Hiruma-Shimizu K, Shimizu H, Thompson GS, Kalverda AP, Patching SG. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications. Mol Membr Biol 2016; 32:139-55. [DOI: 10.3109/09687688.2015.1125536] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Hiroki Shimizu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Hokkaido, Japan,
| | - Gary S. Thompson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
| | - Arnout P. Kalverda
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK,
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK, and
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10
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Kraft TE, Hresko RC, Hruz PW. Expression, purification, and functional characterization of the insulin-responsive facilitative glucose transporter GLUT4. Protein Sci 2015; 24:2008-19. [PMID: 26402434 PMCID: PMC4815238 DOI: 10.1002/pro.2812] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/09/2015] [Accepted: 09/21/2015] [Indexed: 12/24/2022]
Abstract
The insulin-responsive facilitative glucose transporter GLUT4 is of fundamental importance for maintenance of glucose homeostasis. Despite intensive effort, the ability to express and purify sufficient quantities of structurally and functionally intact protein for biophysical analysis has previously been exceedingly difficult. We report here the development of novel methods to express, purify, and functionally reconstitute GLUT4 into detergent micelles and proteoliposomes. Rat GLUT4 containing FLAG and His tags at the amino and carboxy termini, respectively, was engineered and stably transfected into HEK-293 cells. Overexpression in suspension culture yielded over 1.5 mg of protein per liter of culture. Systematic screening of detergent solubilized GLUT4-GFP fusion protein via fluorescent-detection size exclusion chromatography identified lauryl maltose neopentyl glycol (LMNG) as highly effective for isolating monomeric GLUT4 micelles. Preservation of structural integrity and ligand binding was demonstrated via quenching of tryptophan fluorescence and competition of ATB-BMPA photolabeling by cytochalasin B. GLUT4 was reconstituted into lipid nanodiscs and proper folding was confirmed. Reconstitution of purified GLUT4 with amphipol A8-35 stabilized the transporter at elevated temperatures for extended periods of time. Functional activity of purified GLUT4 was confirmed by reconstitution of LMNG-purified GLUT4 into proteoliposomes and measurement of saturable uptake of D-glucose over L-glucose. Taken together, these data validate the development of an efficient means to generate milligram quantities of stable and functionally intact GLUT4 that is suitable for a wide array of biochemical and biophysical analyses.
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Affiliation(s)
- Thomas E Kraft
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, 63110
| | - Richard C Hresko
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, 63110
| | - Paul W Hruz
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, 63110
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri, 63110
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11
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Lantez V, Nikolaidis I, Rechenmann M, Vernet T, Noirclerc-Savoye M. Rapid automated detergent screening for the solubilization and purification of membrane proteins and complexes. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400187] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Violaine Lantez
- Université Grenoble Alpes, IBS; Grenoble France
- CEA, IBS; Grenoble France
- CNRS, IBS; Grenoble France
| | - Ioulia Nikolaidis
- Université Grenoble Alpes, IBS; Grenoble France
- CEA, IBS; Grenoble France
- CNRS, IBS; Grenoble France
- Department of Biochemistry of Membranes; Bijvoet Center for Biomolecular Research, Utrecht University; The Netherlands
| | - Mathias Rechenmann
- Université Grenoble Alpes, IBS; Grenoble France
- CEA, IBS; Grenoble France
- CNRS, IBS; Grenoble France
| | - Thierry Vernet
- Université Grenoble Alpes, IBS; Grenoble France
- CEA, IBS; Grenoble France
- CNRS, IBS; Grenoble France
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12
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Postis V, Rawson S, Mitchell JK, Lee SC, Parslow RA, Dafforn TR, Baldwin SA, Muench SP. The use of SMALPs as a novel membrane protein scaffold for structure study by negative stain electron microscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1848:496-501. [PMID: 25450810 PMCID: PMC4331651 DOI: 10.1016/j.bbamem.2014.10.018] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 10/06/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022]
Abstract
Despite the great progress recently made in resolving their structures, investigation of the structural biology of membrane proteins still presents major challenges. Even with new technical advances such as lipidic cubic phase crystallisation, obtaining well-ordered crystals remains a significant hurdle in membrane protein X-ray crystallographic studies. As an alternative, electron microscopy has been shown to be capable of resolving > 3.5 Å resolution detail in membrane proteins of modest (~ 300 kDa) size, without the need for crystals. However, the conventional use of detergents for either approach presents several issues, including the possible effects on structure of removing the proteins from their natural membrane environment. As an alternative, it has recently been demonstrated that membrane proteins can be effectively isolated, in the absence of detergents, using a styrene maleic acid co-polymer (SMA). This approach yields SMA lipid particles (SMALPs) in which the membrane proteins are surrounded by a small disk of lipid bilayer encircled by polymer. Here we use the Escherichia coli secondary transporter AcrB as a model membrane protein to demonstrate how a SMALP scaffold can be used to visualise membrane proteins, embedded in a near-native lipid environment, by negative stain electron microscopy, yielding structures at a modest resolution in a short (days) timeframe. Moreover, we show that AcrB within a SMALP scaffold is significantly more active than the equivalent DDM stabilised form. The advantages of SMALP scaffolds within electron microscopy are discussed and we conclude that they may prove to be an important tool in studying membrane protein structure and function. Maintaining membrane proteins in a native-like environment is difficult. SMALP scaffolds efficiently extract AcrB from the membrane. We show SMALP scaffolds to be a robust tool for rapid structural analysis by EM.
