1
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Svilenov HL, Arosio P, Menzen T, Tessier P, Sormanni P. Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties. MAbs 2023; 15:2164459. [PMID: 36629855 PMCID: PMC9839375 DOI: 10.1080/19420862.2022.2164459] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Antibody drugs should exhibit not only high-binding affinity for their target antigens but also favorable physicochemical drug-like properties. Such drug-like biophysical properties are essential for the successful development of antibody drug products. The traditional approaches used in antibody drug development require significant experimentation to produce, optimize, and characterize many candidates. Therefore, it is attractive to integrate new methods that can optimize the process of selecting antibodies with both desired target-binding and drug-like biophysical properties. Here, we summarize a selection of techniques that can complement the conventional toolbox used to de-risk antibody drug development. These techniques can be integrated at different stages of the antibody development process to reduce the frequency of physicochemical liabilities in antibody libraries during initial discovery and to co-optimize multiple antibody features during early-stage antibody engineering and affinity maturation. Moreover, we highlight biophysical and computational approaches that can be used to predict physical degradation pathways relevant for long-term storage and in-use stability to reduce the need for extensive experimentation.
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Affiliation(s)
- Hristo L. Svilenov
- Laboratory of General Biochemistry and Physical Pharmacy, Faculty of Pharmaceutical Sciences, Ghent University, Gent, Belgium
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, ETH Zürich, Zürich, Switzerland
| | - Tim Menzen
- Coriolis Pharma Research GmbH, Martinsried, 82152, Germany
| | - Peter Tessier
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
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2
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Jeong SH, Kwon M, Kim SW. Advanced Whole-cell Conversion for D-allulose Production Using an Engineered Corynebacterium glutamicum. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0057-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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3
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Cluet D, Vergier B, Levy NP, Dehau L, Thurman A, Amri I, Spichty M. Titration of apparent in-cellula affinities of protein-protein interactions. Chembiochem 2021; 23:e202100640. [PMID: 34932835 DOI: 10.1002/cbic.202100640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/21/2021] [Indexed: 11/07/2022]
Abstract
A genetic assay permits simultaneous quantification of two interacting proteins and their bound fraction at the single-cell level using flow cytometry. Apparent in-cellula affinities of protein-protein interactions can be extracted from the acquired data through a titration-like analysis. The applicability of this approach is demonstrated on a diverse set of interactions with proteins from different families and organisms and with in-vitro dissociation constants ranging from picomolar to micromolar.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Nicolas-Pierre Levy
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Lucie Dehau
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Alexandre Thurman
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et de Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364, Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire d'Innovation Moléculaire et Applications, Université de Strasbourg -, Centre National de la Recherche Scientifique, Université de Haute-Alsace, 3 bis rue Alfred Werner, 68057, Mulhouse Cedex, France
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4
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Morrison MS, Wang T, Raguram A, Hemez C, Liu DR. Disulfide-compatible phage-assisted continuous evolution in the periplasmic space. Nat Commun 2021; 12:5959. [PMID: 34645844 PMCID: PMC8514426 DOI: 10.1038/s41467-021-26279-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022] Open
Abstract
The directed evolution of antibodies has yielded important research tools and human therapeutics. The dependence of many antibodies on disulfide bonds for stability has limited the application of continuous evolution technologies to antibodies and other disulfide-containing proteins. Here we describe periplasmic phage-assisted continuous evolution (pPACE), a system for continuous evolution of protein-protein interactions in the disulfide-compatible environment of the E. coli periplasm. We first apply pPACE to rapidly evolve novel noncovalent and covalent interactions between subunits of homodimeric YibK protein and to correct a binding-defective mutant of the anti-GCN4 Ω-graft antibody. We develop an intein-mediated system to select for soluble periplasmic expression in pPACE, leading to an eight-fold increase in soluble expression of the Ω-graft antibody. Finally, we evolve disulfide-containing trastuzumab antibody variants with improved binding to a Her2-like peptide and improved soluble expression. Together, these results demonstrate that pPACE can rapidly optimize proteins containing disulfide bonds, broadening the applicability of continuous evolution.
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Affiliation(s)
- Mary S Morrison
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Tina Wang
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - Colin Hemez
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Health Care, Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138, USA.
