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Levitskaya Z, Ser Z, Koh H, Mei WS, Chee S, Sobota RM, Ghadessy JF. Engineering cell-free systems by chemoproteomic-assisted phenotypic screening. RSC Chem Biol 2024; 5:372-385. [PMID: 38576719 PMCID: PMC10989505 DOI: 10.1039/d4cb00004h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 02/16/2024] [Indexed: 04/06/2024] Open
Abstract
Phenotypic screening is a valuable tool to both understand and engineer complex biological systems. We demonstrate the functionality of this approach in the development of cell-free protein synthesis (CFPS) technology. Phenotypic screening identified numerous compounds that enhanced protein production in yeast lysate CFPS reactions. Notably, many of these were competitive ATP kinase inhibitors, with the exploitation of their inherent substrate promiscuity redirecting ATP flux towards heterologous protein expression. Chemoproteomic-guided strain engineering partially phenocopied drug effects, with a 30% increase in protein yield observed upon deletion of the ATP-consuming SSA1 component of the HSP70 chaperone. Moreover, drug-mediated metabolic rewiring coupled with template optimization generated the highest protein yields in yeast CFPS to date using a hitherto less efficient, but more cost-effective glucose energy regeneration system. Our approach highlights the utility of target-agnostic phenotypic screening and target identification to deconvolute cell-lysate complexity, adding to the expanding repertoire of strategies for improving CFPS.
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Affiliation(s)
- Zarina Levitskaya
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Zheng Ser
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Hiromi Koh
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Wang Shi Mei
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Sharon Chee
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - Radoslaw Mikolaj Sobota
- Function Proteomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
| | - John F Ghadessy
- Protein and Peptide Engineering and Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) 8A Biomedical Grove Singapore 138648
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2
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Köck Z, Schnelle K, Persechino M, Umbach S, Schihada H, Januliene D, Parey K, Pockes S, Kolb P, Dötsch V, Möller A, Hilger D, Bernhard F. Cryo-EM structure of cell-free synthesized human histamine 2 receptor/G s complex in nanodisc environment. Nat Commun 2024; 15:1831. [PMID: 38418462 PMCID: PMC10901899 DOI: 10.1038/s41467-024-46096-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 02/14/2024] [Indexed: 03/01/2024] Open
Abstract
Here we describe the cryo-electron microscopy structure of the human histamine 2 receptor (H2R) in an active conformation with bound histamine and in complex with Gs heterotrimeric protein at an overall resolution of 3.4 Å. The complex was generated by cotranslational insertion of the receptor into preformed nanodisc membranes using cell-free synthesis in E. coli lysates. Structural comparison with the inactive conformation of H2R and the inactive and Gq-coupled active state of H1R together with structure-guided functional experiments reveal molecular insights into the specificity of ligand binding and G protein coupling for this receptor family. We demonstrate lipid-modulated folding of cell-free synthesized H2R, its agonist-dependent internalization and its interaction with endogenously synthesized H1R and H2R in HEK293 cells by applying a recently developed nanotransfer technique.
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Affiliation(s)
- Zoe Köck
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt, Germany
| | - Kilian Schnelle
- Department of Biology/Chemistry, Structural Biology section, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | | | - Simon Umbach
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt, Germany
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, University of Marburg, Marburg, Germany
| | - Dovile Januliene
- Department of Biology/Chemistry, Structural Biology section, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Kristian Parey
- Department of Biology/Chemistry, Structural Biology section, University of Osnabrück, Osnabrück, Germany
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany
| | - Steffen Pockes
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, University of Marburg, Marburg, Germany
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt, Germany
| | - Arne Möller
- Department of Biology/Chemistry, Structural Biology section, University of Osnabrück, Osnabrück, Germany.
- Center of Cellular Nanoanalytic Osnabrück (CellNanOs), University of Osnabrück, Osnabrück, Germany.
| | - Daniel Hilger
- Department of Pharmaceutical Chemistry, University of Marburg, Marburg, Germany.
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt, Germany.
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3
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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4
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Choi YN, Cho N, Lee K, Gwon DA, Lee JW, Lee J. Programmable Synthesis of Biobased Materials Using Cell-Free Systems. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2203433. [PMID: 36108274 DOI: 10.1002/adma.202203433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Motivated by the intricate mechanisms underlying biomolecule syntheses in cells that chemistry is currently unable to mimic, researchers have harnessed biological systems for manufacturing novel materials. Cell-free systems (CFSs) utilizing the bioactivity of transcriptional and translational machineries in vitro are excellent tools that allow supplementation of exogenous materials for production of innovative materials beyond the capability of natural biological systems. Herein, recent studies that have advanced the ability to expand the scope of biobased materials using CFS are summarized and approaches enabling the production of high-value materials, prototyping of genetic parts and modules, and biofunctionalization are discussed. By extending the reach of chemical and enzymatic reactions complementary to cellular materials, CFSs provide new opportunities at the interface of materials science and synthetic biology.
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Affiliation(s)
- Yun-Nam Choi
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Namjin Cho
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Kanghun Lee
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Da-Ae Gwon
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Jeong Wook Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Joongoo Lee
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
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5
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Galluccio M, Console L, Pochini L, Scalise M, Giangregorio N, Indiveri C. Strategies for Successful Over-Expression of Human Membrane Transport Systems Using Bacterial Hosts: Future Perspectives. Int J Mol Sci 2022; 23:ijms23073823. [PMID: 35409183 PMCID: PMC8998559 DOI: 10.3390/ijms23073823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/28/2022] [Accepted: 03/28/2022] [Indexed: 02/06/2023] Open
Abstract
Ten percent of human genes encode for membrane transport systems, which are key components in maintaining cell homeostasis. They are involved in the transport of nutrients, catabolites, vitamins, and ions, allowing the absorption and distribution of these compounds to the various body regions. In addition, roughly 60% of FDA-approved drugs interact with membrane proteins, among which are transporters, often responsible for pharmacokinetics and side effects. Defects of membrane transport systems can cause diseases; however, knowledge of the structure/function relationships of transporters is still limited. Among the expression of hosts that produce human membrane transport systems, E. coli is one of the most favorable for its low cultivation costs, fast growth, handiness, and extensive knowledge of its genetics and molecular mechanisms. However, the expression in E. coli of human membrane proteins is often toxic due to the hydrophobicity of these proteins and the diversity in structure with respect to their bacterial counterparts. Moreover, differences in codon usage between humans and bacteria hamper translation. This review summarizes the many strategies exploited to achieve the expression of human transport systems in bacteria, providing a guide to help people who want to deal with this topic.
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Affiliation(s)
- Michele Galluccio
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Lara Console
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Lorena Pochini
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Mariafrancesca Scalise
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
| | - Nicola Giangregorio
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy;
| | - Cesare Indiveri
- Unit of Biochemistry and Molecular Biotechnology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Via P. Bucci 4c, Arcavacata di Rende, 87036 Cosenza, Italy; (M.G.); (L.C.); (L.P.); (M.S.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), National Research Council (CNR), Via Amendola 165/A, 70126 Bari, Italy;
- Correspondence:
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6
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Koo J, Yang J, Park H. Cell-free Systems: Recent Advances and Future Outlook. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Kögler LM, Stichel J, Beck-Sickinger AG. Structural investigations of cell-free expressed G protein-coupled receptors. Biol Chem 2020; 401:97-116. [PMID: 31539345 DOI: 10.1515/hsz-2019-0292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 12/11/2022]
Abstract
G protein-coupled receptors (GPCRs) are of great pharmaceutical interest and about 35% of the commercial drugs target these proteins. Still there is huge potential left in finding molecules that target new GPCRs or that modulate GPCRs differentially. For a rational drug design, it is important to understand the structure, binding and activation of the protein of interest. Structural investigations of GPCRs remain challenging, although huge progress has been made in the last 20 years, especially in the generation of crystal structures of GPCRs. This is mostly caused by issues with the expression yield, purity or labeling. Cell-free protein synthesis (CFPS) is an efficient alternative for recombinant expression systems that can potentially address many of these problems. In this article the use of CFPS for structural investigations of GPCRs is reviewed. We compare different CFPS systems, including the cellular basis and reaction configurations, and strategies for an efficient solubilization. Next, we highlight recent advances in the structural investigation of cell-free expressed GPCRs, with special emphasis on the role of photo-crosslinking approaches to investigate ligand binding sites on GPCRs.
