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Okamura H, Yao T, Nagatsugi F. Reversible Control of Gene Expression by Guest-Modified Adenosines in a Cell-Free System via Host-Guest Interaction. J Am Chem Soc 2024; 146:18513-18523. [PMID: 38941287 PMCID: PMC11240562 DOI: 10.1021/jacs.4c04262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/30/2024]
Abstract
Gene expression technology has become an indispensable tool for elucidating biological processes and developing biotechnology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host-guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand using a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility was fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled tight and reversible control of in vitro transcription and protein expression in the CFE system. This study marks the first utility of the host-guest interaction for gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nanotechnology.
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Affiliation(s)
- Hidenori Okamura
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Takeyuki Yao
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Fumi Nagatsugi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
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2
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Moser C, Muhle-Goll C. Cell-free protein production of a gamma secretase homolog. Protein Expr Purif 2024; 215:106407. [PMID: 38000778 DOI: 10.1016/j.pep.2023.106407] [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] [Received: 08/16/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 11/26/2023]
Abstract
Cleavage of the transmembrane domain (TMD) of amyloid-β precursor protein (APP) by γ-secretase, an intramembrane aspartyl protease, generates Aβ peptides of various lengths that form plaques in the brains of Alzheimer's disease patients. Although the debate has not been finally resolved whether these plaques trigger the onset of Alzheimer's or are side products, disease-related mutations suggest their implication in the etiology of the dementia. These occur both in presenilin, the catalytic subunit of γ-secretase, and in the TMD of APP. Despite two seminal cryo-electron microscopy structures that show the complex of γ-secretase with its substrates APP and Notch, the mechanism of γ-secretase is not yet fully understood. Especially on which basis it selects its substrates is still an enigma. The presenilin homolog PSH from the archaeon Methanoculleus marisnigri JR1 (MCMJR1) is catalytically active without accessory proteins in contrast to γ-secretase making it an excellent model for studies of the basic cleavage process. We here focused on the cell-free expression of PSH screening a range of conditions. Cleavage assays to verify the activity show that not only the yield, but mainly the activity of the protease depends on the careful selection of expression conditions. Optimal results were found for a cell-free expression at relatively low temperature, 20 °C, employing cell lysates prepared from E. coli Rosetta cells. To speed up protein preparation for immediate functional assays, a crude purification protocol was developed. This allows to produce ready-made PSH in a fast and efficient manner in less than two days.
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Affiliation(s)
- Celine Moser
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, 76344 Eggenstein- Leopoldshafen, Germany; Institute of Organic Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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3
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Bruni R, Laguerre A, Kaminska A, McSweeney S, Hendrickson WA, Liu Q. High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics. Protein Sci 2022; 31:639-651. [PMID: 34910339 PMCID: PMC8862427 DOI: 10.1002/pro.4259] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/16/2022]
Abstract
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and apply it to screen 61 eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functionally competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
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Affiliation(s)
- Renato Bruni
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA
| | - Aisha Laguerre
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
Roche DiagnosticsSanta ClaraCaliforniaUSA
| | - Anna‐Maria Kaminska
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Present address:
New York Blood CenterNew YorkNew YorkUSA
| | | | - Wayne A. Hendrickson
- Center on Membrane Protein Production and Analysis (COMPPÅ)New York Structural Biology CenterNew YorkNew YorkUSA,Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Qun Liu
- NSLS‐II, Brookhaven National LaboratoryUptonNew YorkUSA,Biology DepartmentBrookhaven National LaboratoryUptonNew YorkUSA
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4
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A rapid solubility assay of protein domain misfolding for pathogenicity assessment of rare DNA sequence variants. Genet Med 2020; 22:1642-1652. [PMID: 32475984 PMCID: PMC7529867 DOI: 10.1038/s41436-020-0842-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 02/08/2023] Open
Abstract
PURPOSE DNA sequencing technology has unmasked a vast number of uncharacterized single-nucleotide variants in disease-associated genes, and efficient methods are needed to determine pathogenicity and enable clinical care. METHODS We report an E. coli-based solubility assay for assessing the effects of variants on protein domain stability for three disease-associated proteins. RESULTS First, we examined variants in the Kv11.1 channel PAS domain (PASD) associated with inherited long QT syndrome type 2 and found that protein solubility correlated well with reported in vitro protein stabilities. A comprehensive solubility analysis of 56 Kv11.1 PASD variants revealed that disruption of membrane trafficking, the dominant loss-of-function disease mechanism, is largely determined by domain stability. We further validated this assay by using it to identify second-site suppressor PASD variants that improve domain stability and Kv11.1 protein trafficking. Finally, we applied this assay to several cancer-linked P53 tumor suppressor DNA-binding domain and myopathy-linked Lamin A/C Ig-like domain variants, which also correlated well with reported protein stabilities and functional analyses. CONCLUSION This simple solubility assay can aid in determining the likelihood of pathogenicity for sequence variants due to protein misfolding in structured domains of disease-associated genes as well as provide insights into the structural basis of disease.