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5
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Cluet D, Amri I, Vergier B, Léault J, Audibert A, Grosjean C, Calabrési D, Spichty M. A Quantitative Tri-fluorescent Yeast Two-hybrid System: From Flow Cytometry to In cellula Affinities. Mol Cell Proteomics 2020; 19:701-715. [PMID: 32015065 PMCID: PMC7124468 DOI: 10.1074/mcp.tir119.001692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on a small but diverse set of PPIs (eleven protein families from six organisms) with different affinities; the dissociation constants range from 117 pm to 17 μm After only two hours of reaction, expression of the reporter can be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflect the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.
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Affiliation(s)
- David Cluet
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Ikram Amri
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Blandine Vergier
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Jérémie Léault
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Astrid Audibert
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Clémence Grosjean
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Dylan Calabrési
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Martin Spichty
- Laboratoire de Biologie et Modé lisation de la Cellule, Ecole Normale Supé rieure de Lyon, CNRS, Université Lyon 1, Université de Lyon, 46 allée d'Italie, 69364 Lyon cedex 07, France.
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6
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Arslan M, Karadağ D, Kalyoncu S. Protein engineering approaches for antibody fragments: directed evolution and rational design approaches. ACTA ACUST UNITED AC 2019; 43:1-12. [PMID: 30930630 PMCID: PMC6426644 DOI: 10.3906/biy-1809-28] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The number of therapeutic antibodies in preclinical, clinical, or approved phases has been increasing exponentially, mostly due to their known successes. Development of antibody engineering methods has substantially hastened the development of therapeutic antibodies. A variety of protein engineering techniques can be applied to antibodies to improve their afinity and/or biophysical properties such as solubility and stability. Antibody fragments (where all or some parts of constant regions are eliminated while the essential antigen binding region is preserved) are more suitable for protein engineering techniques because there are many in vitro screening technologies available for antibody fragments but not full-length antibodies. Improvement of biophysical characteristics is important in the early development phase because most antibodies fail at the later stage of development and this leads to loss of resources and time. Here, we review directed evolution and rational design methods to improve antibody properties. Recent developments in rational design approaches and antibody display technologies, and especially phage display, which was recently awarded the 2018 Nobel Prize, are discussed to be used in antibody research and development.
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Affiliation(s)
- Merve Arslan
- İzmir Biomedicine and Genome Center , İzmir , Turkey.,İzmir Biomedicine and Genome Institute, Dokuz Eylül University , İzmir , Turkey
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7
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Park JH, Choi MA, Kim YJ, Kim YC, Chang YK, Jeong KJ. Engineering of Klebsiella oxytoca for production of 2,3-butanediol via simultaneous utilization of sugars from a Golenkinia sp. hydrolysate. BIORESOURCE TECHNOLOGY 2017; 245:1386-1392. [PMID: 28601394 DOI: 10.1016/j.biortech.2017.05.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 06/07/2023]
Abstract
The Klebsiella oxytoca was engineered to produce 2,3-butanediol (2,3-BDO) simultaneously utilizing glucose and galactose obtained from a Golenkinia sp. hydrolysate. For efficient uptake of galactose at a high concentration of glucose, Escherichia coli galactose permease (GalP) was introduced, and the expression of galP under a weak-strength promoter resulted in simultaneous consumption of galactose and glucose. Next, to improve the sugar consumption, a gene encoding methylglyoxal synthase (MgsA) known as an inhibitor of multisugar metabolism was deleted, and the mgsA-null mutant showed much faster consumption of both sugars than the wild-type strain did. Finally, we demonstrated that the engineered K. oxytoca could utilize sugar extracts from a Golenkinia sp. hydrolysate and successfully produces 2,3-BDO.
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Affiliation(s)
- Jong Hyun Park
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Min Ah Choi
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Jae Kim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeu-Chun Kim
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, BK21 Plus Program, KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Advanced Biomass R&D Center (ABC), 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea; Institutes for the BioCentury (KIB), KAIST, 291 Daehak-ro Yuseong-gu, Daejeon 34141, Republic of Korea.
