151
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Marek M, Milles S, Schreiber G, Daleke DL, Dittmar G, Herrmann A, Müller P, Pomorski TG. The yeast plasma membrane ATP binding cassette (ABC) transporter Aus1: purification, characterization, and the effect of lipids on its activity. J Biol Chem 2011; 286:21835-43. [PMID: 21521689 DOI: 10.1074/jbc.m111.244525] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The ATP binding cassette (ABC) transporter Aus1 is expressed under anaerobic growth conditions at the plasma membrane of the yeast Saccharomyces cerevisiae and is required for sterol uptake. These observations suggest that Aus1 promotes the translocation of sterols across membranes, but the precise transport mechanism has yet to be identified. In this study, an extraction and purification procedure was developed to characterize the Aus1 transporter. The detergent-solubilized protein was able to bind and hydrolyze ATP. Mutagenesis of the conserved lysine to methionine in the Walker A motif abolished ATP hydrolysis. Likewise, ATP hydrolysis was inhibited by classical inhibitors of ABC transporters. Upon reconstitution into proteoliposomes, the ATPase activity of Aus1 was specifically stimulated by phosphatidylserine (PS) in a stereoselective manner. We also found that Aus1-dependent sterol uptake, but not Aus1 expression and trafficking to the plasma membrane, was affected by changes in cellular PS levels. These results suggest a direct interaction between Aus1 and PS that is critical for the activity of the transporter.
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Affiliation(s)
- Magdalena Marek
- Institute of Biology, Humboldt University of Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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152
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Tokuda N, Igarashi K, Shimamura T, Yurugi-Kobayashi T, Shiroishi M, Ito K, Sugawara T, Asada H, Murata T, Nomura N, Iwata S, Kobayashi T. Cloning, expression and purification of the anion exchanger 1 homologue from the basidiomycete Phanerochaete chrysosporium. Protein Expr Purif 2011; 79:81-7. [PMID: 21515379 DOI: 10.1016/j.pep.2011.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Revised: 04/06/2011] [Accepted: 04/08/2011] [Indexed: 11/27/2022]
Abstract
Anion exchangers are membrane proteins that have been identified in a wide variety of species, where they transport Cl(-) and HCO3(-)across the cell membrane. In this study, we cloned an anion-exchange protein from the genome of the basidiomycete Phanerochaete chrysosporium (PcAEP). PcAEP is a 618-amino acid protein that is homologous to the human anion exchanger (AE1) with 22.9% identity and 40.3% similarity. PcAEP was overexpressed by introducing the PcAEP gene into the genome of Pichia pastoris. As a result, PcAEP localized in the membrane of P. pastoris and was solubilized successfully by n-dodecyl-β-D-maltoside. His-tagged PcAEP was purified as a single band on SDS-PAGE using immobilized metal affinity chromatography and gel filtration chromatography. Purified PcAEP was found to bind to SITS, an inhibitor of the AE family, suggesting that the purified protein is folded properly. PcAEP expressed and purified using the present system could be useful for biological and structural studies of the anion exchange family of proteins.
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Affiliation(s)
- Natsuko Tokuda
- Department of Medical Chemistry, Kyoto University Faculty of Medicine, Sakyo-ku, Kyoto, Japan
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153
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Qin X, Qian J, Xiao C, Zhuang Y, Zhang S, Chu J. Reliable high-throughput approach for screening of engineered constitutive promoters in the yeast Pichia pastoris. Lett Appl Microbiol 2011; 52:634-41. [PMID: 21449926 DOI: 10.1111/j.1472-765x.2011.03051.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop a reliable and sensitive high-throughput approach for the screening of engineered constitutive promoters in the yeast Pichia pastoris. METHODS AND RESULTS The yeast-enhanced green fluorescent protein (yEGFP) was used as the reporter to monitor the promoter strength. After eliminating the interfering components (yeast extract and tryptone) with fluorescence signal from the medium, a high-throughput screening approach was established and optimized to obtain a low standard deviation of cell density (6.9%) and fluorescence (7.4%) in 48-deep-well microplates. Then, 300 clones containing GAP promoter (P(GAP)) variants were screened, exhibiting a wide range in fluorescent intensity from about 8% to 218% of that obtained with P(GAP). Six representative clones with unique promoter sequence were picked for further characterization. A good correlation between yEGFP fluorescence in microplates and shake flasks was observed. Furthermore, the high correlation between fluorescence and transcript levels confirmed that expression was transcriptionally controlled. CONCLUSIONS We developed a reliable high-throughput screening approach that can be used to select engineered constitutive promoters of varying strengths. SIGNIFICANCE AND IMPACT OF THE STUDY This approach is expected to accelerate the selection of constitutive promoters in P. pastoris and can also be applied for the screening of other constitutive expression clones.
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Affiliation(s)
- X Qin
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, China
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154
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Bill RM, Henderson PJF, Iwata S, Kunji ERS, Michel H, Neutze R, Newstead S, Poolman B, Tate CG, Vogel H. Overcoming barriers to membrane protein structure determination. Nat Biotechnol 2011; 29:335-40. [PMID: 21478852 DOI: 10.1038/nbt.1833] [Citation(s) in RCA: 275] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
After decades of slow progress, the pace of research on membrane protein structures is beginning to quicken thanks to various improvements in technology, including protein engineering and microfocus X-ray diffraction. Here we review these developments and, where possible, highlight generic new approaches to solving membrane protein structures based on recent technological advances. Rational approaches to overcoming the bottlenecks in the field are urgently required as membrane proteins, which typically comprise ~30% of the proteomes of organisms, are dramatically under-represented in the structural database of the Protein Data Bank.
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Affiliation(s)
- Roslyn M Bill
- School of Life and Health Sciences, Aston University, Birmingham, UK
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155
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Abstract
The determination of membrane structures presents the structural biologist with many challenges; however, the last two years have seen major advances in our ability to resolve these structures at atomic resolution. My goal here is to summarize some of the most recent advances that have enhanced our prospects for understanding membrane proteins at the level of atomic structure.