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5
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Jang YJ, Lee KH, Yoo TH, Kim DM. Complementary Cell-Free Translational Assay for Quantification of Amino Acids. Anal Chem 2017; 89:9638-9642. [PMID: 28776976 DOI: 10.1021/acs.analchem.7b01956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, we present a simple and economical method that enables rapid quantification of amino acids based on their polymerization into a signal-generating protein. This method harnesses amino acid-deficient cell-free protein synthesis systems that generate fluorescence signals in response to exogenous amino acids. When premixed with assay samples containing the amino acids in question, incubation of the cell-free synthesis reaction mixture rapidly resulted in the production of sfGFP, the fluorescence intensity of which was linearly proportional to the concentration of the amino acids. The assay method achieved a limit of detection as low as ∼100 nM and was successfully applied to the quantification of disease-related amino acids in biological samples. Compared with standard methods in current use that require chemical derivatization of amino acids and chromatographic equipment, the complementation assay method developed in this work enables the direct translation of amino acid titer into measurable biofluorescence intensity in a much shorter period, providing a more affordable and flexible option for the quantification of amino acids.
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Affiliation(s)
- Yeon-Jae Jang
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Kyung-Ho Lee
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University , 206 Worldcup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University , 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
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6
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Harris NJ, Reading E, Ataka K, Grzegorzewski L, Charalambous K, Liu X, Schlesinger R, Heberle J, Booth PJ. Structure formation during translocon-unassisted co-translational membrane protein folding. Sci Rep 2017; 7:8021. [PMID: 28808343 PMCID: PMC5556060 DOI: 10.1038/s41598-017-08522-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/10/2017] [Indexed: 01/16/2023] Open
Abstract
Correctly folded membrane proteins underlie a plethora of cellular processes, but little is known about how they fold. Knowledge of folding mechanisms centres on reversible folding of chemically denatured membrane proteins. However, this cannot replicate the unidirectional elongation of the protein chain during co-translational folding in the cell, where insertion is assisted by translocase apparatus. We show that a lipid membrane (devoid of translocase components) is sufficient for successful co-translational folding of two bacterial α-helical membrane proteins, DsbB and GlpG. Folding is spontaneous, thermodynamically driven, and the yield depends on lipid composition. Time-resolving structure formation during co-translational folding revealed different secondary and tertiary structure folding pathways for GlpG and DsbB that correlated with membrane interfacial and biological transmembrane amino acid hydrophobicity scales. Attempts to refold DsbB and GlpG from chemically denatured states into lipid membranes resulted in extensive aggregation. Co-translational insertion and folding is thus spontaneous and minimises aggregation whilst maximising correct folding.
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Affiliation(s)
- Nicola J Harris
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Eamonn Reading
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Lucjan Grzegorzewski
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Kalypso Charalambous
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK
| | - Xia Liu
- School of Biochemistry, Medical Sciences, University Walk, University of Bristol, Bristol, UK
| | - Ramona Schlesinger
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Dahlem, Germany
| | - Paula J Booth
- Department of Chemistry, Britannia House, 7 Trinity Street, King's College London, London, UK.
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7
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Development of a Cell Marker ELISA for the Detection of Goose T Cell Surface CD8α Molecules. Appl Biochem Biotechnol 2016; 179:531-44. [DOI: 10.1007/s12010-016-2011-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 02/08/2016] [Indexed: 01/13/2023]
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8
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Georgi V, Georgi L, Blechert M, Bergmeister M, Zwanzig M, Wüstenhagen DA, Bier FF, Jung E, Kubick S. On-chip automation of cell-free protein synthesis: new opportunities due to a novel reaction mode. LAB ON A CHIP 2016; 16:269-81. [PMID: 26554896 DOI: 10.1039/c5lc00700c] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Many pharmaceuticals are proteins or their development is based on proteins. Cell-free protein synthesis (CFPS) is an innovative alternative to conventional cell based systems which enables the production of proteins with complex and even new characteristics. However, the short lifetime, low protein production and expensive reagent costs are still limitations of CFPS. Novel automated microfluidic systems might allow continuous, controllable and resource conserving CFPS. The presented microfluidic TRITT platform (TRITT for Transcription - RNA Immobilization & Transfer - Translation) addresses the individual biochemical requirements of the transcription and the translation step of CFPS in separate compartments, and combines the reaction steps by quasi-continuous transfer of RNA templates to enable automated CFPS. In detail, specific RNA templates with 5' and 3' hairpin structures for stabilization against nucleases were immobilized during in vitro transcription by newly designed and optimized hybridization oligonucleotides coupled to magnetizable particles. Transcription compatibility and reusability for immobilization of these functionalized particles was successfully proven. mRNA transfer was realized on-chip by magnetic actuated particle transfer, RNA elution and fluid flow to the in vitro translation compartment. The applicability of the microfluidic TRITT platform for the production of the cytotoxic protein Pierisin with simultaneous incorporation of a non-canonical amino acid for fluorescence labeling was demonstrated. The new reaction mode (TRITT mode) is a modified linked mode that fulfills the precondition for an automated modular reactor system. By continual transfer of new mRNA, the novel procedure overcomes problems caused by nuclease digestion and hydrolysis of mRNA during TL in standard CFPS reactions.
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Affiliation(s)
- V Georgi
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany. and Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - L Georgi
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - M Blechert
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Bergmeister
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - M Zwanzig
- Technische Universität Berlin, Faculty Electrical Engineering Computer Science, Microperipheric Technologies, Berlin, Germany
| | - D A Wüstenhagen
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - F F Bier
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
| | - E Jung
- Fraunhofer Institute for Reliability Microintegration, Department System Integration & Interconnection Technologies, Working Group Medical Microystems, Berlin, Germany.
| | - S Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Potsdam, Germany.