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8
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Wu L, Wang X, Zhang J, Luan T, Bouveret E, Yan X. Flow Cytometric Single-Cell Analysis for Quantitative in Vivo Detection of Protein–Protein Interactions via Relative Reporter Protein Expression Measurement. Anal Chem 2017; 89:2782-2789. [DOI: 10.1021/acs.analchem.6b03603] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lina Wu
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Xu Wang
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Jianqiang Zhang
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Tian Luan
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
| | - Emmanuelle Bouveret
- Laboratory of
Macromolecular System Engineering, Institute of Microbiology
of the Mediterranean, Aix-Marseille Université and Centre National de la Recherche Scientifique, Marseille 13402, France
| | - Xiaomei Yan
- The MOE Key Laboratory
of Spectrochemical Analysis and Instrumentation, The Key Laboratory
for Chemical Biology of Fujian Province, Collaborative Innovation
Center of Chemistry for Energy Materials, Department of
Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, People’s Republic of China
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9
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Xu LM, Zhao JZ, Liu M, Cao YS, Yin JS, Liu HB, Lu T. Recombinant scFv antibodies against infectious pancreatic necrosis virus isolated by flow cytometry. J Virol Methods 2016; 237:204-209. [PMID: 27678027 DOI: 10.1016/j.jviromet.2016.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 07/29/2016] [Accepted: 07/31/2016] [Indexed: 11/28/2022]
Abstract
Infectious pancreatic necrosis is a significant disease of farmed salmonids in China. In this study, a single chain variable fragment (scFv) antibody library derived from rainbow trout (Oncorhynchus mykiss) and viral protein VP2 of a Chinese infectious pancreatic necrosis virus (IPNV) isolate ChRtm213 were co-expressed by a bacterial display technology. The library was subjected to three rounds of screening by flow cytometry (FCM) to select IPNV specific antibodies. Six antibody clones with different mean fluorescence intensities (MFI) were obtained by picking colonies at random. The antibody clones were expressed and purified. The purified IPNV-specific scFv antibodies were used successfully in Western blotting, enzyme linked immunosorbent assay (ELISA) and an immunofluorescence antibody test (IFAT). This method provides a high throughput means to screen an antibody library by flow cytometry, and isolate a panel of antibody that can be used as potential reagents for the detection and study of IPNV that are prevalent in China.
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Affiliation(s)
- Li-Ming Xu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Jing-Zhuang Zhao
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Miao Liu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Yong-Sheng Cao
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Jia-Sheng Yin
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Hong-Bai Liu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
| | - Tongyan Lu
- Heilongjiang River Fishery Research Institute Chinese Academy of Fishery Sciences, Harbin 150070, PR China.
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10
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Chen Y, Bai Y, Guo X, Wang W, Zheng Q, Wang F, Sun D, Li D, Ren G, Yin J. Selection of affinity-improved neutralizing human scFv against HBV PreS1 from CDR3 VH/VL mutant library. Biologicals 2016; 44:271-275. [PMID: 27255707 DOI: 10.1016/j.biologicals.2016.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 05/03/2016] [Accepted: 05/06/2016] [Indexed: 12/17/2022] Open
Abstract
A CDR3 mutant library was constructed from a previously isolated anti-HBV neutralizing Homo sapiens scFv-31 template by random mutant primers PCR. Then the library was displayed on the inner membrane surface in Escherichia coli periplasmic space. Seven scFv clones were isolated from the mutant library through three rounds of screening by flow cytometry. Competition ELISA assay indicates that isolated scFv fragments show more efficient binding ability to HBV PreS1 compared with parental scFv-31. HBV neutralization assay indicated that two clones (scFv-3 and 59) show higher neutralizing activity by blocking the HBV infection to Chang liver cells. Our method provides a new strategy for rapid screening of mutant antibody library for affinity-enhanced scFv clones and the neutralizing scFvs obtained from this study provide a potential alternative of Hepatitis B immune globulin.
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Affiliation(s)
- YanMin Chen
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Yin Bai
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China; The 211th Hospital of People's Liberation Army, Harbin 150080, People's Republic of China.
| | - XiaoChen Guo
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - WenFei Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - Qi Zheng
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - FuXiang Wang
- Harbin Medical University, The Fourth Affiliated Hospital, Nangang District, Harbin 150001, People's Republic of China.
| | - Dejun Sun
- Harbin Pharmaceutical Group Bio-vaccine Co., Ltd., Harbin, 150000, People's Republic of China.
| | - DeShan Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - GuiPing Ren
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
| | - JieChao Yin
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, People's Republic of China.