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Affiliation(s)
- Robert Michael Stroud
- Department of Biochemistry & Biophysics, University of California San Francisco, S-412C Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517 USA
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156
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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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157
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Ihara M, Matsuura N, Yamashita A. High-resolution Native-PAGE for membrane proteins capable of fluorescence detection and hydrodynamic state evaluation. Anal Biochem 2011; 412:217-23. [PMID: 21291856 DOI: 10.1016/j.ab.2011.01.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Revised: 01/20/2011] [Accepted: 01/26/2011] [Indexed: 11/29/2022]
Abstract
An improved native polyacrylamide gel electrophoresis (PAGE) method capable of evaluating the hydrodynamic states of membrane proteins and allowing in-gel fluorescence detection was established. In this method, bis(alkyl) sulfosuccinate is used to provide negative charges for detergent-solubilized membrane proteins to facilitate proper electrophoretic migration without disturbing their native hydrodynamic states. The method achieved high-resolution electrophoretic separation, in good agreement with the elution profiles obtained by size exclusion chromatography. The applicability of in-gel fluorescence detection for tagged green fluorescent protein (GFP) facilitates the analysis of samples without any purification. This method might serve as a general analytical technique for assessing the folding, oligomerization, and protein complex formation of membrane proteins.
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Affiliation(s)
- Makoto Ihara
- Molecular Signaling Research Team, Structural Physiology Research Group, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 679-5148, Japan
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158
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Sonoda Y, Newstead S, Hu NJ, Alguel Y, Nji E, Beis K, Yashiro S, Lee C, Leung J, Cameron AD, Byrne B, Iwata S, Drew D. Benchmarking membrane protein detergent stability for improving throughput of high-resolution X-ray structures. Structure 2011; 19:17-25. [PMID: 21220112 PMCID: PMC3111809 DOI: 10.1016/j.str.2010.12.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 11/30/2010] [Accepted: 12/06/2010] [Indexed: 12/31/2022]
Abstract
Obtaining well-ordered crystals is a major hurdle to X-ray structure determination of membrane proteins. To facilitate crystal optimization, we investigated the detergent stability of 24 eukaryotic and prokaryotic membrane proteins, predominantly transporters, using a fluorescent-based unfolding assay. We have benchmarked the stability required for crystallization in small micelle detergents, as they are statistically more likely to lead to high-resolution structures. Using this information, we have been able to obtain well-diffracting crystals for a number of sodium and proton-dependent transporters. By including in the analysis seven membrane proteins for which structures are already known, AmtB, GlpG, Mhp1, GlpT, EmrD, NhaA, and LacY, it was further possible to demonstrate an overall trend between protein stability and structural resolution. We suggest that by monitoring membrane protein stability with reference to the benchmarks described here, greater efforts can be placed on constructs and conditions more likely to yield high-resolution structures.
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Affiliation(s)
- Yo Sonoda
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Simon Newstead
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Nien-Jen Hu
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Yilmaz Alguel
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Emmanuel Nji
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Konstantinos Beis
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
| | - Shoko Yashiro
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Chiara Lee
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - James Leung
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - Alexander D. Cameron
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Bernadette Byrne
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
| | - So Iwata
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 ODE, UK
- Japan Science and Technology Agency, ERATO, Human Receptor Crystallography Project, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, UK
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159
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Chae PS, Rasmussen SGF, Rana R, Gotfryd K, Chandra R, Goren MA, Kruse AC, Nurva S, Loland CJ, Pierre Y, Drew D, Popot JL, Picot D, Fox BG, Guan L, Gether U, Byrne B, Kobilka B, Gellman SH. Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins. Nat Methods 2010; 7:1003-8. [PMID: 21037590 PMCID: PMC3063152 DOI: 10.1038/nmeth.1526] [Citation(s) in RCA: 332] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Accepted: 09/30/2010] [Indexed: 11/09/2022]
Abstract
The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain difficult to study owing to a lack of suitable detergents. We introduce a class of amphiphiles, each built around a central quaternary carbon atom derived from neopentyl glycol, with hydrophilic groups derived from maltose. Representatives of this maltose-neopentyl glycol (MNG) amphiphile family show favorable behavior relative to conventional detergents, as manifested in multiple membrane protein systems, leading to enhanced structural stability and successful crystallization. MNG amphiphiles are promising tools for membrane protein science because of the ease with which they may be prepared and the facility with which their structures may be varied.
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Affiliation(s)
- Pil Seok Chae
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Rohini Rana
- Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Kamil Gotfryd
- Molecular Neuropharmacology Group Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Richa Chandra
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Michael A. Goren
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Andrew C. Kruse
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Shailika Nurva
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Claus J. Loland
- Molecular Neuropharmacology Group Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Yves Pierre
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, Paris, France
| | - David Drew
- Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Jean-Luc Popot
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, Paris, France
| | - Daniel Picot
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, CNRS/Université Paris-7 UMR 7099, Institut de Biologie Physico-Chimique, Paris, France
| | - Brian G. Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ulrik Gether
- Molecular Neuropharmacology Group Department of Neuroscience and Pharmacology, The Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Bernadette Byrne
- Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Brian Kobilka
- Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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160
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Cysteine-to-serine shuffling using a Saccharomyces cerevisiae expression system improves protein secretion: case of a nonglycosylated mutant of miraculin, a taste-modifying protein. Biotechnol Lett 2010; 33:103-7. [PMID: 20936326 DOI: 10.1007/s10529-010-0399-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 08/27/2010] [Indexed: 10/19/2022]
Abstract
PURPOSE OF WORK Soluble protein expression is an important first step during various types of protein studies. Here, we present the screening strategy of secretable mutant. The strategy aimed to identify those cysteine residues that provoke protein misfolding in the heterologous expression system. Intentional mutagenesis studies should consider the size of the library and the time required for expression screening. Here, we proposed a cysteine-to-serine shuffling mutation strategy (CS shuffling) using a Saccharomyces cerevisiae expression system. This strategy of site-directed shuffling mutagenesis of cysteine-to-serine residues aims to identify the cysteine residues that cause protein misfolding in heterologous expression. In the case of a nonglycosylated mutant of the taste-modifying protein miraculin (MCL), which was used here as a model protein, 25% of all constructs obtained from CS shuffling expressed MCL mutant, and serine mutations were found at Cys47 or Cys92, which are involved in the formation of the disulfide bond. This indicates that these residues had the potential to provoke protein misfolding via incorrect disulfide bonding. The CS shuffling can be performed using a small library and within one week, and is an effective screening strategy of soluble protein expression.