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9
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Henrich E, Hein C, Dötsch V, Bernhard F. Membrane protein production in Escherichia coli cell-free lysates. FEBS Lett 2015; 589:1713-22. [PMID: 25937121 DOI: 10.1016/j.febslet.2015.04.045] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 01/01/2023]
Abstract
Cell-free protein production has become a core technology in the rapidly spreading field of synthetic biology. In particular the synthesis of membrane proteins, highly problematic proteins in conventional cellular production systems, is an ideal application for cell-free expression. A large variety of artificial as well as natural environments for the optimal co-translational folding and stabilization of membrane proteins can rationally be designed. The high success rate of cell-free membrane protein production allows to focus on individually selected targets and to modulate their functional and structural properties with appropriate supplements. The efficiency and robustness of lysates from Escherichia coli strains allow a wide diversity of applications and we summarize current strategies for the successful production of high quality membrane protein samples.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Christopher Hein
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany.
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10
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Eichmann C, Orts J, Tzitzilonis C, Vögeli B, Smrt S, Lorieau J, Riek R. Intermolecular detergent-membrane protein noes for the characterization of the dynamics of membrane protein-detergent complexes. J Phys Chem B 2014; 118:14288-301. [PMID: 25419869 DOI: 10.1021/jp509137q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The interaction between membrane proteins and lipids or lipid mimetics such as detergents is key for the three-dimensional structure and dynamics of membrane proteins. In NMR-based structural studies of membrane proteins, qualitative analysis of intermolecular nuclear Overhauser enhancements (NOEs) or paramagnetic resonance enhancement are used in general to identify the transmembrane segments of a membrane protein. Here, we employed a quantitative characterization of intermolecular NOEs between (1)H of the detergent and (1)H(N) of (2)H-perdeuterated, (15)N-labeled α-helical membrane protein-detergent complexes following the exact NOE (eNOE) approach. Structural considerations suggest that these intermolecular NOEs should show a helical-wheel-type behavior along a transmembrane helix or a membrane-attached helix within a membrane protein as experimentally demonstrated for the complete influenza hemagglutinin fusion domain HAfp23. The partial absence of such a NOE pattern along the amino acid sequence as shown for a truncated variant of HAfp23 and for the Escherichia coli inner membrane protein YidH indicates the presence of large tertiary structure fluctuations such as an opening between helices or the presence of large rotational dynamics of the helices. Detergent-protein NOEs thus appear to be a straightforward probe for a qualitative characterization of structural and dynamical properties of membrane proteins embedded in detergent micelles.
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Affiliation(s)
- Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg , CH-8093 Zürich, Switzerland
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11
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Boland C, Li D, Shah STA, Haberstock S, Dötsch V, Bernhard F, Caffrey M. Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination. Cell Mol Life Sci 2014; 71:4895-4910. [PMID: 25012698 DOI: 10.1007/s00018-014-1655-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 12/17/2022]
Abstract
Membrane proteins are key elements in cell physiology and drug targeting, but getting a high-resolution structure by crystallographic means is still enormously challenging. Novel strategies are in big demand to facilitate the structure determination process that will ultimately hasten the day when sequence information alone can provide a three-dimensional model. Cell-free or in vitro expression enables rapid access to large quantities of high-quality membrane proteins suitable for an array of applications. Despite its impressive efficiency, to date only two membrane proteins produced by the in vitro approach have yielded crystal structures. Here, we have analysed synergies of cell-free expression and crystallisation in lipid mesophases for generating an X-ray structure of the integral membrane enzyme diacylglycerol kinase to 2.28-Å resolution. The quality of cellular and cell-free-expressed kinase samples has been evaluated systematically by comparing (1) spectroscopic properties, (2) purity and oligomer formation, (3) lipid content and (4) functionality. DgkA is the first membrane enzyme crystallised based on cell-free expression. The study provides a basic standard for the crystallisation of cell-free-expressed membrane proteins and the methods detailed here should prove generally useful and contribute to accelerating the pace at which membrane protein structures are solved.
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Affiliation(s)
- Coilín Boland
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Dianfan Li
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Syed Tasadaque Ali Shah
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
| | - Stefan Haberstock
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University of Frankfurt, Germany
| | - Martin Caffrey
- Membrane Structural and Functional Group, School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Ireland
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12
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Stech M, Quast RB, Sachse R, Schulze C, Wüstenhagen DA, Kubick S. A continuous-exchange cell-free protein synthesis system based on extracts from cultured insect cells. PLoS One 2014; 9:e96635. [PMID: 24804975 PMCID: PMC4013096 DOI: 10.1371/journal.pone.0096635] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/09/2014] [Indexed: 11/22/2022] Open
Abstract
In this study, we present a novel technique for the synthesis of complex prokaryotic and eukaryotic proteins by using a continuous-exchange cell-free (CECF) protein synthesis system based on extracts from cultured insect cells. Our approach consists of two basic elements: First, protein synthesis is performed in insect cell lysates which harbor endogenous microsomal vesicles, enabling a translocation of de novo synthesized target proteins into the lumen of the insect vesicles or, in the case of membrane proteins, their embedding into a natural membrane scaffold. Second, cell-free reactions are performed in a two chamber dialysis device for 48 h. The combination of the eukaryotic cell-free translation system based on insect cell extracts and the CECF translation system results in significantly prolonged reaction life times and increased protein yields compared to conventional batch reactions. In this context, we demonstrate the synthesis of various representative model proteins, among them cytosolic proteins, pharmacological relevant membrane proteins and glycosylated proteins in an endotoxin-free environment. Furthermore, the cell-free system used in this study is well-suited for the synthesis of biologically active tissue-type-plasminogen activator, a complex eukaryotic protein harboring multiple disulfide bonds.