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Affiliation(s)
- Lisa Maria Kögler
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Jan Stichel
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
| | - Annette G Beck-Sickinger
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Leipzig University, Brüderstr. 34, D-04103 Leipzig, Germany
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8
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Abstract
Proteins are the main source of drug targets and some of them possess therapeutic potential themselves. Among them, membrane proteins constitute approximately 50% of the major drug targets. In the drug discovery pipeline, rapid methods for producing different classes of proteins in a simple manner with high quality are important for structural and functional analysis. Cell-free systems are emerging as an attractive alternative for the production of proteins due to their flexible nature without any cell membrane constraints. In a bioproduction context, open systems based on cell lysates derived from different sources, and with batch-to-batch consistency, have acted as a catalyst for cell-free synthesis of target proteins. Most importantly, proteins can be processed for downstream applications like purification and functional analysis without the necessity of transfection, selection, and expansion of clones. In the last 5 years, there has been an increased availability of new cell-free lysates derived from multiple organisms, and their use for the synthesis of a diverse range of proteins. Despite this progress, major challenges still exist in terms of scalability, cost effectiveness, protein folding, and functionality. In this review, we present an overview of different cell-free systems derived from diverse sources and their application in the production of a wide spectrum of proteins. Further, this article discusses some recent progress in cell-free systems derived from Chinese hamster ovary and Sf21 lysates containing endogenous translocationally active microsomes for the synthesis of membrane proteins. We particularly highlight the usage of internal ribosomal entry site sequences for more efficient protein production, and also the significance of site-specific incorporation of non-canonical amino acids for labeling applications and creation of antibody drug conjugates using cell-free systems. We also discuss strategies to overcome the major challenges involved in commercializing cell-free platforms from a laboratory level for future drug development.
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Affiliation(s)
- Srujan Kumar Dondapati
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus-Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
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9
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Escherichia coli Extract-Based Cell-Free Expression System as an Alternative for Difficult-to-Obtain Protein Biosynthesis. Int J Mol Sci 2020; 21:ijms21030928. [PMID: 32023820 PMCID: PMC7037961 DOI: 10.3390/ijms21030928] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/15/2020] [Accepted: 01/28/2020] [Indexed: 12/15/2022] Open
Abstract
Before utilization in biomedical diagnosis, therapeutic treatment, and biotechnology, the diverse variety of peptides and proteins must be preliminarily purified and thoroughly characterized. The recombinant DNA technology and heterologous protein expression have helped simplify the isolation of targeted polypeptides at high purity and their structure-function examinations. Recombinant protein expression in Escherichia coli, the most-established heterologous host organism, has been widely used to produce proteins of commercial and fundamental research interests. Nonetheless, many peptides/proteins are still difficult to express due to their ability to slow down cell growth or disrupt cellular metabolism. Besides, special modifications are often required for proper folding and activity of targeted proteins. The cell-free (CF) or in vitro recombinant protein synthesis system enables the production of such difficult-to-obtain molecules since it is possible to adjust reaction medium and there is no need to support cellular metabolism and viability. Here, we describe E. coli-based CF systems, the optimization steps done toward the development of highly productive and cost-effective CF methodology, and the modification of an in vitro approach required for difficult-to-obtain protein production.
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Ayoubi-Joshaghani MH, Dianat-Moghadam H, Seidi K, Jahanban-Esfahalan A, Zare P, Jahanban-Esfahlan R. Cell-free protein synthesis: The transition from batch reactions to minimal cells and microfluidic devices. Biotechnol Bioeng 2020; 117:1204-1229. [PMID: 31840797 DOI: 10.1002/bit.27248] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/23/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022]
Abstract
Thanks to the synthetic biology, the laborious and restrictive procedure for producing a target protein in living microorganisms by biotechnological approaches can now experience a robust, pliant yet efficient alternative. The new system combined with lab-on-chip microfluidic devices and nanotechnology offers a tremendous potential envisioning novel cell-free formats such as DNA brushes, hydrogels, vesicular particles, droplets, as well as solid surfaces. Acting as robust microreactors/microcompartments/minimal cells, the new platforms can be tuned to perform various tasks in a parallel and integrated manner encompassing gene expression, protein synthesis, purification, detection, and finally enabling cell-cell signaling to bring a collective cell behavior, such as directing differentiation process, characteristics of higher order entities, and beyond. In this review, we issue an update on recent cell-free protein synthesis (CFPS) formats. Furthermore, the latest advances and applications of CFPS for synthetic biology and biotechnology are highlighted. In the end, contemporary challenges and future opportunities of CFPS systems are discussed.
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Affiliation(s)
| | | | - Khaled Seidi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Peyman Zare
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, Warsaw, Poland
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
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11
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Calmet P, Cullin C, Cortès S, Vang M, Caudy N, Baccouch R, Dessolin J, Maamar NT, Lecomte S, Tillier B, Alves ID. Cholesterol impacts chemokine CCR5 receptor ligand-binding activity. FEBS J 2019; 287:2367-2385. [PMID: 31738467 DOI: 10.1111/febs.15145] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/27/2019] [Accepted: 11/16/2019] [Indexed: 01/03/2023]
Abstract
The chemokine CCR5 receptor is target of maraviroc, a negative allosteric modulator of CCR5 that blocks the HIV protein gp120 from associating with the receptor, thereby inhibiting virus cellular entry. As noted with other G-protein-coupled receptor family members, the role of the lipid environment in CCR5 signaling remains obscure and very modestly investigated. Controversial literature on the impact of cholesterol (Chol) depletion in HIV infection and CCR5 signaling, including the hypothesis that Chol depletion could inhibit HIV infection, lead us to focus on the understanding of Chol impact in the first stages of receptor activation. To address this aim, the approach chosen was to employ reconstituted model lipid systems of controlled lipid composition containing CCR5 from two distinct expression systems: Pichia pastoris and cell-free expression. The characterization of receptor/ligand interaction in terms of total binding or competition binding assays was independently performed by plasmon waveguide resonance and fluorescence anisotropy, respectively. Maraviroc, a potent receptor antagonist, was the ligand investigated. Additionally, coarse-grained molecular dynamics simulation was employed to investigate Chol impact in the receptor-conformational flexibility and dynamics. Results obtained with receptor produced by different expression systems and using different biophysical approaches clearly demonstrate a considerable impact of Chol in the binding affinity of maraviroc to the receptor and receptor-conformational dynamics. Chol considerably decreases maraviroc binding affinity to the CCR5 receptor. The mechanisms by which this effect occurs seem to involve the adoption of distinct receptor-conformational states with restrained structural dynamics and helical motions in the presence of Chol.
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Affiliation(s)
- Pierre Calmet
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | | | - Maylou Vang
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Nada Caudy
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Rim Baccouch
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | - Jean Dessolin
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | - Sophie Lecomte
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
| | | | - Isabel D Alves
- CBMN, UMR 5248 CNRS, University of Bordeaux, Pessac, France
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12
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Shelby ML, He W, Dang AT, Kuhl TL, Coleman MA. Cell-Free Co-Translational Approaches for Producing Mammalian Receptors: Expanding the Cell-Free Expression Toolbox Using Nanolipoproteins. Front Pharmacol 2019; 10:744. [PMID: 31333463 PMCID: PMC6616253 DOI: 10.3389/fphar.2019.00744] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/07/2019] [Indexed: 12/28/2022] Open
Abstract
Membranes proteins make up more than 60% of current drug targets and account for approximately 30% or more of the cellular proteome. Access to this important class of proteins has been difficult due to their inherent insolubility and tendency to aggregate in aqueous solutions. Understanding membrane protein structure and function demands novel means of membrane protein production that preserve both their native conformational state as well as function. Over the last decade, cell-free expression systems have emerged as an important complement to cell-based expression of membrane proteins due to their simple and customizable experimental parameters. One approach to overcome the solubility and stability limitations of purified membrane proteins is to support them in stable, native-like states within nanolipoprotein particles (NLPs), aka nanodiscs. This has become common practice to facilitate biochemical and biophysical characterization of proteins of interest. NLP technology can be easily coupled with cell-free systems to achieve functional membrane protein production for this purpose. Our approach involves utilizing cell-free expression systems in the presence of NLPs or using co-translation techniques to perform one-pot expression and self-assembly of membrane protein/NLP complexes. We describe how cell-free reactions can be modified to render control over nanoparticle size and monodispersity in support of membrane protein production. These modifications have been exploited to facilitate co-expression of full-length functional membrane proteins such as G-protein-coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). In particular, we summarize the state of the art in NLP-assisted cell-free coexpression of these important classes of membrane proteins as well as evaluate the advances in and prospects for this technology that will drive drug discovery against these targets. We conclude with a prospective on the use of NLPs to produce as well as deliver functional mammalian membrane-bound proteins for a range of applications.