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161
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Suzuki N, Hiraki M, Yamada Y, Matsugaki N, Igarashi N, Kato R, Dikic I, Drew D, Iwata S, Wakatsuki S, Kawasaki M. Crystallization of small proteins assisted by green fluorescent protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:1059-66. [PMID: 20944239 DOI: 10.1107/s0907444910032944] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 08/16/2010] [Indexed: 11/11/2022]
Abstract
The generation of crystal lattice contacts by proteinaceous tags fused to target proteins is an attractive approach to aid in the crystallization of otherwise intractable proteins. Here, the use of green fluorescent protein (GFP) fusions for this purpose is demonstrated, using ubiquitin and the ubiquitin-binding motif (UBM) of Y-family polymerase ι as examples. The structure of the GFP-ubiquitin fusion protein revealed that the crystal lattice was formed by GFP moieties. Ubiquitin was accommodated in the lattice through interactions with the peripheral loops of GFP. However, in the GFP-UBM fusion crystal UBM formed extensive interactions with GFP and these interactions, together with UBM dimerization, mediated the crystal packing. Interestingly, the tyrosine residues that are involved in mediating crystal contacts in both GFP-ubiquitin and GFP-UBM crystals are arranged in a belt on the surface of the β-barrel structure of GFP. Therefore, it is likely that GFP can assist in the crystallization of small proteins and of protein domains in general.
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Affiliation(s)
- Nobuhiro Suzuki
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
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162
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Hsieh JM, Besserer GM, Madej MG, Bui HQ, Kwon S, Abramson J. Bridging the gap: a GFP-based strategy for overexpression and purification of membrane proteins with intra and extracellular C-termini. Protein Sci 2010; 19:868-80. [PMID: 20196076 DOI: 10.1002/pro.365] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Low expression and instability during isolation are major obstacles preventing adequate structure-function characterization of membrane proteins (MPs). To increase the likelihood of generating large quantities of protein, C-terminally fused green fluorescent protein (GFP) is commonly used as a reporter for monitoring expression and evaluating purification. This technique has mainly been restricted to MPs with intracellular C-termini (C(in)) due to GFP's inability to fluoresce in the Escherichia coli periplasm. With the aid of Glycophorin A, a single transmembrane spanning protein, we developed a method to convert MPs with extracellular C-termini (C(out)) to C(in) ones providing a conduit for implementing GFP reporting. We tested this method on eleven MPs with predicted C(out) topology resulting in high level expression. For nine of the eleven MPs, a stable, monodisperse protein-detergent complex was identified using an extended fluorescence-detection size exclusion chromatography procedure that monitors protein stability over time, a critical parameter affecting the success of structure-function studies. Five MPs were successfully cleaved from the GFP tag by site-specific proteolysis and purified to homogeneity. To address the challenge of inefficient proteolysis, we explored expression and purification conditions in the absence of the fusion tag. Contrary to previous studies, optimal expression conditions established with the fusion were not directly transferable for overexpression in the absence of the GFP tag. These studies establish a broadly applicable method for GFP screening of MPs with C(out) topology, yielding sufficient protein suitable for structure-function studies and are superior to expression and purification in the absence GFP fusion tagging.
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Affiliation(s)
- Jennifer M Hsieh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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163
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Bulky high-mannose-type N-glycan blocks the taste-modifying activity of miraculin. Biochim Biophys Acta Gen Subj 2010; 1800:986-92. [DOI: 10.1016/j.bbagen.2010.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 05/17/2010] [Accepted: 06/04/2010] [Indexed: 11/20/2022]
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164
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Kefala G, Ahn C, Krupa M, Esquivies L, Maslennikov I, Kwiatkowski W, Choe S. Structures of the OmpF porin crystallized in the presence of foscholine-12. Protein Sci 2010; 19:1117-25. [PMID: 20196071 DOI: 10.1002/pro.369] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 A, b = 210.5 A, c = 137 A, and beta = 100.5 degrees , and the resolution of 3.8 A. The second structure was solved at the resolution of 4.4 A and was refined in the P321 space group, with unit cell parameters a = 215.5 A, b = 215.5 A, c = 137.5 A, and gamma = 120 degrees . Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Georgia Kefala
- Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, California 92037, USA
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165
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Lee JK, Stroud RM. Unlocking the eukaryotic membrane protein structural proteome. Curr Opin Struct Biol 2010; 20:464-70. [PMID: 20739007 PMCID: PMC3530418 DOI: 10.1016/j.sbi.2010.05.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 05/09/2010] [Indexed: 10/19/2022]
Abstract
Most of the 231 unique membrane protein structures (as of 3/2010) are of bacterial membrane proteins (MPs) expressed in bacteria, or eukaryotic MPs from natural sources. However eukaryotic membrane proteins, especially those with more than three membrane crossings rarely succumb to any suitable expression in bacterial cells. They typically require expression in eukaryotic cells that can provide appropriate endoplasmic reticulum, chaperones, targeting and post-translational processing. In evidence, only approximately 20 eukaryotic MP structures have resulted from heterologous expression. This is required for a general approach to target particular human or pathogen membrane proteins of importance to human health. The first of these appeared in 2005. Our review addresses the special issues that pertain to the expression of eukaryotic and human membrane proteins, and recent advances in the tool kit for crystallization and structure determination.