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Affiliation(s)
- Marlitt Stech
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Robert B. Quast
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Rita Sachse
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Corina Schulze
- Beuth Hochschule für Technik Berlin - University of Applied Sciences Berlin, Life Sciences and Technology, Berlin, Germany
| | - Doreen A. Wüstenhagen
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Biomedical Engineering (IBMT), Branch Potsdam-Golm, Potsdam, Germany
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13
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Tzitzilonis C, Eichmann C, Maslennikov I, Choe S, Riek R. Detergent/nanodisc screening for high-resolution NMR studies of an integral membrane protein containing a cytoplasmic domain. PLoS One 2013; 8:e54378. [PMID: 23349867 PMCID: PMC3551814 DOI: 10.1371/journal.pone.0054378] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 12/11/2012] [Indexed: 11/29/2022] Open
Abstract
Because membrane proteins need to be extracted from their natural environment and reconstituted in artificial milieus for the 3D structure determination by X-ray crystallography or NMR, the search for membrane mimetic that conserve the native structure and functional activities remains challenging. We demonstrate here a detergent/nanodisc screening study by NMR of the bacterial α-helical membrane protein YgaP containing a cytoplasmic rhodanese domain. The analysis of 2D [15N,1H]-TROSY spectra shows that only a careful usage of low amounts of mixed detergents did not perturb the cytoplasmic domain while solubilizing in parallel the transmembrane segments with good spectral quality. In contrast, the incorporation of YgaP into nanodiscs appeared to be straightforward and yielded a surprisingly high quality [15N,1H]-TROSY spectrum opening an avenue for the structural studies of a helical membrane protein in a bilayer system by solution state NMR.
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Affiliation(s)
- Christos Tzitzilonis
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Cédric Eichmann
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
| | - Innokentiy Maslennikov
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Senyon Choe
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Zürich, Switzerland
- Structural Biology Laboratory, The Salk Institute, La Jolla, California, United States of America
- * E-mail:
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14
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Cell-Free Systems: Functional Modules for Synthetic and Chemical Biology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:67-102. [DOI: 10.1007/10_2013_185] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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15
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Mondal S, Shet D, Prasanna C, Atreya HS. High yield expression of proteins in <i>E. coli</i> for NMR studies. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.46099] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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16
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Cell-free protein synthesis of membrane (1,3)-β-d-glucan (curdlan) synthase: co-translational insertion in liposomes and reconstitution in nanodiscs. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:743-57. [PMID: 23063656 DOI: 10.1016/j.bbamem.2012.10.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 09/25/2012] [Accepted: 10/04/2012] [Indexed: 01/07/2023]
Abstract
A membrane-embedded curdlan synthase (CrdS) from Agrobacterium is believed to catalyse a repetitive addition of glucosyl residues from UDP-glucose to produce the (1,3)-β-d-glucan (curdlan) polymer. We report wheat germ cell-free protein synthesis (WG-CFPS) of full-length CrdS containing a 6xHis affinity tag and either Factor Xa or Tobacco Etch Virus proteolytic sites, using a variety of hydrophobic membrane-mimicking environments. Full-length CrdS was synthesised with no variations in primary structure, following analysis of tryptic fragments by MALDI-TOF/TOF Mass Spectrometry. Preparative scale WG-CFPS in dialysis mode with Brij-58 yielded CrdS in mg/ml quantities. Analysis of structural and functional properties of CrdS during protein synthesis showed that CrdS was co-translationally inserted in DMPC liposomes during WG-CFPS, and these liposomes could be purified in a single step by density gradient floatation. Incorporated CrdS exhibited a random orientation topology. Following affinity purification of CrdS, the protein was reconstituted in nanodiscs with Escherichia coli lipids or POPC and a membrane scaffold protein MSP1E3D1. CrdS nanodiscs were characterised by small-angle X-ray scattering using synchrotron radiation and the data obtained were consistent with insertion of CrdS into bilayers. We found CrdS synthesised in the presence of the Ac-AAAAAAD surfactant peptide or co-translationally inserted in liposomes made from E. coli lipids to be catalytically competent. Conversely, CrdS synthesised with only Brij-58 was inactive. Our findings pave the way for future structural studies of this industrially important catalytic membrane protein.