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Affiliation(s)
- Megan L Shelby
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Amanda T Dang
- University of California at Davis, Davis, CA, United States
| | - Tonya L Kuhl
- University of California at Davis, Davis, CA, United States
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, CA, United States.,University of California at Davis, Davis, CA, United States
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13
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Schoborg JA, Jewett MC. Cell-Free Protein Synthesis: An Emerging Technology for Understanding, Harnessing, and Expanding the Capabilities of Biological Systems. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Jennifer A. Schoborg
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering; Northwestern University, 2145 Sheridan Road, Evanston, IL; 60208-3120 USA
- Chemistry of Life Processes Institute; 2170 Campus Drive, Evanston, IL; 60208-3120 USA
- Robert H. Lurie Comprehensive Cancer Center; Northwestern University, 676 N. St Clair St; Suite 1200 Chicago IL 60611-3068 USA
- Simpson Querrey Institute; Northwestern University; 303 E. Superior St; Suite 11-131, Chicago IL 60611-2875 USA
- Center for Synthetic Biology; Northwestern University, 2145 Sheridan Road; Evanston IL 60208-3120 USA
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14
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Patriarchi T, Shen A, He W, Baikoghli M, Cheng RH, Xiang YK, Coleman MA, Tian L. Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. Sci Rep 2018; 8:3556. [PMID: 29476125 PMCID: PMC5824837 DOI: 10.1038/s41598-018-21863-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 02/12/2018] [Indexed: 01/01/2023] Open
Abstract
Modification of membrane receptor makeup is one of the most efficient ways to control input-output signals but is usually achieved by expressing DNA or RNA-encoded proteins or by using other genome-editing methods, which can be technically challenging and produce unwanted side effects. Here we develop and validate a nanodelivery approach to transfer in vitro synthesized, functional membrane receptors into the plasma membrane of living cells. Using β2-adrenergic receptor (β2AR), a prototypical G-protein coupled receptor, as an example, we demonstrated efficient incorporation of a full-length β2AR into a variety of mammalian cells, which imparts pharmacologic control over cellular signaling and affects cellular phenotype in an ex-vivo wound-healing model. Our approach for nanodelivery of functional membrane receptors expands the current toolkit for DNA and RNA-free manipulation of cellular function. We expect this approach to be readily applicable to the synthesis and nanodelivery of other types of GPCRs and membrane receptors, opening new doors for therapeutic development at the intersection between synthetic biology and nanomedicine.
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Affiliation(s)
- Tommaso Patriarchi
- University of California Davis, School of Medicine, Department of Biochemistry and Molecular Medicine, Davis, California, USA
| | - Ao Shen
- University of California Davis, School of Medicine, Department of Pharmacology, Davis, California, USA
| | - Wei He
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Mo Baikoghli
- University of California Davis, Department of Molecular and Cellular Biology, California, USA
| | - R Holland Cheng
- University of California Davis, Department of Molecular and Cellular Biology, California, USA
| | - Yang K Xiang
- University of California Davis, School of Medicine, Department of Pharmacology, Davis, California, USA.,VA Northern California Health care system, Mather, California, USA
| | - Matthew A Coleman
- Lawrence Livermore National Laboratory, Livermore, California, USA. .,University of California Davis School of Medicine, Radiation Oncology, Sacramento, California, USA.
| | - Lin Tian
- University of California Davis, School of Medicine, Department of Biochemistry and Molecular Medicine, Davis, California, USA.
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15
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Expression, Purification and Characterization of the Human Cannabinoid 1 Receptor. Sci Rep 2018; 8:2935. [PMID: 29440756 PMCID: PMC5811539 DOI: 10.1038/s41598-018-19749-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/04/2018] [Indexed: 12/12/2022] Open
Abstract
The human cannabinoid 1 receptor (hCB1) is involved in numerous physiological processes and therefore provides a wide scope of potential therapeutic opportunities to treat maladies such as obesity, cardio-metabolic disorders, substance abuse, neuropathic pain, and multiple sclerosis. Structure-based drug design using the current knowledge of the hCB1 receptor binding site is limited and requires purified active protein. Heterologous expression and purification of functional hCB1 has been the bottleneck for ligand binding structural studies using biophysical methods such as mass spectrometry, x-ray crystallography and NMR. We constructed several plasmids for in-cell or in vitro Escherichia coli (E. coli) based expression of truncated and stabilized hCB1 receptor (hΔCB1 and hΔCB1T4L) variants and evaluated their competency to bind the CP-55,940 ligand. MALDI-TOF MS analysis of in vitro expressed and purified hΔCB1T4Lhis6 variants, following trypsin digestion, generated ~80% of the receptor sequence coverage. Our data demonstrate the feasibility of a cell-free expression system as a promising part of the strategy for the elucidation of ligand binding sites of the hCB1 receptor using a "Ligand Assisted Protein Structure" (LAPS) approach.
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16
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Suzuki Y, Ogasawara T, Tanaka Y, Takeda H, Sawasaki T, Mogi M, Liu S, Maeyama K. Functional G-Protein-Coupled Receptor (GPCR) Synthesis: The Pharmacological Analysis of Human Histamine H1 Receptor (HRH1) Synthesized by a Wheat Germ Cell-Free Protein Synthesis System Combined with Asolectin Glycerosomes. Front Pharmacol 2018; 9:38. [PMID: 29467651 PMCID: PMC5808195 DOI: 10.3389/fphar.2018.00038] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/12/2018] [Indexed: 11/13/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are membrane proteins distributed on the cell surface, and they may be potential drug targets. However, synthesizing GPCRs in vitro can be challenging. Recently, some cell-free protein synthesis systems have been shown to produce a large amount of membrane protein combined with chemical chaperones that include liposomes and glycerol. Liposomes containing high concentrations of glycerol are known as glycerosomes, which are used in new drug delivery systems. Glycerosomes have greater morphological stability than liposomes. Proteoglycerosomes are defined as glycerosomes that contain membrane proteins. Human histamine H1 receptor (HRH1) is one of the most studied GPCRs. In this study, we synthesized wild-type HRH1 (WT-HRH1) proteoglycerosomes and D107A-HRH1, (in which Asp107 was replaced by Ala) in a wheat germ cell-free protein synthesis system combined with asolectin glycerosomes. The mutant HRH1 has been reported to have low affinity for the H1 antagonist. In this study, the amount of synthesized WT-HRH1 in one synthesis reaction was 434 ± 66.6 μg (7.75 ± 1.19 × 103pmol). The specific binding of [3H]pyrilamine to the WT-HRH1 proteoglycerosomes became saturated as the concentration of the radioligand increased. The dissociation constant (Kd) and maximum density (Bmax) of the synthesized WT-HRH1 were 9.76 ± 1.25 nM and 21.4 ± 0.936 pmol/mg protein, respectively. However, specific binding to D107A-HRH1 was reduced compared with WT-HRH1 and the binding did not become saturated. The findings of this study highlight that HRH1 synthesized using a wheat germ cell-free protein synthesis system combined with glycerosomes has the ability to bind to H1 antagonists.