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Affiliation(s)
- John Kyongwon Lee
- Department of Biochemistry & Biophysics, University of California, San Francisco, S-412C Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517. 415-476-4224, FAX: 415-476-1902, ,
| | - Robert Michael Stroud
- Department of Biochemistry & Biophysics, University of California, San Francisco, S-412C Genentech Hall, 600 16th Street, San Francisco, CA 94158-2517. 415-476-4224, FAX: 415-476-1902, ,
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166
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Bonar P, Casey JR. Purification of functional human Cl(-)/HCO(3)(-) exchanger, AE1, over-expressed in Saccharomyces cerevisiae. Protein Expr Purif 2010; 74:106-15. [PMID: 20609390 DOI: 10.1016/j.pep.2010.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Revised: 06/30/2010] [Accepted: 06/30/2010] [Indexed: 01/29/2023]
Abstract
There is no high-resolution structure for the membrane domain of the human erythrocyte anion exchanger, AE1 (Band 3). In this report, we have developed an expression and purification strategy for AE1 to be used in crystallization trials. Saccharomyces cerevisiae strain BJ5457 was transformed with an expression vector encoding the AE1 membrane domain (AE1MD, amino acids 388-911), fused C-terminally to an epitope tag, corresponding to the nine C-terminal amino acids of rhodopsin. The fusion protein, AE1MD-Rho, was expressed at a concentration of 0.3 mg/l of culture. Confocal immunofluorescence microscopy and sucrose gradient ultracentrifugation revealed that AE1MD-Rho did not process to the plasma membrane of S. cerevisiae, but was retained in an intracellular membrane fraction. Treatment with the endoglycosidase, PNGase F, showed that AE1MD-Rho is not N-glycosylated. AE1MD-Rho solubilized from yeast membranes, with Fos-choline detergent, was purified to 93% homogeneity in a single-step, using a 1D4 antibody affinity resin, in amounts up to 2.5 mg from 18 l of culture. The ability of purified AE1MD-Rho to transport sulfate was examined in reconstituted vesicles. The rate of sulfate efflux mediated by vesicles reconstituted with AE1MD-Rho was indistinguishable from vesicles with purified erythrocyte-source AE1. Using this purification strategy, sufficient amounts of functional, homogeneous AE1MD-Rho can be purified to enable crystallization trials.
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Affiliation(s)
- Pamela Bonar
- Membrane Protein Research Group, Department of Physiology, School of Molecular and Systems Medicine, University of Alberta, Edmonton, Canada T6G 2H7
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167
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Sonoda Y, Cameron A, Newstead S, Omote H, Moriyama Y, Kasahara M, Iwata S, Drew D. Tricks of the trade used to accelerate high-resolution structure determination of membrane proteins. FEBS Lett 2010; 584:2539-47. [PMID: 20394746 DOI: 10.1016/j.febslet.2010.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Revised: 04/01/2010] [Accepted: 04/08/2010] [Indexed: 10/19/2022]
Abstract
The rate at which X-ray structures of membrane proteins are solved is on a par with that of soluble proteins in the late 1970s. There are still many obstacles facing the membrane protein structural community. Recently, there have been several technical achievements in the field that have started to dramatically accelerate structural studies. Here, we summarize these so-called 'tricks-of-the-trade' and include case studies of several mammalian transporters.
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Affiliation(s)
- Yo Sonoda
- Division of Molecular Biosciences, Imperial College London, London, UK
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168
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Van Pham ST, Engman H, Dahlgren LG, Cornvik T, Eshaghi S. A systematic approach to isolate mono-disperse membrane proteins - purification of zinc transporter ZntB. Protein Expr Purif 2010; 72:48-54. [PMID: 20159043 DOI: 10.1016/j.pep.2010.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 02/11/2010] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
Obtaining mono-disperse and stable protein is a requirement for successful structural and biochemical investigation of proteins. For membrane proteins, such preparation is one of the major hurdles, which consequently has contributed to the slow progress in studying them. During the past few years, many screening methods have been developed to make studies of membrane proteins more efficient. Despite these advances, many membrane proteins remain challenging to even isolate in a stable and homogeneous form. The bacterial zinc transporter ZntB is such a protein, for which no isolation procedure has been reported. Here, we present a systematic approach to obtain homogeneous and mono-disperse zinc transporter ZntB in quantities sufficient for structural and biochemical studies. Important aspects of this study that can be applied to other membrane proteins are also discussed.
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Affiliation(s)
- Sally Thanh Van Pham
- Centre for Biomedical Structural Biology, School of Biological Sciences, Nanyang Technological University, Singapore
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169
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Leung J, Karachaliou M, Alves C, Diallinas G, Byrne B. Expression and purification of a functional uric acid-xanthine transporter (UapA). Protein Expr Purif 2010; 72:139-46. [PMID: 20153431 DOI: 10.1016/j.pep.2010.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/03/2010] [Indexed: 11/19/2022]
Abstract
The Nucleobase-Ascorbate Transporters (NATs) family includes carriers with fundamental functions in uptake of key cellular metabolites, such as uric acid or vitamin C. The best studied example of a NAT transporter is the uric acid-xanthine permease (UapA) from the model ascomycete Aspergillus nidulans. Detailed genetic and biochemical analyses have revealed much about the mechanism of action of this protein; however, the difficulties associated with handling eukaryotic membrane proteins have limited efforts to elucidate the precise structure-function relationships of UapA by structural analysis. In this manuscript, we describe the heterologous overexpression of functional UapA as a fusion with GFP in different strains of Saccharomyces cerevisiae. The UapA-GFP construct expressed to 2.3 mg/L in a pep4Delta deletion strain lacking a key vacuolar endopeptidase and 3.8 mg/L in an npi1-1 mutant strain with defective Rsp5 ubiquitin ligase activity. Epifluorescence microscopy revealed that the UapA-GFP was predominately localized to the plasma membrane in both strains, although a higher intensity of fluorescence was observed for the npi1-1 mutant strain plasma membrane. In agreement with these observations, the npi1-1 mutant strain demonstrated a approximately 5-fold increase in uptake of [(3)H]-xanthine compared to the pep4Delta deletion strain. Despite yielding the best results for functional expression, in-gel fluorescence of the UapA-GFP expressed in the npi1-1 mutant strain revealed that the protein was subject to significant proteolytic degradation. Large scale expression of the protein using the pep4Delta deletion strain followed by purification produced mg quantities of pure, monodispersed protein suitable for further structural and functional studies. In addition, this work has generated a yeast cell based system for performing reverse genetics and other targeted approaches, in order to further understand the mechanism of action of this important model protein.