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17
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Long AR, O'Brien CC, Alder NN. The cell-free integration of a polytopic mitochondrial membrane protein into liposomes occurs cotranslationally and in a lipid-dependent manner. PLoS One 2012; 7:e46332. [PMID: 23050015 PMCID: PMC3457961 DOI: 10.1371/journal.pone.0046332] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/31/2012] [Indexed: 01/19/2023] Open
Abstract
The ADP/ATP Carrier (AAC) is the most abundant transporter of the mitochondrial inner membrane. The central role that this transporter plays in cellular energy production highlights the importance of understanding its structure, function, and the basis of its pathologies. As a means of preparing proteoliposomes for the study of membrane proteins, several groups have explored the use of cell-free translation systems to facilitate membrane protein integration directly into preformed unilamellar vesicles without the use of surfactants. Using AAC as a model, we report for the first time the detergent-free reconstitution of a mitochondrial inner membrane protein into liposomes using a wheat germ-based in vitro translation system. Using a host of independent approaches, we demonstrate the efficient integration of AAC into vesicles with an inner membrane-mimetic lipid composition and, more importantly, that the integrated AAC is functionally active in transport. By adding liposomes at different stages of the translation reaction, we show that this direct integration is obligatorily cotranslational, and by synthesizing stable ribosome-bound nascent chain intermediates, we show that the nascent AAC polypeptide interacts with lipid vesicles while ribosome-bound. Finally, we show that the presence of the phospholipid cardiolipin in the liposomes specifically enhances AAC translation rate as well as the efficiency of vesicle association and integration. In light of these results, the possible mechanisms of liposome-assisted membrane protein integration during cell-free translation are discussed with respect to the mode of integration and the role of specific lipids.
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Affiliation(s)
- Ashley R. Long
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Catherine C. O'Brien
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Nathan N. Alder
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
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18
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Production of functional antibody fragments in a vesicle-based eukaryotic cell-free translation system. J Biotechnol 2012; 164:220-31. [PMID: 22982167 DOI: 10.1016/j.jbiotec.2012.08.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 08/15/2012] [Accepted: 08/30/2012] [Indexed: 12/17/2022]
Abstract
Cell-free protein synthesis is of increasing interest for the rapid and high-throughput synthesis of many proteins, in particular also antibody fragments. In this study, we present a novel strategy for the production of single chain antibody fragments (scFv) in a eukaryotic in vitro translation system. This strategy comprises the cell-free expression, isolation and label-free interaction analysis of a model antibody fragment synthesized in two differently prepared insect cell lysates. These lysates contain translocationally active microsomal structures derived from the endoplasmic reticulum (ER), allowing for posttranslational modifications of cell-free synthesized proteins. Both types of these insect cell lysates enable the synthesis and translocation of scFv into ER-derived vesicles. However, only the one that has a specifically adapted redox potential yields functional active antibody fragments. We have developed a new methodology for the isolation of functional target proteins based on the translocation of cell-free produced scFv into microsomal structures and subsequent collection of protein-enriched vesicles. Antibody fragments that have been released from these vesicles are shown to be well suited for label-free binding studies. Altogether, these results show the potential of insect cell lysates for the production, purification and selection of antibody fragments in an easy-to-handle and time-saving manner.
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19
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Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods 2012; 9:834-9. [PMID: 22609626 DOI: 10.1038/nmeth.2033] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/25/2012] [Indexed: 12/31/2022]
Abstract
Although nearly half of today's major pharmaceutical drugs target human integral membrane proteins (hIMPs), only 30 hIMP structures are currently available in the Protein Data Bank, largely owing to inefficiencies in protein production. Here we describe a strategy for the rapid structure determination of hIMPs, using solution NMR spectroscopy with systematically labeled proteins produced via cell-free expression. We report new backbone structures of six hIMPs, solved in only 18 months from 15 initial targets. Application of our protocols to an additional 135 hIMPs with molecular weight <30 kDa yielded 38 hIMPs suitable for structural characterization by solution NMR spectroscopy without additional optimization.
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20
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Cotranslational cis-phosphorylation of the COOH-terminal tail is a key priming step in the maturation of cAMP-dependent protein kinase. Proc Natl Acad Sci U S A 2012; 109:E1221-9. [PMID: 22493239 DOI: 10.1073/pnas.1202741109] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
cAMP-dependent protein kinase A (PKA), ubiquitously expressed in mammalian cells, regulates a plethora of cellular processes through its ability to phosphorylate many protein substrates, including transcription factors, ion channels, apoptotic proteins, transporters, and metabolic enzymes. The PKA catalytic subunit has two phosphorylation sites, a well-studied site in the activation loop (Thr(197)) and another site in the C-terminal tail (Ser(338)) for which the role of phosphorylation is unknown. We show here, using in vitro studies and experiments with S49 lymphoma cells, that cis-autophosphorylation of Ser(338) occurs cotranslationally, when PKA is associated with ribosomes and precedes posttranslational phosphorylation of the activation loop Thr(197). Ser(338) phoshorylation is not required for PKA activity or formation of the holoenzyme complex; however, it is critical for processing and maturation of PKA, and it is a prerequisite for phosphorylation of Thr(197). After Thr(197) and Ser(338) are phosphorylated, both sites are remarkably resistant to phosphatases. Phosphatase resistance of the activation loop, a unique feature of both PKA and PKG, reflects the distinct way that signal transduction dynamics are controlled by cyclic nucleotide-dependent PKs.