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11
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Goldblum RM, Ning B, Judy BM, Holthauzen LMF, van Bavel J, Kamijo A, Midoro-Horiuti T. A single mouse monoclonal antibody, E58 modulates multiple IgE epitopes on group 1 cedar pollen allergens. Mol Immunol 2016; 74:106-12. [PMID: 27174188 DOI: 10.1016/j.molimm.2016.04.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 10/21/2022]
Abstract
We recently described a dominant role for conformational epitopes on the group 1 allergen of the mountain cedar (Juniperus ashei, Cupressaceae), Jun a 1, in pollen hypersensitivity in South Central U.S.A. Since these epitopes are surface exposed and are likely to be flexible, they may be susceptible to molecular or physical perturbations. This may make Jun a 1 a potential target for new forms of therapy for cedar pollinosis. Here, we describe a mouse monoclonal antibody, termed E58, which binds to the group 1 allergens of the cedar pollens from three highly populated regions of the world (central U.S.A., France and Japan). Upon binding to these allergens, E58 strongly reduces the binding of patient's IgE antibodies to these dominant allergens. This characteristic of E58, and potentially other similar antibodies, suggests an opportunity to develop preventative or therapeutic agents that may inhibit cedar pollen sensitization or prevent their allergic reactions.
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Affiliation(s)
- Randall M Goldblum
- Department of Pediatrics, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0366, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1068, USA
| | - Bo Ning
- Department of Pediatrics, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0366, USA
| | - Barbara M Judy
- Department of Pediatrics, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0366, USA
| | - Luis Marcelo F Holthauzen
- Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1068, USA
| | - Julius van Bavel
- Isis Clinical Research, LLC, 6836 Austin Center Blvd. Ste 180, Austin, TX 78731, USA
| | - Atsushi Kamijo
- Department of Pediatrics, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0366, USA
| | - Terumi Midoro-Horiuti
- Department of Pediatrics, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-0366, USA.
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12
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Development of high-affinity single chain Fv against foot-and-mouth disease virus. Enzyme Microb Technol 2016; 84:50-5. [DOI: 10.1016/j.enzmictec.2015.12.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/10/2015] [Accepted: 12/17/2015] [Indexed: 11/19/2022]
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13
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High throughput screening of scFv antibodies against viral hemorrhagic septicaemia virus by flow cytometry. J Virol Methods 2015; 219:18-22. [DOI: 10.1016/j.jviromet.2015.03.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 11/17/2022]
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14
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Zhou Y, Xie ZG. A neutralizing scFv antibody against infectious bursal disease virus screened by flow cytometry. J Immunol Methods 2015; 424:80-4. [PMID: 26003676 DOI: 10.1016/j.jim.2015.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/11/2015] [Accepted: 05/12/2015] [Indexed: 11/29/2022]
Abstract
Infectious bursal disease (IBD) is considered a vital viral disease that threatens the poultry industry worldwide. In this study, a recombinant single chain variable fragment (scFv) antibody library derived from chickens immunized with VP2 protein of infectious bursal disease virus (IBDV) was constructed. The library was subjected to three rounds of screening by flow cytometry (FCM) against VP2/IBDV through a bacteria display technology, resulting in the enrichment of scFvs. Three scFv clones with different fluorescence intensity were obtained by colony pick up at random. The obtained scFv antibodies were expressed and purified. Relative affinity assay showed the three clones had different sensitivity to VP2, in accordance with fluorescence activity cell sorting analysis (FACS). The potential use of the isolated IBDV-specific scFv antibodies was demonstrated by the successful application of these antibodies in Western blotting and ELISA assay. What's more, in vitro neutralization measurement showed that one of the three isolated antibodies possessed the neutralization function against IBDV. This study provides new strategies for screening of antibody library, and scFv antibodies isolated in this study may be utilized as lead candidates for further development of diagnostic or therapeutic antibodies for detection and treatment of IBDV infection.
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Affiliation(s)
- Yao Zhou
- College of Life Sciences and Agro-forest, Qiqihar University, Qiqihar 161000, PR China
| | - Zhi-Gang Xie
- College of Life Sciences and Agro-forest, Qiqihar University, Qiqihar 161000, PR China.