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Affiliation(s)
- James Leung
- Division of Molecular Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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170
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N-terminal chimaeras with signal sequences enhance the functional expression and alter the subcellular localization of heterologous membrane-bound inorganic pyrophosphatases in yeast. Biochem J 2010; 426:147-57. [PMID: 20025609 DOI: 10.1042/bj20091491] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Expression of heterologous multispanning membrane proteins in Saccharomyces cerevisiae is a difficult task. Quite often, the use of multicopy plasmids where the foreign gene is under the control of a strong promoter does not guarantee efficient production of the corresponding protein. In the present study, we show that the expression level and/or subcellular localization in S. cerevisiae of a heterologous type of multispanning membrane protein, the proton-translocating inorganic pyrophosphatase (H+-PPase), can be changed by fusing it with various suitable N-terminal signal sequences. Chimaeric proteins were constructed by adding the putative N-terminal extra domain of Trypanosoma cruzi H+-PPase or the bona fide signal sequence of S. cerevisiae invertase Suc2p to H+-PPase polypeptides of different organisms (from bacteria to plants) and expressed in a yeast conditional mutant deficient in its cytosolic PPi hydrolysis activity when grown on glucose. Chimaeric constructs not only substantially enhanced H+-PPase expression levels in transformed mutant cells, but also allowed functional complementation in those cases in which native H+-PPase failed to accomplish it. Activity assays and Western blot analyses demonstrated further the occurrence of most H+-PPase in internal membrane fractions of these cells. The addition of N-terminal signal sequences to the vacuolar H+-PPase AVP1 from the plant Arabidopsis thaliana, a protein efficiently expressed in yeast in its natural form, alters the subcellular distribution of the chimaeras, suggesting further progression along the secretory sorting pathways, as shown by density gradient ultracentrifugation and in vivo fluorescence microscopy of the corresponding GFP (green fluorescent protein)-H+-PPase fusion proteins.
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171
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Iizasa E, Mitsutomi M, Nagano Y. Direct binding of a plant LysM receptor-like kinase, LysM RLK1/CERK1, to chitin in vitro. J Biol Chem 2010; 285:2996-3004. [PMID: 19951949 PMCID: PMC2823440 DOI: 10.1074/jbc.m109.027540] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 11/19/2009] [Indexed: 11/06/2022] Open
Abstract
Plants induce immune responses against fungal pathogens by recognition of chitin, which is a component of the fungal cell wall. Recent studies have revealed that LysM receptor-like kinase 1/chitin elicitor receptor kinase 1 (LysM RLK1/CERK1) is a critical component for the immune responses to chitin in Arabidopsis thaliana. However, the molecular mechanism of the chitin recognition by LysM RLK1 still remains unknown. Here, we present the first evidence for direct binding of LysM RLK1 to chitin. We expressed LysM RLK1 fused with yeast-enhanced green fluorescent protein (LysM RLK1-yEGFP) in yeast cells. Binding studies using the solubilized LysM RLK1-yEGFP and several insoluble polysaccharides having similar structures showed that LysM RLK1-yEGFP specifically binds to chitin. Subsequently, the fluorescence microscopic observation of the solubilized LysM RLK1-yEGFP binding to chitin beads revealed that the binding was saturable and had a high affinity, with a K(d) of approximately 82 nm. This binding was competed by the addition of soluble glycol chitin or high concentration of chitin oligosaccharides having 4-8 residues of N-acetyl glucosamine. However, the competition of these chitin oligosaccharides is weaker than that of glycol chitin. These data suggest that LysM RLK1 has a higher affinity for chitin having a longer residue of N-acetyl glucosamine. We also found that LysM RLK1-yEGFP was autophosphorylated in vitro and that chitin does not affect the phosphorylation of LysM RLK1-yEGFP. Our results provide a new dimension to chitin elicitor perception in plants.
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Affiliation(s)
- Ei'ichi Iizasa
- From the Analytical Research Center for Experimental Sciences and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Masaru Mitsutomi
- the Department of Applied Biochemistry and Food Science, Saga University, 1 Honjo-machi, Saga 840-8502 and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Yukio Nagano
- From the Analytical Research Center for Experimental Sciences and
- the United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
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172
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Practical considerations of membrane protein instability during purification and crystallisation. Methods Mol Biol 2010; 601:187-203. [PMID: 20099147 DOI: 10.1007/978-1-60761-344-2_12] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Crystallisation of integral membranes requires milligrams of purified protein in a homogeneous, monodisperse state, and crucially, the membrane protein must also be fully functional and stable. The stability of membrane proteins in solution is dependent on the type of detergents used, but unfortunately the use of the most stabilising detergent can often decrease the probability of obtaining crystals that diffract to high resolution, especially of small membrane proteins. A number of strategies have been developed to facilitate the purification of membrane proteins in a functional form, which have led to new possibilities for structure determination.
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173
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Freigassner M, Pichler H, Glieder A. Tuning microbial hosts for membrane protein production. Microb Cell Fact 2009; 8:69. [PMID: 20040113 PMCID: PMC2807855 DOI: 10.1186/1475-2859-8-69] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 12/29/2009] [Indexed: 12/22/2022] Open
Abstract
The last four years have brought exciting progress in membrane protein research. Finally those many efforts that have been put into expression of eukaryotic membrane proteins are coming to fruition and enable to solve an ever-growing number of high resolution structures. In the past, many skilful optimization steps were required to achieve sufficient expression of functional membrane proteins. Optimization was performed individually for every membrane protein, but provided insight about commonly encountered bottlenecks and, more importantly, general guidelines how to alleviate cellular limitations during microbial membrane protein expression. Lately, system-wide analyses are emerging as powerful means to decipher cellular bottlenecks during heterologous protein production and their use in microbial membrane protein expression has grown in popularity during the past months. This review covers the most prominent solutions and pitfalls in expression of eukaryotic membrane proteins using microbial hosts (prokaryotes, yeasts), highlights skilful applications of our basic understanding to improve membrane protein production. Omics technologies provide new concepts to engineer microbial hosts for membrane protein production.
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Affiliation(s)
- Maria Freigassner
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
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174
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Koth CMM, Payandeh J. Strategies for the cloning and expression of membrane proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2009; 76:43-86. [PMID: 20663478 DOI: 10.1016/s1876-1623(08)76002-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Despite the determination of thousands of high-resolution structures of soluble proteins, many features of integral membrane proteins render them difficult targets for the structural biologist. Among these, the most important challenge is in expressing sufficient quantities of active protein to support downstream purification and structure determination efforts. Over 190 unique membrane protein structures have now been solved, and noticeable trends in successful expression strategies are beginning to emerge. A number of groups have also explored high-throughput (HTP) methods for membrane protein expression, with varying degrees of success. Here we review the current state of expressing membrane proteins for functional and structural studies. We first survey successful methods that have already yielded levels of membrane protein expression sufficient for structure determination. HTP methods are also examined since these aim to explore large numbers of targets and can predict reasonable starting points for many membrane proteins. Since HTP techniques may fail, particularly for certain classes of eukaryotic targets, detailed strategies for the expression of two prominent classes of eukaryotic protein families, G-protein-coupled receptors and ion channels, are also summarized.