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21
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Isaksson L, Enberg J, Neutze R, Göran Karlsson B, Pedersen A. Expression screening of membrane proteins with cell-free protein synthesis. Protein Expr Purif 2012; 82:218-25. [DOI: 10.1016/j.pep.2012.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 12/22/2011] [Accepted: 01/03/2012] [Indexed: 12/22/2022]
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22
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Corin K, Baaske P, Ravel DB, Song J, Brown E, Wang X, Wienken CJ, Jerabek-Willemsen M, Duhr S, Luo Y, Braun D, Zhang S. Designer lipid-like peptides: a class of detergents for studying functional olfactory receptors using commercial cell-free systems. PLoS One 2011; 6:e25067. [PMID: 22132066 PMCID: PMC3223156 DOI: 10.1371/journal.pone.0025067] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/26/2011] [Indexed: 01/18/2023] Open
Abstract
A crucial bottleneck in membrane protein studies, particularly G-protein coupled receptors, is the notorious difficulty of finding an optimal detergent that can solubilize them and maintain their stability and function. Here we report rapid production of 12 unique mammalian olfactory receptors using short designer lipid-like peptides as detergents. The peptides were able to solubilize and stabilize each receptor. Circular dichroism showed that the purified olfactory receptors had alpha-helical secondary structures. Microscale thermophoresis suggested that the receptors were functional and bound their odorants. Blot intensity measurements indicated that milligram quantities of each olfactory receptor could be produced with at least one peptide detergent. The peptide detergents' capability was comparable to that of the detergent Brij-35. The ability of 10 peptide detergents to functionally solubilize 12 olfactory receptors demonstrates their usefulness as a new class of detergents for olfactory receptors, and possibly other G-protein coupled receptors and membrane proteins.
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Affiliation(s)
- Karolina Corin
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Deepali B. Ravel
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Junyao Song
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emily Brown
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Xiaoqiang Wang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong, China
| | - Christoph J. Wienken
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Moran Jerabek-Willemsen
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Stefan Duhr
- NanoTemper Technologies GmbH, München, Germany
| | - Yuan Luo
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, United States of America
| | - Dieter Braun
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University Munich, München, Germany
| | - Shuguang Zhang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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23
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Corin K, Baaske P, Ravel DB, Song J, Brown E, Wang X, Geissler S, Wienken CJ, Jerabek-Willemsen M, Duhr S, Braun D, Zhang S. A robust and rapid method of producing soluble, stable, and functional G-protein coupled receptors. PLoS One 2011; 6:e23036. [PMID: 22039398 PMCID: PMC3201940 DOI: 10.1371/journal.pone.0023036] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Accepted: 07/04/2011] [Indexed: 11/20/2022] Open
Abstract
Membrane proteins, particularly G-protein coupled receptors (GPCRs), are notoriously difficult to express. Using commercial E. coli cell-free systems with the detergent Brij-35, we could rapidly produce milligram quantities of 13 unique GPCRs. Immunoaffinity purification yielded receptors at >90% purity. Secondary structure analysis using circular dichroism indicated that the purified receptors were properly folded. Microscale thermophoresis, a novel label-free and surface-free detection technique that uses thermal gradients, showed that these receptors bound their ligands. The secondary structure and ligand-binding results from cell-free produced proteins were comparable to those expressed and purified from HEK293 cells. Our study demonstrates that cell-free protein production using commercially available kits and optimal detergents is a robust technology that can be used to produce sufficient GPCRs for biochemical, structural, and functional analyses. This robust and simple method may further stimulate others to study the structure and function of membrane proteins.
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Affiliation(s)
- Karolina Corin
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | | | - Deepali B. Ravel
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Junyao Song
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Emily Brown
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Xiaoqiang Wang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- Center for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong, People's Republic of China
| | | | - Christoph J. Wienken
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University München, München, Germany
| | | | - Stefan Duhr
- NanoTemper Technologies GmbH, München, Germany
| | - Dieter Braun
- Systems Biophysics, Functional Nanosystems, Ludwig-Maximilians University München, München, Germany
| | - Shuguang Zhang
- Center for Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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24
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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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25
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Rath P, Demange P, Saurel O, Tropis M, Daffé M, Dötsch V, Ghazi A, Bernhard F, Milon A. Functional expression of the PorAH channel from Corynebacterium glutamicum in cell-free expression systems: implications for the role of the naturally occurring mycolic acid modification. J Biol Chem 2011; 286:32525-32. [PMID: 21799011 DOI: 10.1074/jbc.m111.276956] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
PorA and PorH are two small membrane proteins from the outer membrane of Corynebacterium glutamicum, which have been shown to form heteromeric ion channels and to be post-translationally modified by mycolic acids. Any structural details of the channel could not be analyzed so far due to tremendous difficulties in the production of sufficient amounts of protein samples. Cell-free (CF) expression is a new and remarkably successful strategy for the production of membrane proteins for which toxicity, membrane targeting, and degradation are key issues. In addition, reaction conditions can easily be modified to modulate the quality of synthesized protein samples. We developed an efficient CF expression strategy to produce the channel subunits devoid of post-translational modifications. (15)N-labeled PorA and PorH samples were furthermore characterized by NMR and gave well resolved spectra, opening the way for structural studies. The comparison of ion channel activities of CF-expressed proteins with channels isolated from C. glutamicum gave clear insights on the influence of the mycolic acid modification of the two subunits on their functional properties.