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15
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Bi-specific antibodies with high antigen-binding affinity identified by flow cytometry. Int Immunopharmacol 2014; 24:463-473. [PMID: 25526913 DOI: 10.1016/j.intimp.2014.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/25/2023]
Abstract
Using conventional approaches, the antigen-binding affinity of a novel format of bi-specific antibody (BsAb) cannot be determined until purified BsAb is obtained. Here, we show that new lipoprotein A (NlpA)-based bacteria display technology, combined with flow cytometry (FCM), can be used to detect antigen-binding affinity of BsAbs, in the absence of expression and purification work. Two formats of BsAb, scFv2-CH/CL and Diabody-CH/CL, specific for human interleukin 1β (hIL-1β) and human interleukin 17A (hIL-17A), were constructed and displayed in Escherichia coli using NlpA-based bacteria display technology. Conversion of these cells to spheroplasts, and their incubation with fluorescently conjugated antigens resulted in the selective labeling of spheroplasts expressing BsAb; enabling their antigen-binding affinity to be analyzed with FCM. The association and dissociation of BsAbs for binding to hIL-1β and hIL-17A were analyzed using FCM-based assays. The results showed that antigen-binding affinity of Diabody-CH/CL was significantly higher than that of scFv2-CH/CL. To confirm these results of FCM-based assays, BsAbs were expressed, purified and subjected to relative affinity measurements, in vitro and in vivo bioactivity analysis. The results showed that Diabody-CH/CL had greater relative affinities for both antigens, resulting in better blocking bioactivities on cellular level and effects on alleviating joint inflammation, and cartilage destruction and bone damage in collagen induced arthritis (CIA) mice model. These results indicate that BsAbs with good antigen-binding affinity can be identified by FCM-based assays without expression and purification work, and the indentified BsAb can serve as a lead compound for further drug development.
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16
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Yim SS, Bang HB, Kim YH, Lee YJ, Jeong GM, Jeong KJ. Rapid isolation of antibody from a synthetic human antibody library by repeated fluorescence-activated cell sorting (FACS). PLoS One 2014; 9:e108225. [PMID: 25303314 PMCID: PMC4193741 DOI: 10.1371/journal.pone.0108225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 08/27/2014] [Indexed: 11/19/2022] Open
Abstract
Antibodies and their derivatives are the most important agents in therapeutics and diagnostics. Even after the significant progress in the technology for antibody screening from huge libraries, it takes a long time to isolate an antibody, which prevents a prompt action against the spread of a disease. Here, we report a new strategy for isolating desired antibodies from a combinatorial library in one day by repeated fluorescence-activated cell sorting (FACS). First, we constructed a library of synthetic human antibody in which single-chain variable fragment (scFv) was expressed in the periplasm of Escherichia coli. After labeling the cells with fluorescent antigen probes, the highly fluorescent cells were sorted by using a high-speed cell sorter, and these cells were reused without regeneration in the next round of sorting. After repeating this sorting, the positive clones were completely enriched in several hours. Thus, we screened the library against three viral antigens, including the H1N1 influenza virus, Hepatitis B virus, and Foot-and-mouth disease virus. Finally, the potential antibody candidates, which show KD values between 10 and 100 nM against the target antigens, could be successfully isolated even though the library was relatively small (∼106). These results show that repeated FACS screening without regeneration of the sorted cells can be a powerful method when a rapid response to a spreading disease is required.
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Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Hyun Bae Bang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Young Hwan Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Yong Jae Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Gu Min Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
| | - Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST) (BK21 plus program), Daejeon, Republic of Korea
- Institute for the BioCentury, KAIST, Daejeon, Republic of Korea
- * E-mail:
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17
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Epitope mapping of the infectious hematopoietic necrosis virus glycoprotein by flow cytometry. Biotechnol Lett 2014; 36:2109-16. [DOI: 10.1007/s10529-014-1586-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/04/2014] [Indexed: 11/24/2022]
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18
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Jeong GM, Kim YS, Jeong KJ. A human kringle domain-based fluorescence-linked immunosorbent assay system. Anal Biochem 2014; 451:63-8. [DOI: 10.1016/j.ab.2014.01.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/04/2014] [Accepted: 01/31/2014] [Indexed: 10/25/2022]
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19
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scFv antibodies against infectious bursal disease virus isolated from a combinatorial antibody library by flow cytometry. Biotechnol Lett 2014; 36:1029-35. [DOI: 10.1007/s10529-014-1463-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 01/08/2014] [Indexed: 11/26/2022]
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20
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Guo M, Xu LM, Zhou B, Yin JC, Ye XL, Ren GP, Li DS. Anchored periplasmic expression (APEx)-based bacterial display for rapid and high-throughput screening of B cell epitopes. Biotechnol Lett 2013; 36:609-16. [DOI: 10.1007/s10529-013-1400-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 10/24/2013] [Indexed: 11/30/2022]