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Affiliation(s)
- Christopher M M Koth
- Department of Structural Biology, Genentech, South San Francisco, California 94080, USA
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175
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Vernier G, Wang J, Jennings LD, Sun J, Fischer A, Song L, Collier RJ. Solubilization and characterization of the anthrax toxin pore in detergent micelles. Protein Sci 2009; 18:1882-95. [PMID: 19609933 DOI: 10.1002/pro.199] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Proteolytically activated Protective Antigen (PA) moiety of anthrax toxin self-associates to form a heptameric ring-shaped oligomer (the prepore). Acidic pH within the endosome converts the prepore to a pore that serves as a passageway for the toxin's enzymatic moieties to cross the endosomal membrane. Prepore is stable in solution under mildly basic conditions, and lowering the pH promotes a conformational transition to an insoluble pore-like state. N-tetradecylphosphocholine (FOS14) was the only detergent among 110 tested that prevented aggregation without dissociating the multimer into its constituent subunits. FOS14 maintained the heptamers as monodisperse, insertion-competent 440-kDa particles, which formed channels in planar phospholipid bilayers with the same unitary conductance and ability to translocate a model substrate protein as channels formed in the absence of detergent. Electron paramagnetic resonance analysis detected pore-like conformational changes within PA on solubilization with FOS14, and electron micrograph images of FOS14-solubilized pore showed an extended, mushroom-shaped structure. Circular dichroïsm measurements revealed an increase in alpha helix and a decrease in beta structure in pore formation. Spectral changes caused by a deletion mutation support the hypothesis that the 2beta2-2beta3 loop transforms into the transmembrane segment of the beta-barrel stem of the pore. Changes caused by selected point mutations indicate that the transition to alpha structure is dependent on residues of the luminal 2beta11-2beta12 loop that are known to affect pore formation. Stabilizing the PA pore in solution with FOS14 may facilitate further structural analysis and a more detailed understanding of the folding pathway by which the pore is formed.
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Affiliation(s)
- Gregory Vernier
- Department of Microbiology and Molecular Genetics, Harvard Medical School, 200 Longwood Ave., Boston, Massachusetts 02115, USA
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176
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Palladino P, Rossi F, Ragone R. Effective critical micellar concentration of a zwitterionic detergent: a fluorimetric study on n-dodecyl phosphocholine. J Fluoresc 2009; 20:191-6. [PMID: 19756982 DOI: 10.1007/s10895-009-0537-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 08/25/2009] [Indexed: 11/27/2022]
Abstract
We have investigated the effect of ionic strength on the aggregation behavior of n-dodecyl phosphocholine. On the basis of the classical Corrin-Harkins relation, the critical micellar concentration of this detergent decreases with a biphasic trend on lithium chloride addition. It is nearly constant below 150 mM salt, with a mean value of 0.91 mM, whereas it undergoes a dramatic 80-fold decrease in 7 M LiCl. Such a drop in the critical micellar concentration could be explained by the effect of salting out and the implication of phosphocholine head groups on the organization of surrounding water. Knowledge of the effective critical micellar concentration of n-dodecyl phosphocholine could be useful in the purification of membrane proteins in non-denaturing conditions.
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Affiliation(s)
- Pasquale Palladino
- Dipartimento delle Scienze Biologiche & C.I.R.Pe.B., Università Federico II, via Mezzocannone 16, 80134, Naples, Italy
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177
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Hammon J, Palanivelu DV, Chen J, Patel C, Minor DL. A green fluorescent protein screen for identification of well-expressed membrane proteins from a cohort of extremophilic organisms. Protein Sci 2009; 18:121-33. [PMID: 19177357 DOI: 10.1002/pro.18] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Green fluorescent protein (GFP) fusion proteins provide a potentially facile tool for identification of well expressed, properly behaved membrane proteins for biochemical and structural study. Here, we present a GFP-expression survey of >300 membrane proteins from 18 bacterial and archaeal extremophiles, organisms expected to be rich sources of membrane proteins having robust biophysical properties. We find that GFP-fusion fluorescence intensity is an excellent indicator of over-expression potential. By employing a follow-up optimization protocol using a suite of non-GFP constructs and different expression temperatures, we obtain 0.5-15 mg L(-1) expression levels for 90% of the tested candidate proteins that pass the GFP screen. Evaluation of the results suggests that certain organisms may serve as better sources of well-expressed membrane proteins than others, that the degree to which codon usage matches the expression host is uncorrelated with success rate, and that the combination of GFP screening and expression optimization is essential for producing biochemically tractable quantities of material.
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Affiliation(s)
- Justus Hammon
- Cardiovascular Research Institute, Department of Biochemistry and Biophysics, Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158-2330, USA
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178
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Raimunda D, Bollo M, Beaugé L, Berberián G. Squid nerve Na+/Ca2+ exchanger expressed in Saccharomyces cerevisiae: Up-regulation by a phosphorylated cytosolic protein (ReP1–NCXSQ) is identical to that of native exchanger in situ. Cell Calcium 2009; 45:499-508. [DOI: 10.1016/j.ceca.2009.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 03/12/2009] [Accepted: 03/17/2009] [Indexed: 01/11/2023]
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179
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Sugawara T, Ito K, Shiroishi M, Tokuda N, Asada H, Yurugi-Kobayashi T, Shimamura T, Misaka T, Nomura N, Murata T, Abe K, Iwata S, Kobayashi T. Fluorescence-based optimization of human bitter taste receptor expression in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2009; 382:704-10. [DOI: 10.1016/j.bbrc.2009.03.089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Accepted: 03/17/2009] [Indexed: 10/21/2022]
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180
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Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. JOURNAL OF STRUCTURAL AND FUNCTIONAL GENOMICS 2009; 10:9-16. [PMID: 19031011 PMCID: PMC2756966 DOI: 10.1007/s10969-008-9046-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 10/24/2008] [Indexed: 11/28/2022]
Abstract
Persistent hurdles impede the successful determination of high-resolution crystal structures of eukaryotic integral membrane proteins (IMP). We designed a high-throughput structural genomics oriented pipeline that seeks to minimize effort in uncovering high-quality, responsive non-redundant targets for crystallization. This "discovery-oriented" pipeline sidesteps two significant bottlenecks in the IMP structure determination pipeline: expression and membrane extraction with detergent. In addition, proteins that enter the pipeline are then rapidly vetted by their presence in the included volume on a size-exclusion column--a hallmark of well-behaved IMP targets. A screen of 384 rationally selected eukaryotic IMPs in baker's yeast Saccharomyces cerevisiae is outlined to demonstrate the results expected when applying this discovery-oriented pipeline to whole-organism membrane proteomes.
