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Kim NH, Kang S, Park GH, Shim G, Kang TH, Yu YG. A robust antibody discovery platform for difficult-to-express G protein-coupled receptors. Protein Sci 2023; 32:e4520. [PMID: 36419382 PMCID: PMC9793966 DOI: 10.1002/pro.4520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCRs) are in the spotlight as drug targets due to the fact that multiple research results have verified the correlation between the activation of GPCRs and disease indications. This is because the GPCRs are present across the cell membranes, which interact with either extracellular ligands or other types of compartments and simultaneously mediate intracellular signaling. Despite the importance of the GPCRs as drug targets, they are too difficult to express in soluble forms. Currently, the difficulty of preparing functional GPCRs and the lack of efficient antibody screening methods are the most challenging steps in the discovery of antibodies targeting GPCRs. In this study, we developed a powerful platform that facilitates isolating GPCR-specific antibodies by obviating difficulties in GPCR preparation. The strategies include (i) conjugation of the P9 peptide, an envelope protein of Pseudomonas phi6, to the N-terminus of GPCRs to improve the expression level of the GPCRs in Escherichia coli, (ii) stabilization of the GPCRs in their active forms with amphiphilic poly-γ-glutamate (APG) to shield the seven hydrophobic transmembrane domains, and (iii) further limiting the size of the APG complex to improve the chance to isolate antibodies targeting the proteins-of-interest. Capitalizing on the above strategies, we could prepare GPCR proteins in their active forms as facile as other general-soluble antigen proteins. Furthermore, this protocol was validated to be successful in discovering three individual GPCR-specific antibodies targeting glucagon-like peptide-1 receptor, C-X-C chemokine receptor type 4, and prostaglandin E2 receptor 4 in this study.
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Affiliation(s)
- Nam Hyuk Kim
- Department of ChemistryKookmin UniversitySeoulRepublic of Korea
- Antibody Research InstituteKookmin UniversitySeoulRepublic of Korea
| | - Sumin Kang
- Department of ChemistryKookmin UniversitySeoulRepublic of Korea
- Antibody Research InstituteKookmin UniversitySeoulRepublic of Korea
| | - Ga Hyeon Park
- Biopharmaceutical Chemistry Major, School of Applied ChemistryKookmin UniversitySeoulRepublic of Korea
| | - Goeun Shim
- Biopharmaceutical Chemistry Major, School of Applied ChemistryKookmin UniversitySeoulRepublic of Korea
| | - Tae Hyun Kang
- Department of ChemistryKookmin UniversitySeoulRepublic of Korea
- Antibody Research InstituteKookmin UniversitySeoulRepublic of Korea
- Biopharmaceutical Chemistry Major, School of Applied ChemistryKookmin UniversitySeoulRepublic of Korea
- Department of Biopharmaceutical ChemistryKookmin UniversitySeoulRepublic of Korea
| | - Yeon Gyu Yu
- Department of ChemistryKookmin UniversitySeoulRepublic of Korea
- Antibody Research InstituteKookmin UniversitySeoulRepublic of Korea
- Biopharmaceutical Chemistry Major, School of Applied ChemistryKookmin UniversitySeoulRepublic of Korea
- Department of Biopharmaceutical ChemistryKookmin UniversitySeoulRepublic of Korea
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2
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Kang S, Kim NH, Yu YG. Identification of novel positive allosteric modulators of GLP1R that stimulate its interaction with ligands and G α subunits. Biochem Biophys Res Commun 2021; 583:162-168. [PMID: 34739856 DOI: 10.1016/j.bbrc.2021.10.071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022]
Abstract
Glucagon-like peptide-1 (GLP-1) is a major incretin hormone that enhances the release of insulin from pancreatic β-cells by activating the glucagon-like peptide-1 receptor (GLP1R), which belongs to secretin-like class B of G protein-coupled receptors (GPCRs). Owing to the absence of small molecule agonist drugs to GLP1R, focus has been placed on chemical modulators that bind to the allosteric site of GLP1R. In this study, we identified novel small-molecule positive allosteric modulators of GLP1R from a chemical library consisting of commercial drug compounds using an assay system that measures the direct interaction between a purified GLP1R and its ligand, exendin-4. Two newly identified compounds, benzethonium and tamoxifen, significantly enhanced the affinity of peptide ligands for GLP1R although they lacked agonist activity by themselves. In addition, benzethonium augmented the ligand-induced accumulation of cAMP in GLP1R-transfected HEK293T cells. These compounds significantly increased the affinity of GLP1R to the alpha-subunit of G proteins, suggesting that they stabilize GLP1R in a conformation with a higher affinity to peptide ligand as well as G proteins. These compounds may lead to the design of an orally active positive allosteric modulator for GLP1R.
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Affiliation(s)
- Sumin Kang
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea
| | - Nam Hyuk Kim
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea
| | - Yeon Gyu Yu
- Department of Chemistry, Kookmin University, 861-1 Jeongneung-dong, Seongbuk-gu, Seoul, 136-702, Republic of Korea.
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3
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Royes J, Biou V, Dautin N, Tribet C, Miroux B. Inducible intracellular membranes: molecular aspects and emerging applications. Microb Cell Fact 2020; 19:176. [PMID: 32887610 PMCID: PMC7650269 DOI: 10.1186/s12934-020-01433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
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Affiliation(s)
- Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France. .,Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France.
| | - Valérie Biou
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Tribet
- Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France.