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21
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Park JH, Kwon HW, Jeong KJ. Development of a plasmid display system with an Oct-1 DNA-binding domain suitable for in vitro screening of engineered proteins. J Biosci Bioeng 2013; 116:246-52. [DOI: 10.1016/j.jbiosc.2013.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
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22
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Yim SS, An SJ, Kang M, Lee J, Jeong KJ. Isolation of fully synthetic promoters for high-level gene expression in Corynebacterium glutamicum. Biotechnol Bioeng 2013; 110:2959-69. [PMID: 23633298 DOI: 10.1002/bit.24954] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/26/2013] [Accepted: 04/22/2013] [Indexed: 12/17/2022]
Abstract
Corynebacterium glutamicum is an important industrial organism that is widely used in the production of amino acids, nucleotides and vitamins. To extend its product spectrum and improve productivity, C. glutamicum needs to undergo further engineering, including the development of applicable promoter system. Here, we isolated new promoters from the fully synthetic promoter library consisting of 70-bp random sequences in C. glutamicum. Using green fluorescent protein (GFP) as a reporter, highly fluorescent cells were screened from the library by fluorescent activated cell sorting (FACS). Twenty potential promoters of various strengths were isolated and characterized through extensive analysis of DNA sequences and mRNA transcripts. Among 20 promoters, 6 promoters which have different strengths were selected and their activities were successfully demonstrated using two model proteins (antibody fragment and endoxylanase). Finally, the strongest promoter (P(H36)) was employed for the secretory production of endoxylanase in fed-batch cultivation, achieving production levels of 746 mg/L in culture supernatant. This is the first report of synthetic promoters constructed in C. glutamicum, and our screening strategy together with the use of synthetic promoters of various strengths will contribute to the future engineering of C. glutamicum.
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Affiliation(s)
- Sung Sun Yim
- Department of Chemical and Biomolecular Engineering, KAIST, 335 Gwahagno, Yuseong-gu, Daejeon, 305-701, Republic of Korea
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23
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An SJ, Yim SS, Jeong KJ. Development of a secretion system for the production of heterologous proteins in Corynebacterium glutamicum using the Porin B signal peptide. Protein Expr Purif 2013; 89:251-7. [PMID: 23597779 DOI: 10.1016/j.pep.2013.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 10/27/2022]
Abstract
Corynebacterium glutamicum is one of the useful hosts for the secretory production of heterologous proteins because of intrinsic attributes such as the presence of few endogenous proteins and proteases in culture medium. Here, we report the development of a new secretory system for the production of heterologous proteins by using the porin B (PorB) signal peptide in C. glutamicum. We examined two different endoxylanases and an antibody fragment (scFv) as model proteins for secretory production. In the flask cultivations, all the examined proteins were successfully produced as active forms into the culture medium with high efficiency. For the high-level production of endoxylanase, fed-batch cultivation was also performed in a lab-scale (5L) bioreactor, and the endoxylanases were efficiently secreted in the culture medium at levels as high as 615mg/L. From the culture supernatant, the secreted endoxylanases could be purified with high purity via one-step affinity column chromatography.
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Affiliation(s)
- Seul Ji An
- Department of Chemical and Biomolecular Engineering, KAIST, Yuseong-gu, Daejeon 305-701, Republic of Korea
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24
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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25
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Ramesh B, Sendra VG, Cirino PC, Varadarajan N. Single-cell characterization of autotransporter-mediated Escherichia coli surface display of disulfide bond-containing proteins. J Biol Chem 2012; 287:38580-9. [PMID: 23019324 DOI: 10.1074/jbc.m112.388199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Autotransporters (ATs) are a family of bacterial proteins containing a C-terminal β-barrel-forming domain that facilitates the translocation of N-terminal passenger domain whose functions range from adhesion to proteolysis. Genetic replacement of the native passenger domain with heterologous proteins is an attractive strategy not only for applications such as biocatalysis, live-cell vaccines, and protein engineering but also for gaining mechanistic insights toward understanding AT translocation. The ability of ATs to efficiently display functional recombinant proteins containing multiple disulfides has remained largely controversial. By employing high-throughput single-cell flow cytometry, we have systematically investigated the ability of the Escherichia coli AT Antigen 43 (Ag43) to display two different recombinant reporter proteins, a single-chain antibody (M18 scFv) that contains two disulfides and chymotrypsin that contains four disulfides, by varying the signal peptide and deleting the different domains of the native protein. Our results indicate that only the C-terminal β-barrel and the threaded α-helix are essential for efficient surface display of functional recombinant proteins containing multiple disulfides. These results imply that there are no inherent constraints for functional translocation and display of disulfide bond-containing proteins mediated by the AT system and should open new avenues for protein display and engineering.