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Affiliation(s)
- Vincent Postis
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK; Biomedicine Research Group, Faculty of Health and Social Sciences, Leeds Beckett University, LS1 3HE, UK
| | - Shaun Rawson
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Jennifer K Mitchell
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Rosemary A Parslow
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Tim R Dafforn
- School of Biosciences, University of Birmingham, Birmingham, Edgbaston B15 2TT, UK
| | - Stephen A Baldwin
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK.
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13
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Detergent quantification in membrane protein samples and its application to crystallization experiments. Amino Acids 2013; 45:1293-302. [PMID: 24105076 DOI: 10.1007/s00726-013-1600-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The structural characterization of membrane proteins remains a challenging field, largely because the use of stabilizing detergents is required. Researchers must first select a suitable detergent for the solubility and stability of their protein during in vitro studies. In addition, an appropriate concentration of detergent in membrane protein samples can be essential for protein solubility, stability, and experimental success. For example, in membrane protein crystallography, detergent concentration in the crystallization drop can be a critical parameter influencing crystal growth. Over the past decade, multiple techniques have been developed for the measurement of detergent concentration using a wide variety of strategies. These methods include colorimetric reactions, which target specific detergent classes, and analytical techniques applicable to a wide variety of detergents. This review will summarize and discuss the available options. It will be a useful resource to those selecting a strategy that best fits their experimental requirements and available instruments.
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14
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Pollock NL, McDevitt CA, Collins R, Niesten PHM, Prince S, Kerr ID, Ford RC, Callaghan R. Improving the stability and function of purified ABCB1 and ABCA4: the influence of membrane lipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:134-47. [PMID: 24036079 DOI: 10.1016/j.bbamem.2013.09.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 08/27/2013] [Accepted: 09/03/2013] [Indexed: 12/17/2022]
Abstract
ATP Binding Cassette (ABC) transporters play prominent roles in numerous cellular processes and many have been implicated in human diseases. Unfortunately, detailed mechanistic information on the majority of ABC transporters has not yet been elucidated. The slow rate of progress of molecular and high resolution structural studies may be attributed to the difficulty in the investigation of integral membrane proteins. These difficulties include the expression of functional, non-aggregated protein in heterologous systems. Furthermore, the extraction of membrane proteins from source material remains a major bottle-neck in the process since there are relatively few guidelines for selection of an appropriate detergent to achieve optimal extraction. Whilst affinity tag strategies have simplified the purification of membrane proteins; many challenges remain. For example, the chromatographic process and associated steps can rapidly lead to functional inactivation, random aggregation, or even precipitation of the target protein. Furthermore, optimisation of high yield and purity, does not guarantee successful structure determination. Based on this series of potential issues, any investigation into structure-function of membrane proteins requires a systematic evaluation of preparation quality. In particular, the evaluation should focus on function, homogeneity and mono-dispersity. The present investigation provides a detailed assessment of the quality of purified ATP Binding Cassette (ABC) transporters; namely ABCB1 (P-gp) and ABCA4 (ABCR). A number of suggestions are provided to facilitate the production of functional, homogeneous and mono-disperse preparations using the insect cell expression system. Finally, the ABCA4 samples have been used to provide structural insights into this essential photo-receptor cell protein.