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4
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Lama R, Pereiro P, Novoa B, Coll J. Sea Bass Immunization to Downsize the Betanodavirus Protein Displayed in the Surface of Inactivated Repair-Less Bacteria. Vaccines (Basel) 2019; 7:E94. [PMID: 31434322 PMCID: PMC6789578 DOI: 10.3390/vaccines7030094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/20/2023] Open
Abstract
: This work describes immunization of European sea bass (Dicentrarchus labrax) juveniles against viral nervous necrosis virus (VNNV), a betanodavirus causing worldwide mortalities in many fish species. Protection was obtained with the so-called spinycterin vehicles consisting of irreversibly DNA-damaged DNA-repair-less Escherichia coli displaying at their surface a downsized VNNV coat antigen. In this work we have i) maximized bacterial expression levels by downsizing the coat protein of VNNV to a fragment (frgC91-220) containing most of its previously determined antigenicity, ii) developed a scalable autoinduction culture media for E.coli based in soy-bean rather than in casein hydrolysates, iii) enriched surface expression by screening different anchors from several prokaryotic sources (anchor + frgC91-220 recombinant products), iv) preserved frgC91-220 antigenicity by inactivating bacteria by irreversible DNA-damage by means of Ciprofloxacin, and v) increased safety using a repair-less E.coli strain as chassis for the spinycterins. These spinycterins protected fish against VNNV challenge with partial (Nmistic + frgC91-220) or total (YBEL + frgC91-220) levels of protection, in contrast to fish immunized with frgC91-220 spinycterins. The proposed spinycterin platform has high levels of environmental safety and cost effectiveness and required no adjuvants, thus providing potential to further develop VNNV vaccines for sustainable aquaculture.
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Affiliation(s)
- Raquel Lama
- Institute of Marine Research (IIM). Spanish National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | | | - Beatriz Novoa
- Institute of Marine Research (IIM). Spanish National Research Council (CSIC), Eduardo Cabello 6, 36208 Vigo, Spain
| | - Julio Coll
- National Institute for Agricultural and Food Research and Technology (INIA), Biotechnology Department, La Coruña road, 28040 Madrid, Spain.
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Jung JH, Han S, Ju M, Jung ST, Yu YG. Isolation of Single Chain Antibodies Specific to Lysophosphatidic Acid Receptor 1 (LPA
1
) from a M13 Phage Display Library Using Purified LPA
1
Stabilized in Nanodiscs. B KOREAN CHEM SOC 2019. [DOI: 10.1002/bkcs.11751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ji Hae Jung
- Department of Applied ChemistryKookmin University Seoul 02707 South Korea
| | - Seong‐Gu Han
- Department of Applied ChemistryKookmin University Seoul 02707 South Korea
| | - Man‐Seok Ju
- Department of Applied ChemistryKookmin University Seoul 02707 South Korea
| | - Sang Taek Jung
- Graduate School of MedicineKorea University Seoul 02841 South Korea
| | - Yeon Gyu Yu
- Department of Applied ChemistryKookmin University Seoul 02707 South Korea
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6
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Lyytinen OL, Starkova D, Poranen MM. Microbial production of lipid-protein vesicles using enveloped bacteriophage phi6. Microb Cell Fact 2019; 18:29. [PMID: 30732607 PMCID: PMC6366064 DOI: 10.1186/s12934-019-1079-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Background Cystoviruses have a phospholipid envelope around their nucleocapsid. Such a feature is unique among bacterial viruses (i.e., bacteriophages) and the mechanisms of virion envelopment within a bacterial host are largely unknown. The cystovirus Pseudomonas phage phi6 has an envelope that harbors five viral membrane proteins and phospholipids derived from the cytoplasmic membrane of its Gram-negative host. The phi6 major envelope protein P9 and the non-structural protein P12 are essential for the envelopment of its virions. Co-expression of P9 and P12 in a Pseudomonas host results in the formation of intracellular vesicles that are potential intermediates in the phi6 virion assembly pathway. This study evaluated the minimum requirements for the formation of phi6-specific vesicles and the possibility to localize P9-tagged heterologous proteins into such structures in Escherichia coli. Results Using transmission electron microscopy, we detected membranous structures in the cytoplasm of E. coli cells expressing P9. The density of the P9-specific membrane fraction was lower (approximately 1.13 g/cm3 in sucrose) than the densities of the bacterial cytoplasmic and outer membrane fractions. A P9-GFP fusion protein was used to study the targeting of heterologous proteins into P9 vesicles. Production of the GFP-tagged P9 vesicles required P12, which protected the fusion protein against proteolytic cleavage. Isolated vesicles contained predominantly P9-GFP, suggesting selective incorporation of P9-tagged fusion proteins into the vesicles. Conclusions Our results demonstrate that the phi6 major envelope protein P9 can trigger formation of cytoplasmic membrane structures in E. coli in the absence of any other viral protein. Intracellular membrane structures are rare in bacteria, thus making them ideal chasses for cell-based vesicle production. The possibility to locate heterologous proteins into the P9-lipid vesicles facilitates the production of vesicular structures with novel properties. Such products have potential use in biotechnology and biomedicine. Electronic supplementary material The online version of this article (10.1186/s12934-019-1079-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Outi L Lyytinen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland
| | - Daria Starkova
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.,Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, Mira St. 14, St. Petersburg, 197101, Russia
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014, Helsinki, Finland.
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7
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Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology. Viruses 2019; 11:E76. [PMID: 30669250 PMCID: PMC6356626 DOI: 10.3390/v11010076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
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Affiliation(s)
- Sari Mäntynen
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Lotta-Riina Sundberg
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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8
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Son SH, Baek SI, Ju MS, Han SG, Jung ST, Yu YG. Development of Single-Chain Antibodies Specific to Lysophosphatidic Acid Receptor 2. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sang Hyeon Son
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
| | - Seung-il Baek
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
| | - Man-Seok Ju
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
| | - Seong-Gu Han
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
| | - Sang Taek Jung
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
| | - Yeon Gyu Yu
- Department of Applied Chemistry; Kookmin University; Seoul 02707 South Korea
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