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Affiliation(s)
- Yasuyuki Suzuki
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Japan
| | | | - Yuki Tanaka
- Advanced Research Support Center, Division of Analytical Bio-Medicine, Ehime University, Toon, Japan
| | | | | | - Masaki Mogi
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Japan
| | - Shuang Liu
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Japan
| | - Kazutaka Maeyama
- Department of Pharmacology, Ehime University Graduate School of Medicine, Toon, Japan
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17
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Wang J, Liu Y, Zhang J, Han Z, Wang W, Liu Y, Wei D, Huang W. Cell-free expression, purification, and characterization of the functional β2-adrenergic receptor for multianalyte detection of β-agonists. BIOCHEMISTRY (MOSCOW) 2017; 82:1346-1353. [DOI: 10.1134/s0006297917110128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Sonnabend A, Spahn V, Stech M, Zemella A, Stein C, Kubick S. Production of G protein-coupled receptors in an insect-based cell-free system. Biotechnol Bioeng 2017; 114:2328-2338. [PMID: 28574582 PMCID: PMC5599999 DOI: 10.1002/bit.26346] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 04/21/2017] [Accepted: 05/31/2017] [Indexed: 02/06/2023]
Abstract
The biochemical analysis of human cell membrane proteins remains a challenging task due to the difficulties in producing sufficient quantities of functional protein. G protein‐coupled receptors (GPCRs) represent a main class of membrane proteins and drug targets, which are responsible for a huge number of signaling processes regulating various physiological functions in living cells. To circumvent the current bottlenecks in GPCR studies, we propose the synthesis of GPCRs in eukaryotic cell‐free systems based on extracts generated from insect (Sf21) cells. Insect cell lysates harbor the fully active translational and translocational machinery allowing posttranslational modifications, such as glycosylation and phosphorylation of de novo synthesized proteins. Here, we demonstrate the production of several GPCRs in a eukaryotic cell‐free system, performed within a short time and in a cost‐effective manner. We were able to synthesize a variety of GPCRs ranging from 40 to 133 kDa in an insect‐based cell‐free system. Moreover, we have chosen the μ opioid receptor (MOR) as a model protein to analyze the ligand binding affinities of cell‐free synthesized MOR in comparison to MOR expressed in a human cell line by “one‐point” radioligand binding experiments. Biotechnol. Bioeng. 2017;114: 2328–2338. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Viola Spahn
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Marlitt Stech
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
| | - Christoph Stein
- Department of Anesthesiology and Intensive Care Medicine, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses Potsdam-Golm (IZI-BB), Am Muehlenberg 13, Potsdam 14476, Germany
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19
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Zemella A, Grossmann S, Sachse R, Sonnabend A, Schaefer M, Kubick S. Qualifying a eukaryotic cell-free system for fluorescence based GPCR analyses. Sci Rep 2017. [PMID: 28623260 PMCID: PMC5473880 DOI: 10.1038/s41598-017-03955-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Membrane proteins are key elements in cell-mediated processes. In particular, G protein-coupled receptors (GPCRs) have attracted increasing interest since they affect cellular signaling. Furthermore, mutations in GPCRs can cause acquired and inheritable diseases. Up to date, there still exist a number of GPCRs that has not been structurally and functionally analyzed due to difficulties in cell-based membrane protein production. A promising approach for membrane protein synthesis and analysis has emerged during the last years and is known as cell-free protein synthesis (CFPS). Here, we describe a simply portable method to synthesize GPCRs and analyze their ligand-binding properties without the requirement of additional supplements such as liposomes or nanodiscs. This method is based on eukaryotic cell lysates containing translocationally active endogenous endoplasmic reticulum-derived microsomes where the insertion of GPCRs into biologically active membranes is supported. In this study we present CFPS in combination with fast fluorescence-based screening methods to determine the localization, orientation and ligand-binding properties of the endothelin B (ET-B) receptor upon expression in an insect-based cell-free system. To determine the functionality of the cell-free synthesized ET-B receptor, we analyzed the binding of its ligand endothelin-1 (ET-1) in a qualitative fluorescence-based assay and in a quantitative radioligand binding assay.
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Affiliation(s)
- Anne Zemella
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Solveig Grossmann
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Rita Sachse
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Andrei Sonnabend
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany
| | - Michael Schaefer
- Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Härtelstraße 16-18, 04107, Leipzig, Germany
| | - Stefan Kubick
- Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalysis and Bioprocesses, Potsdam-Golm, Am Mühlenberg 13, 14476, Potsdam, Germany.
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20
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Shilling PJ, Bumbak F, Scott DJ, Bathgate RAD, Gooley PR. Characterisation of a cell-free synthesised G-protein coupled receptor. Sci Rep 2017; 7:1094. [PMID: 28439124 PMCID: PMC5430785 DOI: 10.1038/s41598-017-01227-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/27/2017] [Indexed: 02/03/2023] Open
Abstract
G-protein coupled receptors are the largest family of integral membrane proteins found within the human genome. They function as receptors and modulators to a wide range of ligands and responses which are crucial for human health. GPCR study, specifically the investigation of structure and interaction to cognate ligands, is of high priority. Limitations for structural study can be traced in part, to obtaining suitable quantities of recombinant protein. We sought to address the limitations of traditional recombinant technologies by utilising an Escherichia coli based cell-free protein synthesis (CFPS) approach for production of a thermostable neurotensin receptor 1 (en2NTS1). Initial results were promising, with a high amount (up to 2 mg/mL) of en2NTS1 produced, that had attained correct secondary structure. Meanwhile, concurrent experiments indicated that CFPS produced en2NTS1 showed non-competitive binding to the peptide ligand neurotensin8-13 when compared to E. coli produced en2NTS1. 1H-13C HMQC SOFAST NMR spectra were indicative of disrupted tertiary structure for CFPS produced 13CH3-methionine labelled en2NTS1. The results obtained, indicate CFPS produced en2NTS1 is not forming a discrete tertiary structure and that further development of the CFPS technique needs to be carried out.
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Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
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21
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Malhotra K, Alder NN. Reconstitution of Mitochondrial Membrane Proteins into Nanodiscs by Cell-Free Expression. Methods Mol Biol 2017; 1567:155-178. [PMID: 28276018 DOI: 10.1007/978-1-4939-6824-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The isolation and characterization of mitochondrial membrane proteins is technically challenging because they natively reside within the specialized environment of the lipid bilayer, an environment that must be recapitulated to some degree during reconstitution to ensure proper folding, stability, and function. Here we describe protocols for the assembly of a membrane protein into lipid bilayer nanodiscs in a series of cell-free reactions. Cell-free expression of membrane proteins circumvents problems attendant with in vivo expression such as cytotoxicity, low expression levels, and the formation of inclusion bodies. Nanodiscs are artificial membrane systems comprised of discoidal lipid bilayer particles bound by annuli of amphipathic scaffold protein that shield lipid acyl chains from water. They are therefore excellent platforms for membrane protein reconstitution and downstream solution-based biochemical and biophysical analysis. This chapter details the procedures for the reconstitution of a mitochondrial membrane protein into nanodiscs using two different types of approaches: cotranslational and posttranslational assembly. These strategies are broadly applicable for different mitochondrial membrane proteins. They are also applicable for the use of nanodiscs with distinct lipid compositions that are biomimetic for different mitochondrial membranes and that recapitulate lipid profiles associated with pathological disorders in lipid metabolism.
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Affiliation(s)
- Ketan Malhotra
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269, USA.,Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, Sterling Hall of Medicine, New Haven, CT, 06520, USA
| | - Nathan N Alder
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Storrs, CT, 06269, USA.
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22
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The power, pitfalls and potential of the nanodisc system for NMR-based studies. Biol Chem 2016; 397:1335-1354. [DOI: 10.1515/hsz-2016-0224] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/19/2016] [Indexed: 12/21/2022]
Abstract
Abstract
The choice of a suitable membrane mimicking environment is of fundamental importance for the characterization of structure and function of membrane proteins. In this respect, usage of the lipid bilayer nanodisc technology provides a unique potential for nuclear magnetic resonance (NMR)-based studies. This review summarizes the recent advances in this field, focusing on (i) the strengths of the system, (ii) the bottlenecks that may be faced, and (iii) promising capabilities that may be explored in future studies.