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Affiliation(s)
- Franklin A Hays
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA 94158-2517, USA.
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181
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182
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NEWSTEAD SIMON, HOBBS JEANETTE, JORDAN DAVINA, CARPENTER ELISABETHP, IWATA SO. Insights into outer membrane protein crystallization. Mol Membr Biol 2008; 25:631-8. [PMID: 19023694 PMCID: PMC2885437 DOI: 10.1080/09687680802526574] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Outer membrane proteins are structurally distinct from those that reside in the inner membrane and play important roles in bacterial pathogenicity and human metabolism. X-ray crystallography studies on >40 different outer membrane proteins have revealed that the transmembrane portion of these proteins can be constructed from either beta-sheets or less commonly from alpha-helices. The most common architecture is the beta-barrel, which can be formed from either a single anti-parallel sheet, fused at both ends to form a barrel or from multiple peptide chains. Outer membrane proteins exhibit considerable rigidity and stability, making their study through x-ray crystallography particularly tractable. As the number of structures of outer membrane proteins increases a more rational approach to their crystallization can be made. Herein we analyse the crystallization data from 53 outer membrane proteins and compare the results to those obtained for inner membrane proteins. A targeted sparse matrix screen for outer membrane protein crystallization is presented based on the present analysis.
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Affiliation(s)
- SIMON NEWSTEAD
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - JEANETTE HOBBS
- Molecular Dimensions Ltd, Unit 7 Acorn Business Centre, Oaks Drive, Newmarket, Suffolk, CB8 7SY, UK
| | - DAVINA JORDAN
- Molecular Dimensions Ltd, Unit 7 Acorn Business Centre, Oaks Drive, Newmarket, Suffolk, CB8 7SY, UK
| | - ELISABETH P. CARPENTER
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 ODE, UK
| | - SO IWATA
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
- Membrane Protein Laboratory, Diamond Light Source Ltd, Harwell Science and Innovation Campus, Chilton, Didcot, OX11 ODE, UK
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183
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Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJW, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol 2008; 385:820-30. [PMID: 19061901 DOI: 10.1016/j.jmb.2008.11.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 10/26/2008] [Accepted: 11/12/2008] [Indexed: 10/21/2022]
Abstract
A medium-throughput approach is used to rapidly identify membrane proteins from a eukaryotic organism that are most amenable to expression in amounts and quality adequate to support structure determination. The goal was to expand knowledge of new membrane protein structures based on proteome-wide coverage. In the first phase, membrane proteins from the budding yeast Saccharomyces cerevisiae were selected for homologous expression in S. cerevisiae, a system that can be adapted to expression of membrane proteins from other eukaryotes. We performed medium-scale expression and solubilization tests on 351 rationally selected membrane proteins from S. cerevisiae. These targets are inclusive of all annotated and unannotated membrane protein families within the organism's membrane proteome. Two hundred seventy-two targets were expressed, and of these, 234 solubilized in the detergent n-dodecyl-beta-D-maltopyranoside. Furthermore, we report the identity of a subset of targets that were purified to homogeneity to facilitate structure determinations. The extensibility of this approach is demonstrated with the expression of 10 human integral membrane proteins from the solute carrier superfamily. This discovery-oriented pipeline provides an efficient way to select proteins from particular membrane protein classes, families, or organisms that may be more suited to structure analysis than others.
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Affiliation(s)
- Min Li
- Membrane Protein Expression Center, University of California at San Francisco, San Francisco, CA 94158-2517, USA
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184
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Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity. Proc Natl Acad Sci U S A 2008; 105:14808-13. [PMID: 18812512 DOI: 10.1073/pnas.0803103105] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We outline a powerful method for the directed evolution of integral membrane proteins in the inner membrane of Escherichia coli. For a mammalian G protein-coupled receptor, we arrived at a sequence with an order-of-magnitude increase in functional expression that still retains the biochemical properties of wild type. This mutant also shows enhanced heterologous expression in eukaryotes (12-fold in Pichia pastoris and 3-fold in HEK293T cells) and greater stability when solubilized and purified, indicating that the biophysical properties of the protein had been under the pressure of selection. These improvements arise from multiple small contributions, which would be difficult to assemble by rational design. In a second screen, we rapidly pinpointed a single amino acid substitution in wild type that abolishes antagonist binding while retaining agonist-binding affinity. These approaches may alleviate existing bottlenecks in structural studies of these targets by providing sufficient quantities of stable variants in defined conformational states.
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185
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Niu Y, Kong J, Xu Y. A Novel GFP-Fused Eukaryotic Membrane Protein Expression System in Lactococcus lactis and Its Application to Overexpression of an Elongase. Curr Microbiol 2008; 57:423-8. [DOI: 10.1007/s00284-008-9223-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Accepted: 06/17/2008] [Indexed: 11/24/2022]
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186
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Hibi T, Aoki S, Oda K, Munemasa S, Ozaki S, Shirai O, Murata Y, Uozumi N. Purification of the functional plant membrane channel KAT1. Biochem Biophys Res Commun 2008; 374:465-9. [DOI: 10.1016/j.bbrc.2008.07.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 07/09/2008] [Indexed: 10/21/2022]
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187
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Carpenter EP, Beis K, Cameron AD, Iwata S. Overcoming the challenges of membrane protein crystallography. Curr Opin Struct Biol 2008; 18:581-6. [PMID: 18674618 PMCID: PMC2580798 DOI: 10.1016/j.sbi.2008.07.001] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 07/03/2008] [Indexed: 11/23/2022]
Abstract
Membrane protein structural biology is still a largely unconquered area, given that approximately 25% of all proteins are membrane proteins and yet less than 150 unique structures are available. Membrane proteins have proven to be difficult to study owing to their partially hydrophobic surfaces, flexibility and lack of stability. The field is now taking advantage of the high-throughput revolution in structural biology and methods are emerging for effective expression, solubilisation, purification and crystallisation of membrane proteins. These technical advances will lead to a rapid increase in the rate at which membrane protein structures are solved in the near future.