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Affiliation(s)
- Naomi L Pollock
- Nuffield Department of Clinical Laboratory Sciences, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
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15
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Postis VGL, Rawlings AE, Lesiuk A, Baldwin SA. Use of Escherichia coli for the production and purification of membrane proteins. Methods Mol Biol 2013; 998:33-54. [PMID: 23529419 DOI: 10.1007/978-1-62703-351-0_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Individual types of ion channels and other membrane proteins are typically expressed only at low levels in their native membranes, rendering their isolation by conventional purification techniques difficult. The heterologous over-expression of such proteins is therefore usually a prerequisite for their purification in amounts suitable for structural and for many functional investigations. The most straightforward expression host, suitable for prokaryote membrane proteins and some proteins from eukaryotes, is the bacterium Escherichia coli. Here we describe the use of this expression system for production of functionally active polytopic membrane proteins and methods for their purification by affinity chromatography in amounts up to tens of milligrams.
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Affiliation(s)
- Vincent G L Postis
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds, UK
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16
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Abstract
Urea is exploited as a nitrogen source by bacteria, and its breakdown products, ammonia and bicarbonate, are employed to counteract stomach acidity in pathogens such as Helicobacter pylori. Uptake in the latter is mediated by UreI, a UAC (urea amide channel) family member. In the present paper, we describe the structure and function of UACBc, a homologue from Bacillus cereus. The purified channel was found to be permeable not only to urea, but also to other small amides. CD and IR spectroscopy revealed a structure comprising mainly α-helices, oriented approximately perpendicular to the membrane. Consistent with this finding, site-directed fluorescent labelling indicated the presence of seven TM (transmembrane) helices, with a cytoplasmic C-terminus. In detergent, UACBc exists largely as a hexamer, as demonstrated by both cross-linking and size-exclusion chromatography. A 9 Å (1 Å=0.1 nm) resolution projection map obtained by cryo-electron microscopy of two-dimensional crystals shows that the six protomers are arranged in a planar hexameric ring. Each exhibits six density features attributable to TM helices, surrounding a putative central channel, while an additional helix is peripherally located. Bioinformatic analyses allowed individual TM regions to be tentatively assigned to the density features, with the resultant model enabling identification of residues likely to contribute to channel function.
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17
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Miller JL, Tate CG. Engineering an ultra-thermostable β(1)-adrenoceptor. J Mol Biol 2011; 413:628-38. [PMID: 21907721 DOI: 10.1016/j.jmb.2011.08.057] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 08/26/2011] [Accepted: 08/29/2011] [Indexed: 02/04/2023]
Abstract
Conformational thermostabilisation of G-protein-coupled receptors is a successful strategy for their structure determination. The thermostable mutants tolerate short-chain detergents, such as octylglucoside and nonylglucoside, which are ideal for crystallography, and in addition, the receptors are preferentially in a single conformational state. The first thermostabilised receptor to have its structure determined was the β(1)-adrenoceptor mutant β(1)AR-m23 bound to the antagonist cyanopindolol, and recently, additional structures have been determined with agonist bound. Here, we describe further stabilisation of β(1)AR-m23 by the addition of three thermostabilising mutations (I129V, D322K, and Y343L) to make a mutant receptor that is 31 °C more thermostable than the wild-type receptor in dodecylmaltoside and is 13 °C more thermostable than β(1)AR-m23 in nonylglucoside. Although a number of thermostabilisation methods were tried, including rational design of disulfide bonds and engineered zinc bridges, the two most successful strategies to improve the thermostability of β(1)AR-m23 were an engineered salt bridge and leucine scanning mutagenesis. The three additional thermostabilising mutations did not significantly affect the pharmacological properties of β(1)AR-m23, but the new mutant receptor was significantly more stable in short-chain detergents such as heptylthioglucoside and denaturing detergents such as SDS.
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High throughput platforms for structural genomics of integral membrane proteins. Curr Opin Struct Biol 2011; 21:517-22. [PMID: 21807498 DOI: 10.1016/j.sbi.2011.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Revised: 06/20/2011] [Accepted: 07/07/2011] [Indexed: 11/20/2022]
Abstract
Structural genomics approaches on integral membrane proteins have been postulated for over a decade, yet specific efforts are lagging years behind their soluble counterparts. Indeed, high throughput methodologies for production and characterization of prokaryotic integral membrane proteins are only now emerging, while large-scale efforts for eukaryotic ones are still in their infancy. Presented here is a review of recent literature on actively ongoing structural genomics of membrane protein initiatives, with a focus on those aimed at implementing interesting techniques aimed at increasing our rate of success for this class of macromolecules.