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23
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Rues RB, Dötsch V, Bernhard F. Co-translational formation and pharmacological characterization of beta1-adrenergic receptor/nanodisc complexes with different lipid environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1306-16. [PMID: 26922884 DOI: 10.1016/j.bbamem.2016.02.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/17/2016] [Accepted: 02/24/2016] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors are of key significance for biomedical research. Streamlined approaches for their efficient recombinant production are of pivotal interest in order to explore their intrinsic conformational dynamics and complex ligand binding behavior. We have systematically optimized the co-translational association and folding of G protein-coupled receptors with defined membranes of nanodiscs by cell-free expression approaches. Each optimization step was quantified and the ligand binding active fraction of the receptor samples could drastically be improved. The strategy was exemplified with a stabilized and a non-stabilized derivative of the turkey beta1-adrenergic receptor. Systematic lipid screens with preformed nanodiscs revealed that generation of ligand binding active conformations of the analyzed beta1-adrenergic receptors strongly depends on lipid charge, flexibility and chain length. The lipid composition of the nanodisc membranes modulates the affinities to a variety of ligands of both receptor derivatives. In addition, the thermostabilization procedure had a significant impact on specific ligand affinities of the receptor and abolished or reduced the binding of certain antagonists. Both receptors were highly stable after purification with optimized nanodisc membranes. The procedure avoids any detergent contact of the receptors and sample production takes less than two days. Moreover, even non-stabilized receptors can be analyzed and their prior purification is not necessary for the formation of nanodisc complexes. The established process appears therefore to be suitable as a new platform for the functional or even structural characterization of recombinant G protein-coupled receptors associated with defined lipid environments.
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Affiliation(s)
- Ralf-Bernhardt Rues
- 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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24
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Tanimoto Y, Okada K, Hayashi F, Morigaki K. Evaluating the Raftophilicity of Rhodopsin Photoreceptor in a Patterned Model Membrane. Biophys J 2015; 109:2307-16. [PMID: 26636942 PMCID: PMC4675817 DOI: 10.1016/j.bpj.2015.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 10/07/2015] [Accepted: 10/08/2015] [Indexed: 01/09/2023] Open
Abstract
Lipid rafts in the cell membrane are believed to affect various membrane functions, including the signaling by G-protein coupled receptors (GPCRs). However, the regulatory roles of lipid rafts on GPCRs' functions are still poorly understood, partially owing to the lack of the methods to quantitatively evaluate the affinity of membrane proteins to lipid raft (raftophilicity). Here, we describe a methodology to gauge the raftophilicity of a representative GPCR in vertebrate photoreceptor, i.e., rhodopsin (Rh), and its cognate G protein transducin (Gt) by using a patterned model membrane. We generated a substrate-supported planar lipid bilayer that has patterned regions of liquid-ordered (Lo) and liquid-disordered (Ld) membrane domains. We reconstituted Rh and Gt into the patterned membrane and observed their lateral distribution and diffusion. Mobile and functional Rh molecules could be reconstituted through the rapid dilution of solubilized Rh, by optimizing the reconstitution conditions including the chamber design, protein/detergent concentrations, and solution mixing. We determined the partition and diffusion coefficients of Rh and Gt in the Lo-rich and Ld-rich regions. Both Rh and Gt were predominantly localized in the Ld phase, suggesting their low affinity to lipid rafts. Patterned model membrane offers a robust and scalable platform for systematically and quantitatively studying the functional roles of lipid rafts in biological membranes including retinal disk membranes.
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Affiliation(s)
- Yasushi Tanimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Keisuke Okada
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Fumio Hayashi
- Graduate School of Science, Kobe University, Kobe, Japan.
| | - Kenichi Morigaki
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan; Research Center for Environmental Genomics, Kobe University, Kobe, Japan.
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25
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Wang J, She Y, Wang M, Jin M, Li Y, Wang J, Liu Y. Multiresidue Method for Analysis of β Agonists in Swine Urine by Enzyme Linked Receptor Assay Based on β2 Adrenergic Receptor Expressed in HEK293 Cells. PLoS One 2015; 10:e0139176. [PMID: 26422475 PMCID: PMC4589316 DOI: 10.1371/journal.pone.0139176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 09/08/2015] [Indexed: 11/23/2022] Open
Abstract
A novel enzyme-linked receptor assay (ELRA) based on β2-adrenergic receptor (β2-AR) has been developed for rapid and high-throughput detection of β-adrenergic agonists (β-agonists) in urine. Human embryonic kidney cells (HEK293) were introduced as the expression system to enhance the functionality of the recombinant β2-AR, and the attempt to detect β-agonists in swine urine using such approaches was accomplished unprecedentedly. In this article, a recombinant porcine β2-AR was produced in the inner membrane of HEK293 cells and purified from crude membrane protein by nickel-nitrilotriacetic acid affinity chromatography. After activity identification, the recombinant receptor was used in the development of direct competitive ELRA. Several parameters such as blocking buffer and blocking process were optimized and the performance of the system was determined. The IC50 concentrations of clenbuterol, salbutamol, and ractopamine were 34, 53 and 63 μg/L, and the average recovery rates were 68.2%, 60.3% and 65.5%, respectively. ELRA based on β2-AR shows a series of advantages such as safety, easy operation, and high efficiency, making it promising for the rapid screening of β-agonists in animal urine.
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Affiliation(s)
- Jian Wang
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
- Department of Food Science, Hebei North University, Zhangjiakou, 075000, P. R. China
| | - Yongxin She
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Miao Wang
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Maojun Jin
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Yongfei Li
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
| | - Jing Wang
- Institute of Quality Standards and Testing Technology for Agro-products of CAAS, Key Laboratory of Agro-Product Quality and Safety, Ministry of Agriculture, Beijing, 100081, P. R. China
- * E-mail:
| | - Yuan Liu
- Department of Food Science, Hebei North University, Zhangjiakou, 075000, P. R. China
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26
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Jin Q, Chen H, Wang X, Zhao L, Xu Q, Wang H, Li G, Yang X, Ma H, Wu H, Ji X. The Effects of the Recombinant CCR5 T4 Lysozyme Fusion Protein on HIV-1 Infection. PLoS One 2015; 10:e0131894. [PMID: 26154172 PMCID: PMC4496087 DOI: 10.1371/journal.pone.0131894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 06/08/2015] [Indexed: 12/03/2022] Open
Abstract
Background Insertion of T4 lysozyme (T4L) into the GPCR successfully enhanced GPCR protein stability and solubilization. However, the biological functions of the recombinant GPCR protein have not been analyzed. Methods We engineered the CCR5-T4L mutant and expressed and purified the soluble recombinant protein using an E.coli expression system. The antiviral effects of this recombinant protein in THP-1 cell lines, primary human macrophages, and PBMCs from different donors were investigated. We also explored the possible mechanisms underlying the observed antiviral effects. Results Our data showed the biphasic inhibitory and promotion effects of different concentrations of soluble recombinant CCR5-T4L protein on R5 tropic human immunodeficiency virus-1 (HIV-1) infection in THP-1 cell lines, human macrophages, and PBMCs from clinical isolates. We demonstrated that soluble recombinant CCR5-T4L acts as a HIV-1 co-receptor, interacts with wild type CCR5, down-regulates the surface CCR5 expression in human macrophages, and interacts with CCL5 to inhibit macrophage migration. Using binding assays, we further determined that recombinant CCR5-T4L and [125I]-CCL5 compete for the same binding site on wild type CCR5. Conclusions Our results suggest that recombinant CCR5-T4L protein marginally promotes HIV-1 infection at low concentrations and markedly inhibits infection at higher concentrations. This recombinant protein may be helpful in the future development of anti-HIV-1 therapeutic agents.