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Affiliation(s)
- Parthasarathi Rath
- Centre National de la Recherche Scientifique, CNRS UMR 5089, Institut de Pharmacologie et de Biologie Structurale, 205 Route de Narbonne, Toulouse F-31077, Cedex 04, France
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26
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Klammt C, Perrin MH, Maslennikov I, Renault L, Krupa M, Kwiatkowski W, Stahlberg H, Vale W, Choe S. Polymer-based cell-free expression of ligand-binding family B G-protein coupled receptors without detergents. Protein Sci 2011; 20:1030-41. [PMID: 21465615 DOI: 10.1002/pro.636] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 02/23/2011] [Accepted: 03/25/2011] [Indexed: 12/13/2022]
Abstract
G-protein coupled receptors (GPCRs) constitute the largest family of intercellular signaling molecules and are estimated to be the target of more than 50% of all modern drugs. As with most integral membrane proteins (IMPs), a major bottleneck in the structural and biochemical analysis of GPCRs is their expression by conventional expression systems. Cell-free (CF) expression provides a relatively new and powerful tool for obtaining preparative amounts of IMPs. However, in the case of GPCRs, insufficient homogeneity of the targeted protein is a problem as the in vitro expression is mainly done with detergents, in which aggregation and solubilization difficulties, as well as problems with proper folding of hydrophilic domains, are common. Here, we report that using CF expression with the help of a fructose-based polymer, NV10 polymer (NVoy), we obtained preparative amounts of homogeneous GPCRs from the three GPCR families. We demonstrate that two GPCR B family members, corticotrophin-releasing factor receptors 1 and 2β are not only solubilized in NVoy but also have functional ligand-binding characteristics with different agonists and antagonists in a detergent-free environment as well. Our findings open new possibilities for functional and structural studies of GPCRs and IMPs in general.
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Affiliation(s)
- Christian Klammt
- Structural Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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27
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Michán C, Daniels C, Fernández M, Solano J, De La Campa AM, Ramos JL. Sugar (ribose), spice (peroxidase) and all things nice (laccase hair-dyes). Microb Biotechnol 2011; 3:131-3. [PMID: 21255315 PMCID: PMC3836576 DOI: 10.1111/j.1751-7915.2010.00167.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Carmen Michán
- Universidad de Córdoba, Campus de Rabanales, Department. of Biochemistry and Molecular Biology, Edificio Severo Ochoa C-6, 2a Planta, 14071, Córdoba, Spain
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28
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Junge F, Haberstock S, Roos C, Stefer S, Proverbio D, Dötsch V, Bernhard F. Advances in cell-free protein synthesis for the functional and structural analysis of membrane proteins. N Biotechnol 2011; 28:262-71. [DOI: 10.1016/j.nbt.2010.07.002] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Revised: 06/28/2010] [Accepted: 07/04/2010] [Indexed: 11/25/2022]
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29
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Miot M, Betton JM. Reconstitution of the Cpx signaling system from cell-free synthesized proteins. N Biotechnol 2010; 28:277-81. [PMID: 20601270 DOI: 10.1016/j.nbt.2010.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 06/16/2010] [Indexed: 11/29/2022]
Abstract
Cell-free expression has received growing attention as an effective system to produce integral membrane proteins for biochemical studies. We have applied this technology for the production of the histidine kinase CpxA, an integral membrane sensor that regulates an envelope stress response in Escherichia coli. All phosphotransfer activities of detergent-solubilized CpxA synthesized in vitro have been characterized and compared with those of CpxA solubilized from bacterial membranes. The results demonstrate the simplicity and efficiency of this technology for purifying large quantities of functional membrane proteins.
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Affiliation(s)
- Marika Miot
- Unité de Biochimie Structurale, Institut Pasteur, URA-CNRS 2185, 75724 Paris cedex 15, France
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30
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Schwarz D, Daley D, Beckhaus T, Dötsch V, Bernhard F. Cell-free expression profiling of E. coli
inner membrane proteins. Proteomics 2010; 10:1762-79. [DOI: 10.1002/pmic.200900485] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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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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32
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Schlegel S, Klepsch M, Gialama D, Wickström D, Slotboom DJ, de Gier JW. Revolutionizing membrane protein overexpression in bacteria. Microb Biotechnol 2009; 3:403-11. [PMID: 21255339 PMCID: PMC3815807 DOI: 10.1111/j.1751-7915.2009.00148.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The bacterium Escherichia coli is the most widely used expression host for overexpression trials of membrane proteins. Usually, different strains, culture conditions and expression regimes are screened for to identify the optimal overexpression strategy. However, yields are often not satisfactory, especially for eukaryotic membrane proteins. This has initiated a revolution of membrane protein overexpression in bacteria. Recent studies have shown that it is feasible to (i) engineer or select for E. coli strains with strongly improved membrane protein overexpression characteristics, (ii) use bacteria other than E. coli for the expression of membrane proteins, (iii) engineer or select for membrane protein variants that retain functionality but express better than the wild‐type protein, and (iv) express membrane proteins using E. coli‐based cell‐free systems.
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Affiliation(s)
- Susan Schlegel
- Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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33
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Schwarz D, Dötsch V, Bernhard F. Production of membrane proteins using cell-free expression systems. Proteomics 2009; 8:3933-46. [PMID: 18763710 DOI: 10.1002/pmic.200800171] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Production of membrane proteins (MPs) is a challenging task as their hydrophobic nature and their specific requirements in cellular expression systems frequently prevent an efficient synthesis. Cell-free (CF) expression systems have been developed in recent times as promising tools by offering completely new approaches to synthesize MPs directly into artificial hydrophobic environments. A considerable variety of CF produced MPs has been characterized by functional and structural approaches and the high success rates and the rapidly accumulating data on quality and expression efficiencies increasingly attract attention. In addition, CF expression is a highly dynamic and versatile technique and new modifications for improved performance as well as for extended applications for the labeling, throughput expression and proteomic analysis of MPs are rapidly emerging.