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Fan J, Huang B, Wang X, Zhang XC. Thermal precipitation fluorescence assay for protein stability screening. J Struct Biol 2011; 175:465-8. [PMID: 21600987 DOI: 10.1016/j.jsb.2011.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 04/22/2011] [Accepted: 05/05/2011] [Indexed: 10/18/2022]
Abstract
A simple and reliable method of protein stability assessment is desirable for high throughput expression screening of recombinant proteins. Here we described an assay termed thermal precipitation fluorescence (TPF) which can be used to compare thermal stabilities of recombinant protein samples directly from cell lysate supernatants. In this assay, target membrane proteins are expressed as recombinant fusions with a green fluorescence protein tag and solubilized with detergent, and the fluorescence signals are used to report the quantity of the fusion proteins in the soluble fraction of the cell lysate. After applying a heat shock, insoluble protein aggregates are removed by centrifugation. Subsequently, the amount of remaining protein in the supernatant is quantified by in-gel fluorescence analysis and compared to samples without a heat shock treatment. Over 60 recombinant membrane proteins from Escherichia coli were subject to this screening in the presence and absence of a few commonly used detergents, and the results were analyzed. Because no sophisticated protein purification is required, this TPF technique is suitable to high throughput expression screening of recombinant membrane proteins as well as soluble ones and can be used to prioritize target proteins based on their thermal stabilities for subsequent large scale expression and structural studies.
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Affiliation(s)
- Junping Fan
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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Magliery TJ, Lavinder JJ, Sullivan BJ. Protein stability by number: high-throughput and statistical approaches to one of protein science's most difficult problems. Curr Opin Chem Biol 2011; 15:443-51. [PMID: 21498105 DOI: 10.1016/j.cbpa.2011.03.015] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/18/2011] [Accepted: 03/18/2011] [Indexed: 01/24/2023]
Abstract
Most proteins are only barely stable, which impedes research, complicates therapeutic applications, and makes proteins susceptible to pathologically destabilizing mutations. Our ability to predict the thermodynamic consequences of even single point mutations is still surprisingly limited, and established methods of measuring stability are slow. Recent advances are bringing protein stability studies into the high-throughput realm. Some methods are based on inferential read-outs such as activity, proteolytic resistance or split-protein fragment reassembly. Other methods use miniaturization of direct measurements, such as intrinsic fluorescence, H/D exchange, cysteine reactivity, aggregation and hydrophobic dye binding (DSF). Protein engineering based on statistical analysis (consensus and correlated occurrences of amino acids) is promising, but much work remains to understand and implement these methods.
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Affiliation(s)
- Thomas J Magliery
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA.
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Fan J, Heng J, Dai S, Shaw N, Zhou B, Huang B, He Z, Wang Y, Jiang T, Li X, Liu Z, Wang X, Zhang XC. An efficient strategy for high throughput screening of recombinant integral membrane protein expression and stability. Protein Expr Purif 2011; 78:6-13. [PMID: 21354311 DOI: 10.1016/j.pep.2011.02.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/14/2011] [Accepted: 02/18/2011] [Indexed: 02/05/2023]
Abstract
Membrane proteins account for about 30% of the genomes sequenced to date and play important roles in a variety of cellular functions. However, determining the three-dimensional structures of membrane proteins continues to pose a major challenge for structural biologists due to difficulties in recombinant expression and purification. We describe here a high throughput pipeline for Escherichia coli based membrane protein expression and purification. A ligation-independent cloning (LIC)-based vector encoding a C-terminal green fluorescence protein (GFP) tag was used for cloning in a high throughput mode. The GFP tag facilitated expression screening in E. coli through both cell culture fluorescence measurements and in-gel fluorescence imaging. Positive candidates from the GFP screening were subsequently sub-cloned into a LIC-based, GFP free vector for further expression and purification. The expressed, C-terminal His-tagged membrane proteins were purified via membrane enrichment and Ni-affinity chromatography. Thermofluor technique was applied to screen optimal buffers and detergents for the purified membrane proteins. This pipeline has been successfully tested for membrane proteins from E. coli and can be potentially expanded to other prokaryotes.
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Affiliation(s)
- Junping Fan
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China
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