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Affiliation(s)
- Qingwen Jin
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
- Department of Neurology, Nanjing First Hospital, 68 Changle Road, Nanjing, Jiangsu Province, China
| | - Hong Chen
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Xingxia Wang
- Department of Neurology, The People’s Hospital of Jiangsu Province, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Liandong Zhao
- Department of Neurology, The Second Hospital of Huaian, 62 Huaihai South Road, Huaian, Jiangsu Province, China
| | - Qingchen Xu
- Department of Neurology, Nanjing First Hospital, 68 Changle Road, Nanjing, Jiangsu Province, China
| | - Huijuan Wang
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
| | - Guanyu Li
- Department of Neurology, Mingji Hospital of Nanjing, Jiangsu Province, 71 Riverside West Road, Nanjing, Jiangsu Province, China
| | - Xiaofan Yang
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
| | - Hongming Ma
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas, United States of America
| | - Haoquan Wu
- Department of Biomedical Sciences, Texas Tech University Health Sciences Center, 5001 El Paso Drive, El Paso, Texas, United States of America
| | - Xiaohui Ji
- Department of Microbiology and Immunology, Nanjing Medical University, 140 Hanzhong Road, Nanjing, Jiangsu Province, China
- * E-mail:
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Malhotra K, Alder NN. Advances in the use of nanoscale bilayers to study membrane protein structure and function. Biotechnol Genet Eng Rev 2015; 30:79-93. [PMID: 25023464 DOI: 10.1080/02648725.2014.921502] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Within the last decade, nanoscale lipid bilayers have emerged as powerful experimental systems in the analysis of membrane proteins (MPs) for both basic and applied research. These discoidal lipid lamellae are stabilized by annuli of specially engineered amphipathic polypeptides (nanodiscs) or polymers (SMALPs/Lipodisqs®). As biomembrane mimetics, they are well suited for the reconstitution of MPs within a controlled lipid environment. Moreover, because they are water-soluble, they are amenable to solution-based biochemical and biophysical experimentation. Hence, due to their solubility, size, stability, and monodispersity, nanoscale lipid bilayers offer technical advantages over more traditional MP analytic approaches such as detergent solubilization and reconstitution into lipid vesicles. In this article, we review some of the most recent advances in the synthesis of polypeptide- and polymer-bound nanoscale lipid bilayers and their application in the study of MP structure and function.
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Affiliation(s)
- Ketan Malhotra
- a Department of Molecular and Cell Biology , University of Connecticut , Storrs , CT 06269 , USA
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Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
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Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
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29
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Abstract
Cell-free expression has emerged as a new standard for the production of membrane proteins. The reduction of expression complexity in cell-free systems eliminates central bottlenecks and allows the reliable and efficient synthesis of many different types of membrane proteins. Furthermore, the open accessibility of cell-free reactions enables the co-translational solubilization of cell-free expressed membrane proteins in a large variety of supplied additives. Hydrophobic environments can therefore be adjusted according to the requirements of individual membrane protein targets. We present different approaches for the preparative scale cell-free production of G-protein-coupled receptors using the extracts of Escherichia coli cells. We exemplify expression conditions implementing detergents, nanodiscs, or liposomes. The generated protein samples could be directly used for further functional characterization.
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30
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Folding membrane proteins in vitro: A table and some comments. Arch Biochem Biophys 2014; 564:314-26. [DOI: 10.1016/j.abb.2014.06.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/17/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
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31
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The ligand binding ability of dopamine D1 receptors synthesized using a wheat germ cell-free protein synthesis system with liposomes. Eur J Pharmacol 2014; 745:117-22. [PMID: 25446930 DOI: 10.1016/j.ejphar.2014.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 10/06/2014] [Accepted: 10/08/2014] [Indexed: 01/15/2023]
Abstract
G-protein coupled receptors (GPCRs) share a common seven-transmembrane topology and mediate cellular responses to a variety of extracellular signals. However, structural and functional approaches to GPCRs have often been limited by the difficulty of producing a sufficient amount of receptor protein using conventional expression systems. We synthesized human dopamine D1 receptors using a wheat cell-free protein synthesis system with liposomes and then analyzed their receptor binding ability. We determined the specific binding of [(3)H]SCH23390 to the synthesized receptors generated from a cell-free protein synthesis system or rat striatal membranes. From Scatchard plot analysis, the dissociation constant (Kd) and the maximum density (Bmax) of the synthesized receptors were 6.61±0.06 nM and 1.85±0.05 pmol/mg protein, respectively. The same analysis for rat striatal membrane gave a Kd of 2.67±0.05 nM and Bmax of 0.70±0.10 pmol/mg protein. Using a competition binding assay, Ki values of antagonists, SCH23390, LE300 and SKF83566, for the synthetic receptors were the same as those for rat striatal membranes, but Ki values of agonists, A68930, SKF38393 and dopamine, were 5-17 fold higher than those for rat striatal membranes. These results suggest that the dopamine D1 receptors synthesized in liposomes have a functional binding capacity. The different patterns of binding of antagonists and agonists to the synthetic receptors and rat striatal membranes indicate that G proteins are involved in agonist binding to dopamine D1 receptors. The cell-free protein synthesis method with liposomes will be invaluable for the functional analysis of GPCRs.
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Hein C, Henrich E, Orbán E, Dötsch V, Bernhard F. Hydrophobic supplements in cell-free systems: Designing artificial environments for membrane proteins. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300050] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Christopher Hein
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Erik Henrich
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Erika Orbán
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Volker Dötsch
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
| | - Frank Bernhard
- Centre for Biomolecular Magnetic Resonance; Institute for Biophysical Chemistry; Goethe-University of Frankfurt/Main; Frankfurt am Main Germany
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Zheng X, Dong S, Zheng J, Li D, Li F, Luo Z. Expression, stabilization and purification of membrane proteins via diverse protein synthesis systems and detergents involving cell-free associated with self-assembly peptide surfactants. Biotechnol Adv 2014; 32:564-74. [PMID: 24566241 DOI: 10.1016/j.biotechadv.2014.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 06/13/2013] [Accepted: 02/17/2014] [Indexed: 12/21/2022]
Abstract
G-protein coupled receptors (GPCRs) are involved in regulating most of physiological actions and metabolism in the bodies, which have become most frequently addressed therapeutic targets for various disorders and diseases. Purified GPCR-based drug discoveries have become routine that approaches to structural study, novel biophysical and biochemical function analyses. However, several bottlenecks that GPCR-directed drugs need to conquer the problems including overexpression, solubilization, and purification as well as stabilization. The breakthroughs are to obtain efficient protein yield and stabilize their functional conformation which are both urgently requiring of effective protein synthesis system methods and optimal surfactants. Cell-free protein synthesis system is superior to the high yields and post-translation modifications, and early signs of self-assembly peptide detergents also emerged to superiority in purification of membrane proteins. We herein focus several predominant protein synthesis systems and surfactants involving the novel peptide detergents, and uncover the advantages of cell-free protein synthesis system with self-assembling peptide detergents in purification of functional GPCRs. This review is useful to further study in membrane proteins as well as the new drug exploration.
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Affiliation(s)
- Xuan Zheng
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Shuangshuang Dong
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China
| | - Jie Zheng
- College of laboratory Medicine, Chongqing Medical University, Chongqing, China
| | - Duanhua Li
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Feng Li
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China
| | - Zhongli Luo
- College of Basic Medical Sciences, Molecular Medicine and Cancer Research Center, Chongqing Medical University, Chongqing, China.
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34
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Roos C, Kai L, Haberstock S, Proverbio D, Ghoshdastider U, Ma Y, Filipek S, Wang X, Dötsch V, Bernhard F. High-level cell-free production of membrane proteins with nanodiscs. Methods Mol Biol 2014; 1118:109-130. [PMID: 24395412 DOI: 10.1007/978-1-62703-782-2_7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This chapter addresses two major bottlenecks in cell-free membrane protein production. Firstly, we describe the optimization of expression templates for obtaining membrane proteins in preparative scales. We present details for a newly established tag variation screen providing high success rates in improving expression efficiencies while having only minimal impacts on the target protein structure. Secondly, we present protocols for the efficient co-translational insertion of membrane proteins into defined lipid bilayers. We describe the production of nanodiscs and their implementation into cell-free expression reactions for the co-translational reconstitution of membrane proteins. In addition we give guidelines for the loading of nanodiscs with different lipids in order to systematically analyze effects of lipids on the translocation, functional folding, and stability of cell-free expressed membrane proteins.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Frankfurt/Main, Germany
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35
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Functional properties of cell-free expressed human endothelin A and endothelin B receptors in artificial membrane environments. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2182-92. [DOI: 10.1016/j.bbamem.2013.05.031] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 01/06/2023]
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36
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Frassanito AM, Barsanti L, Passarelli V, Evangelista V, Gualtieri P. A second rhodopsin-like protein in Cyanophora paradoxa: gene sequence and protein expression in a cell-free system. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 125:188-93. [PMID: 23851421 DOI: 10.1016/j.jphotobiol.2013.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 06/07/2013] [Accepted: 06/17/2013] [Indexed: 12/15/2022]
Abstract
Here we report the identification and expression of a second rhodopsin-like protein in the alga Cyanophora paradoxa (Glaucophyta), named Cyanophopsin_2. This new protein was identified due to a serendipity event, since the RACE reaction performed to complete the sequence of Cyanophopsin_1, (the first rhodopsin-like protein of C. paradoxa identified in 2009 by our group), amplified a 619 bp sequence corresponding to a portion of a new gene of the same protein family. The full sequence consists of 1175 bp consisting of 849 bp coding DNA sequence and 4 introns of 326 bp. The protein is characterized by an N-terminal region of 47 amino acids, followed by a region with 7 α-helices of 213 amino acids and a C-terminal region of 22 amino acids. This protein showed high identity with Cyanophopsin_1 and other rhodopsin-like proteins of Archea, Bacteria, Fungi and Algae. Cyanophosin_2 (CpR2) was expressed in a cell-free expression system, and characterized by means of absorption spectroscopy.