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Affiliation(s)
- Elisabeth P Carpenter
- Membrane Protein Laboratory, Imperial College London, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 ODE, United Kingdom
- Division of Molecular Biosciences, Membrane Protein Crystallography Group and Membrane Protein Laboratory, Imperial College, London SW7 2AZ, United Kingdom
| | - Konstantinos Beis
- Membrane Protein Laboratory, Imperial College London, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 ODE, United Kingdom
- Division of Molecular Biosciences, Membrane Protein Crystallography Group and Membrane Protein Laboratory, Imperial College, London SW7 2AZ, United Kingdom
| | - Alexander D Cameron
- Membrane Protein Laboratory, Imperial College London, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 ODE, United Kingdom
- Division of Molecular Biosciences, Membrane Protein Crystallography Group and Membrane Protein Laboratory, Imperial College, London SW7 2AZ, United Kingdom
| | - So Iwata
- Membrane Protein Laboratory, Imperial College London, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 ODE, United Kingdom
- Division of Molecular Biosciences, Membrane Protein Crystallography Group and Membrane Protein Laboratory, Imperial College, London SW7 2AZ, United Kingdom
- ERATO Human Receptor Crystallography Project, 3rd Floor, Building A, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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188
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Drew D, Newstead S, Sonoda Y, Kim H, von Heijne G, Iwata S. GFP-based optimization scheme for the overexpression and purification of eukaryotic membrane proteins in Saccharomyces cerevisiae. Nat Protoc 2008; 3:784-98. [PMID: 18451787 DOI: 10.1038/nprot.2008.44] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
It is often difficult to produce eukaryotic membrane proteins in large quantities, which is a major obstacle for analyzing their biochemical and structural features. To date, yeast has been the most successful heterologous overexpression system in producing eukaryotic membrane proteins for high-resolution structural studies. For this reason, we have developed a protocol for rapidly screening and purifying eukaryotic membrane proteins in the yeast Saccharomyces cerevisiae. Using this protocol, in 1 week many genes can be rapidly cloned by homologous recombination into a 2 micro GFP-fusion vector and their overexpression potential determined using whole-cell and in-gel fluorescence. The quality of the overproduced eukaryotic membrane protein-GFP fusions can then be evaluated over several days using confocal microscopy and fluorescence size-exclusion chromatography (FSEC). This protocol also details the purification of targets that pass our quality criteria, and can be scaled up for a large number of eukaryotic membrane proteins in either an academic, structural genomics or commercial environment.
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Affiliation(s)
- David Drew
- Membrane Protein Crystallography Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College of London, London SW7 2AZ, UK
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189
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Ito K, Sugawara T, Shiroishi M, Tokuda N, Kurokawa A, Misaka T, Makyio H, Yurugi-Kobayashi T, Shimamura T, Nomura N, Murata T, Abe K, Iwata S, Kobayashi T. Advanced method for high-throughput expression of mutated eukaryotic membrane proteins in Saccharomyces cerevisiae. Biochem Biophys Res Commun 2008; 371:841-5. [PMID: 18474222 DOI: 10.1016/j.bbrc.2008.04.182] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 04/29/2008] [Indexed: 11/20/2022]
Abstract
Crystallization of eukaryotic membrane proteins is a challenging, iterative process. The protein of interest is often modified in an attempt to improve crystallization and diffraction results. To accelerate this process, we took advantage of a GFP-fusion yeast expression system that uses PCR to direct homologous recombination and gene cloning. We explored the possibility of employing more than one PCR fragment to introduce various mutations in a single step, and found that when up to five PCR fragments were co-transformed into yeast, the recombination frequency was maintained as the number of fragments was increased. All transformants expressed the model membrane protein, while the resulting plasmid from each clone contained the designed mutations only. Thus, we have demonstrated a technique allowing the expression of mutant membrane proteins within 5 days, combining a GFP-fusion expression system and yeast homologous recombination.
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Affiliation(s)
- Keisuke Ito
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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190
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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191
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Abstract
Overexpression of membrane proteins in Escherichia coli frequently leads to the formation of aggregates or inclusion bodies, which is undesirable for most studies. Ideally, one would like to optimize the expression conditions by monitoring simultaneously and rapidly both the amounts of properly folded and aggregated membrane protein, a requirement not met by any of the currently available methods. Here, we describe a simple gel-based approach with green fluorescent protein as folding indicator to detect well folded and aggregated proteins simultaneously. The method allows for rapid screening and, importantly, pinpointing the most likely bottlenecks in protein production.
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192
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Newstead S, Ferrandon S, Iwata S. Rationalizing alpha-helical membrane protein crystallization. Protein Sci 2008; 17:466-72. [PMID: 18218713 DOI: 10.1110/ps.073263108] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
X-ray crystallography is currently the most successful method for determining the three-dimensional structure of membrane proteins. Nevertheless, growing the crystals required for this technique presents one of the major bottlenecks in this area of structural biology. This is especially true for the alpha-helical type membrane proteins that are of particular interest due to their medical relevance. To address this problem we have undertaken a detailed analysis of the crystallization conditions from 121 alpha-helical membrane protein structures deposited in the Protein Data Bank. This information has been analyzed so that the success of different parameters can be easily compared for different membrane protein families. Concurrent with this analysis, we also present the new sparse matrix crystallization screen MemGold.
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Affiliation(s)
- Simon Newstead
- Division of Molecular Biosciences, Membrane Protein Crystallography Group, Wolfson Laboratory, Imperial College London, London SW7 2AZ, United Kingdom
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