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Affiliation(s)
- Daniel Schwarz
- Centre for Biomolecular Magnetic Resonance, University of Frankfurt/Main, Institute for Biophysical Chemistry, Frankfurt/Main, Germany
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34
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Newby ZER, O'Connell JD, Gruswitz F, Hays FA, Harries WEC, Harwood IM, Ho JD, Lee JK, Savage DF, Miercke LJW, Stroud RM. A general protocol for the crystallization of membrane proteins for X-ray structural investigation. Nat Protoc 2009; 4:619-37. [PMID: 19360018 PMCID: PMC4075773 DOI: 10.1038/nprot.2009.27] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Protein crystallography is used to generate atomic resolution structures of protein molecules. These structures provide information about biological function, mechanism and interaction of a protein with substrates or effectors including DNA, RNA, cofactors or other small molecules, ions and other proteins. This technique can be applied to membrane proteins resident in the membranes of cells. To accomplish this, membrane proteins first need to be either heterologously expressed or purified from a native source. The protein has to be extracted from the lipid membrane with a mild detergent and purified to a stable, homogeneous population that may then be crystallized. Protein crystals are then used for X-ray diffraction to yield atomic resolution structures of the desired membrane protein target. Below, we present a general protocol for the growth of diffraction quality membrane protein crystals. The process of protein crystallization is highly variable, and obtaining diffraction quality crystals can require weeks to months or even years in some cases.
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Affiliation(s)
- Zachary E R Newby
- Department of Biochemistry and Biophysics, University of California in San Francisco, 600 16th Street, San Francisco, California 94158-2517, USA
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35
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Efficient cell-free production of olfactory receptors: detergent optimization, structure, and ligand binding analyses. Proc Natl Acad Sci U S A 2008; 105:15726-31. [PMID: 18840687 DOI: 10.1073/pnas.0804766105] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
High-level production of membrane proteins, particularly of G protein-coupled receptors (GPCRs) in heterologous cell systems encounters a number of difficulties from their inherent hydrophobicity in their transmembrane domains, which frequently cause protein aggregation and cytotoxicity and thus reduce the protein yield. Recent advances in cell-free protein synthesis circumvent those problems to produce membrane proteins with a yield sometimes exceeding the cell-based approach. Here, we report cell-free production of a human olfactory receptor 17-4 (hOR17-4) using the wheat germ extract. Using the simple method, we also successful produced two additional olfactory receptors. To obtain soluble olfactory receptors and to increase yield, we directly added different detergents in varying concentrations to the cell-free reaction. To identify a purification buffer system that maintained the receptor in a nonaggregated form, we developed a method that uses small-volume size-exclusion column chromatography combined with rapid and sensitive dot-blot detection. Different buffer components including salt concentration, various detergents and detergent concentration, and reducing agent and its concentrations were evaluated for their ability to maintain the cell-free produced protein stable and nonaggregated. The purified olfactory receptor displays a typical a alpha-helical CD spectrum. Surface plasmon resonance measurements were used to show binding of a known ligand undecanal to hOR17-4. Our approach to produce a high yield of purified olfactory receptor is a milestone toward obtaining a large quantity of olfactory receptors for designing bionic sensors. Furthermore, this simple approach may be broadly useful not only for other classes of GPCRs but also for other membrane proteins.
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Optimized in vitro and in vivo expression of proteorhodopsin: A seven-transmembrane proton pump. Protein Expr Purif 2008; 58:103-13. [DOI: 10.1016/j.pep.2007.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2007] [Revised: 10/15/2007] [Accepted: 10/18/2007] [Indexed: 11/19/2022]
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Zhao KQ, Hurst R, Slater MR, Bulleit RF. Functional protein expression from a DNA based wheat germ cell-free system. ACTA ACUST UNITED AC 2007; 8:199-208. [PMID: 18034374 DOI: 10.1007/s10969-007-9035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 11/01/2007] [Indexed: 11/29/2022]
Abstract
Wheat germ based eukaryotic cell-free systems have been shown to be applicable for both functional and structural analyses of proteins. However, the existing methods might require specialized instrumentation and/or a separate mRNA synthesis step. We have developed a DNA based, highly productive, coupled transcription/translation wheat germ cell-free system that incorporates the normally separate mRNA synthesis step and does not require specialized instrumentation. Using a small-volume batch reaction with fluorescence labeling, DNA templates predicted to encode proteins could be quickly screened for their ability to direct the expression of proteins of the appropriate size. Protein yield can be increased as much as 2 to 4-fold in this system using a dialysis reaction, reaching approximately 200-440 microg/ml in 10-20 h. Furthermore, enzyme activities can be assayed directly in the extract without further purification. Simple purification with affinity tags can be achieved in one-step and with minor modifications, efficient SeMet and [U-15N] labeling of >95% can be accomplished in this system. Thus, this efficient cell-free expression system can facilitate both functional and structural proteomics.
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Affiliation(s)
- Kate Qin Zhao
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA.
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Schwarz D, Junge F, Durst F, Frölich N, Schneider B, Reckel S, Sobhanifar S, Dötsch V, Bernhard F. Preparative scale expression of membrane proteins in Escherichia coli-based continuous exchange cell-free systems. Nat Protoc 2007; 2:2945-57. [PMID: 18007631 DOI: 10.1038/nprot.2007.426] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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