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37
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Ritz S, Hulko M, Zerfass C, May S, Hospach I, Krasteva N, Nelles G, Sinner EK. Cell-free expression of a mammalian olfactory receptor and unidirectional insertion into small unilamellar vesicles (SUVs). Biochimie 2013; 95:1909-16. [PMID: 23816872 DOI: 10.1016/j.biochi.2013.06.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/20/2013] [Indexed: 01/29/2023]
Abstract
Although the identification of the multigene family encoding mammalian olfactory receptors were identified more than 20 years ago, we are far from understanding olfactory perception because of the difficulties in functional expression of these receptors in heterologous cell systems. Cell-free (CF) or in vitro expression systems offer an elegant alternative route to cell based protein expression, as the functional expression of membrane proteins can be directly achieved from the genetic template without the need of cell cultivation and protein isolation. Here we investigated in detail the cell-free expression and membrane insertion of the olfactory receptor OR5 in dependence of different experimental conditions like probing different origins of the cell-free expression system (from bacteria, via plants and insects toward mammalian system) and lipid composition of the respective extracts. We provided substantial biochemical indications by radioactive labeling based on [(35)S]-methionine, followed by proteolytic digestion, and we found that the insertion of the olfactory receptor OR5 into liposomes resulted in an unidirectional orientation with the binding side exposed into the aqueous space, resembling the native orientation in the cilia of the olfactory neurons. We report the different results in synthesis capacity for the different in vitro systems employed as we like to demonstrate the first in vitro kit toward and ex situ and ex vivo odorant receptor array.
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Affiliation(s)
- Sandra Ritz
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.
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38
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He W, Luo J, Bourguet F, Xing L, Yi SK, Gao T, Blanchette C, Henderson PT, Kuhn E, Malfatti M, Murphy WJ, Cheng RH, Lam KS, Coleman MA. Controlling the diameter, monodispersity, and solubility of ApoA1 nanolipoprotein particles using telodendrimer chemistry. Protein Sci 2013; 22:1078-86. [PMID: 23754445 DOI: 10.1002/pro.2292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/15/2013] [Accepted: 05/28/2013] [Indexed: 12/16/2022]
Abstract
Nanolipoprotein particles (NLPs) are nanometer-scale discoidal particles that feature a phospholipid bilayer confined within an apolipoprotein "scaffold," which are useful for solubilizing hydrophobic molecules such as drugs and membrane proteins. NLPs are synthesized either by mixing the purified apolipoprotein with phospholipids and other cofactors or by cell-free protein synthesis followed by self-assembly of the nanoparticles in the reaction mixture. Either method can be problematic regarding the production of homogeneous and monodispersed populations of NLPs, which also currently requires multiple synthesis and purification steps. Telodendrimers (TD) are branched polymers made up of a dendritic oligo-lysine core that is conjugated to linear polyethylene glycol (PEG) on one end, and the lysine "branches" are terminated with cholic acid moieties that enable the formation of nanomicelles in aqueous solution. We report herein that the addition of TD during cell-free synthesis of NLPs produces unique hybrid nanoparticles that have drastically reduced polydispersity as compared to NLPs made in the absence of TD. This finding was supported by dynamic light scattering, fluorescence correlation spectroscopy, and cryo transmission electron microscopy (Cryo-EM). These techniques demonstrate the ability of TDs to modulate both the NLP size (6-30 nm) and polydispersity. The telodendrimer NLPs (TD-NLPs) also showed 80% less aggregation as compared to NLPs alone. Furthermore, the versatility of these novel nanoparticles was shown through direct conjugation of small molecules such as fluorescent dyes directly to the TD as well as the insertion of a functional membrane protein.
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Affiliation(s)
- Wei He
- NSF Center for Biophotonics Science and Technology, Sacramento, California, 95817, USA
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39
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Ruehrer S, Michel H. ExploitingLeishmania tarentolaecell-free extracts for the synthesis of human solute carriers. Mol Membr Biol 2013; 30:288-302. [DOI: 10.3109/09687688.2013.807362] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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40
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Braun CJ, Lachnit C, Becker P, Henkes LM, Arrigoni C, Kast SM, Moroni A, Thiel G, Schroeder I. Viral potassium channels as a robust model system for studies of membrane-protein interaction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:1096-103. [PMID: 23791706 DOI: 10.1016/j.bbamem.2013.06.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 05/31/2013] [Accepted: 06/08/2013] [Indexed: 11/15/2022]
Abstract
The viral channel KcvNTS belongs to the smallest K(+) channels known so far. A monomer of a functional homotetramer contains only 82 amino acids. As a consequence of the small size the protein is almost fully submerged into the membrane. This suggests that the channel is presumably sensitive to its lipid environment. Here we perform a comparative analysis for the function of the channel protein embedded in three different membrane environments. 1. Single-channel currents of KcvNTS were recorded with the patch clamp method on the plasma membrane of HEK293 cells. 2. They were also measured after reconstitution of recombinant channel protein into classical planar lipid bilayers and 3. into horizontal bilayers derived from giant unilamellar vesicles (GUVs). The recombinant channel protein was either expressed and purified from Pichia pastoris or from a cell-free expression system; for the latter a new approach with nanolipoprotein particles was used. The data show that single-channel activity can be recorded under all experimental conditions. The main functional features of the channel like a large single-channel conductance (80pS), high open-probability (>50%) and the approximate duration of open and closed dwell times are maintained in all experimental systems. An apparent difference between the approaches was only observed with respect to the unitary conductance, which was ca. 35% lower in HEK293 cells than in the other systems. The reason for this might be explained by the fact that the channel is tagged by GFP when expressed in HEK293 cells. Collectively the data demonstrate that the small viral channel exhibits a robust function in different experimental systems. This justifies an extrapolation of functional data from these systems to the potential performance of the channel in the virus/host interaction. This article is part of a Special Issue entitled: Viral Membrane Proteins-Channels for Cellular Networking.
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Affiliation(s)
- Christian J Braun
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Christine Lachnit
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Patrick Becker
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Leonhard M Henkes
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Cristina Arrigoni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Stefan M Kast
- Physikalische Chemie III, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Anna Moroni
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy; CNR-IBF, Via Celoria 26, 20133 Milano, Italy
| | - Gerhard Thiel
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany
| | - Indra Schroeder
- Membrane Biophysics, Technical University of Darmstadt, Schnittspahnstrasse 3, 64287 Darmstadt, Germany.
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Roos C, Zocher M, Müller D, Münch D, Schneider T, Sahl HG, Scholz F, Wachtveitl J, Ma Y, Proverbio D, Henrich E, Dötsch V, Bernhard F. Characterization of co-translationally formed nanodisc complexes with small multidrug transporters, proteorhodopsin and with the E. coli MraY translocase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3098-106. [DOI: 10.1016/j.bbamem.2012.08.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/10/2012] [Accepted: 08/10/2012] [Indexed: 10/28/2022]
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Gao T, Petrlova J, He W, Huser T, Kudlick W, Voss J, Coleman MA. Characterization of de novo synthesized GPCRs supported in nanolipoprotein discs. PLoS One 2012; 7:e44911. [PMID: 23028674 PMCID: PMC3460959 DOI: 10.1371/journal.pone.0044911] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 08/09/2012] [Indexed: 02/05/2023] Open
Abstract
The protein family known as G-protein coupled receptors (GPCRs) comprises an important class of membrane-associated proteins, which remains a difficult family of proteins to characterize because their function requires a native-like lipid membrane environment. This paper focuses on applying a single step method leading to the formation of nanolipoprotein particles (NLPs) capable of solubilizing functional GPCRs for biophysical characterization. NLPs were used to demonstrate increased solubility for multiple GPCRs such as the Neurokinin 1 Receptor (NK1R), the Adrenergic Receptor â2 (ADRB2) and the Dopamine Receptor D1 (DRD1). All three GPCRs showed affinity for their specific ligands using a simple dot blot assay. The NK1R was characterized in greater detail to demonstrate correct folding of the ligand pocket with nanomolar specificity. Electron paramagnetic resonance (EPR) spectroscopy validated the correct folding of the NK1R binding pocket for Substance P (SP). Fluorescence correlation spectroscopy (FCS) was used to identify SP-bound NK1R-containing NLPs and measure their dissociation rate in an aqueous environment. The dissociation constant was found to be 83 nM and was consistent with dot blot assays. This study represents a unique combinational approach involving the single step de novo production of a functional GPCR combined with biophysical techniques to demonstrate receptor association with the NLPs and binding affinity to specific ligands. Such a combined approach provides a novel path forward to screen and characterize GPCRs for drug discovery as well as structural studies outside of the complex cellular environment.
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Affiliation(s)
- Tingjuan Gao
- NSF Center for Biophotonics Science and Technology, University of California Davis Medical Center, Sacramento, California, United States of America
- Department of Biochemistry and Molecular Medicine, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Jitka Petrlova
- Department of Biochemistry and Molecular Medicine, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Wei He
- Department of Radiation Oncology, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Thomas Huser
- NSF Center for Biophotonics Science and Technology, University of California Davis Medical Center, Sacramento, California, United States of America
| | - Wieslaw Kudlick
- Life Technologies, Carlsbad, California, United States of America
| | - John Voss
- Department of Biochemistry and Molecular Medicine, University of California Davis Medical Center, Sacramento, California, United States of America
- * E-mail: (JV); (MAC)
| | - Matthew A. Coleman
- NSF Center for Biophotonics Science and Technology, University of California Davis Medical Center, Sacramento, California, United States of America
- Department of Radiation Oncology, University of California Davis Medical Center, Sacramento, California, United States of America
- Lawrence Livermore National Laboratory, Livermore, California, United States of America
- * E-mail: (JV); (MAC)
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Roos C, Kai L, Proverbio D, Ghoshdastider U, Filipek S, Dötsch V, Bernhard F. Co-translational association of cell-free expressed membrane proteins with supplied lipid bilayers. Mol Membr Biol 2012; 30:75-89. [PMID: 22716775 DOI: 10.3109/09687688.2012.693212] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Routine strategies for the cell-free production of membrane proteins in the presence of detergent micelles and for their efficient co-translational solubilization have been developed. Alternatively, the expression in the presence of rationally designed lipid bilayers becomes interesting in particular for biochemical studies. The synthesized membrane proteins would be directed into a more native-like environment and cell-free expression of transporters, channels or other membrane proteins in the presence of supplied artificial membranes could allow their subsequent functional analysis without any exposure to detergents. In addition, lipid-dependent effects on activity and stability of membrane proteins could systematically be studied. However, in contrast to the generally efficient detergent solubilization, the successful stabilization of membrane proteins with artificial membranes appears to be more difficult. A number of strategies have therefore been explored in order to optimize the co-translational association of membrane proteins with different forms of supplied lipid bilayers including liposomes, bicelles, microsomes or nanodiscs. In this review, we have compiled the current state-of-the-art of this technology and we summarize parameters which have been indicated as important for the co-translational association of cell-free synthesized membrane proteins with supplied membranes.
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Affiliation(s)
- Christian Roos
- Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe-University of Frankfurt/Main, Germany
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Haberstock S, Roos C, Hoevels Y, Dötsch V, Schnapp G, Pautsch A, Bernhard F. A systematic approach to increase the efficiency of membrane protein production in cell-free expression systems. Protein Expr Purif 2012; 82:308-16. [PMID: 22342679 DOI: 10.1016/j.pep.2012.01.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/25/2012] [Accepted: 01/27/2012] [Indexed: 10/14/2022]
Abstract
High amounts of membrane protein samples are needed for structural or functional analysis and a first bottleneck is often to obtain sufficient production efficiencies. The reduced complexity of protein production in cell-free expression systems results in a frequent correlation of efficiency problems with the essential transcription/translation process. We present a systematic tag variation strategy for the rapid improvement of cell-free expression efficiencies of membrane proteins based on the optimization of translation initiation. A small number of rationally designed short expression tags is attached via overlap PCR to the 5-prime end of the target protein coding sequence. The generated pool of DNA templates is analyzed in a cell-free expression screen and the most efficient template is selected for further preparative scale protein production. The expression tags can be minimized to only a few codons and no further impact on the coding sequence is required. The complete process takes only few days and the synthesized PCR fragments can be used directly as templates for preparative scale cell-free reactions. The strategy is exemplified with the production of a set of G-protein coupled receptors and yield improvements of up to 32-fold were obtained. All proteins were finally synthesized in amounts sufficient for further quality optimization and initial crystallization screens.
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Affiliation(s)
- Stefan Haberstock
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt-am-Main, Germany
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Luo Z, Zhang S. Designer nanomaterials using chiral self-assembling peptide systems and their emerging benefit for society. Chem Soc Rev 2012; 41:4736-54. [DOI: 10.1039/c2cs15360b] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Lyukmanova EN, Shenkarev ZO, Khabibullina NF, Kopeina GS, Shulepko MA, Paramonov AS, Mineev KS, Tikhonov RV, Shingarova LN, Petrovskaya LE, Dolgikh DA, Arseniev AS, Kirpichnikov MP. Lipid-protein nanodiscs for cell-free production of integral membrane proteins in a soluble and folded state: comparison with detergent micelles, bicelles and liposomes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:349-58. [PMID: 22056981 DOI: 10.1016/j.bbamem.2011.10.020] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/03/2011] [Accepted: 10/18/2011] [Indexed: 11/26/2022]
Abstract
Production of integral membrane proteins (IMPs) in a folded state is a key prerequisite for their functional and structural studies. In cell-free (CF) expression systems membrane mimicking components could be added to the reaction mixture that promotes IMP production in a soluble form. Here lipid-protein nanodiscs (LPNs) of different lipid compositions (DMPC, DMPG, POPC, POPC/DOPG) have been compared with classical membrane mimicking media such as detergent micelles, lipid/detergent bicelles and liposomes by their ability to support CF synthesis of IMPs in a folded and soluble state. Three model membrane proteins of different topology were used: homodimeric transmembrane (TM) domain of human receptor tyrosine kinase ErbB3 (TM-ErbB3, 1TM); voltage-sensing domain of K(+) channel KvAP (VSD, 4TM); and bacteriorhodopsin from Exiguobacterium sibiricum (ESR, 7TM). Structural and/or functional properties of the synthesized proteins were analyzed. LPNs significantly enhanced synthesis of the IMPs in a soluble form regardless of the lipid composition. A partial disintegration of LPNs composed of unsaturated lipids was observed upon co-translational IMP incorporation. Contrary to detergents the nanodiscs resulted in the synthesis of ~80% active ESR and promoted correct folding of the TM-ErbB3. None of the tested membrane mimetics supported CF synthesis of correctly folded VSD, and the protocol of the domain refolding was developed. The use of LPNs appears to be the most promising approach to CF production of IMPs in a folded state. NMR analysis of (15)N-Ile-TM-ErbB3 co-translationally incorporated into LPNs shows the great prospects of this membrane mimetics for structural studies of IMPs produced by CF systems.
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Affiliation(s)
- E N Lyukmanova
- Russian Academy of Sciences, Moscow, Russian Federation.
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