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Affiliation(s)
- Balakrishnan Ramesh
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA
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26
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Yang C, Xie H, Zhang JK, Su BL. Anchoring proteins to Escherichia coli cell membranes using hydrophobic anchors derived from a Bacillus subtilis integral membrane protein. Protein Expr Purif 2012; 85:60-5. [DOI: 10.1016/j.pep.2012.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 06/11/2012] [Accepted: 06/20/2012] [Indexed: 12/01/2022]
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27
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Löfblom J. Bacterial display in combinatorial protein engineering. Biotechnol J 2011; 6:1115-29. [DOI: 10.1002/biot.201100129] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 06/15/2011] [Accepted: 06/20/2011] [Indexed: 12/17/2022]
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28
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Jeong KJ, Jang SH, Velmurugan N. Recombinant antibodies: engineering and production in yeast and bacterial hosts. Biotechnol J 2011; 6:16-27. [PMID: 21170983 DOI: 10.1002/biot.201000381] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
After the appearance of the first FDA-approved antibody 25 years ago, antibodies have become major therapeutic agents in the treatment of many human diseases, including cancer and infectious diseases, and the use of antibodies as therapeutic/diagnostic agents is expected to increase in the future. So far, a variety of strategies have been devised for engineering of these fascinating molecules to develop superior properties and functions. Recent progress in systems biology has provided more information about the structures and cellular networks of antibodies, and, in addition, recent development of biotechnology tools, particularly in regard to high-throughput screening, has made it possible to perform more intensive engineering on these substances. Based on a sound understanding and new technologies, antibodies are now being developed as more powerful drugs. In this review, we highlight the recent, significant progress that has been made in antibody engineering, with a particular focus on Fc engineering and glycoengineering for improved functions, and cellular engineering for enhanced production of antibodies in yeast and bacterial hosts.
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Affiliation(s)
- Ki Jun Jeong
- Department of Chemical and Biomolecular Engineering, KAIST, Daejeon, Korea.
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29
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Dube DH, Li B, Greenblatt EJ, Nimer S, Raymond AK, Kohler JJ. A two-hybrid assay to study protein interactions within the secretory pathway. PLoS One 2010; 5:e15648. [PMID: 21209940 PMCID: PMC3011011 DOI: 10.1371/journal.pone.0015648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 11/18/2010] [Indexed: 11/18/2022] Open
Abstract
Interactions of transcriptional activators are difficult to study using transcription-based two-hybrid assays due to potent activation resulting in false positives. Here we report the development of the Golgi two-hybrid (G2H), a method that interrogates protein interactions within the Golgi, where transcriptional activators can be assayed with negligible background. The G2H relies on cell surface glycosylation to report extracellularly on protein-protein interactions occurring within the secretory pathway. In the G2H, protein pairs are fused to modular domains of the reporter glycosyltransferase, Och1p, and proper cell wall formation due to Och1p activity is observed only when a pair of proteins interacts. Cells containing interacting protein pairs are identified by selectable phenotypes associated with Och1p activity and proper cell wall formation: cells that have interacting proteins grow under selective conditions and display weak wheat germ agglutinin (WGA) binding by flow cytometry, whereas cells that lack interacting proteins display stunted growth and strong WGA binding. Using this assay, we detected the interaction between transcription factor MyoD and its binding partner Id2. Interfering mutations along the MyoD:Id2 interaction interface ablated signal in the G2H assay. Furthermore, we used the G2H to detect interactions of the activation domain of Gal4p with a variety of binding partners. Finally, selective conditions were used to enrich for cells encoding interacting partners. The G2H detects protein-protein interactions that cannot be identified via traditional two-hybrid methods and should be broadly useful for probing previously inaccessible subsets of the interactome, including transcriptional activators and proteins that traffic through the secretory pathway.
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Affiliation(s)
- Danielle H. Dube
- Department of Chemistry and Biochemistry, Bowdoin College, Brunswick, Maine, United States of America
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Bin Li
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ethan J. Greenblatt
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Biophysics Program, Stanford University, Stanford, California, United States of America
| | - Sadeieh Nimer
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Amanda K. Raymond
- Department of Chemistry, Stanford University, Stanford, California, United States of America
| | - Jennifer J. Kohler
- Department of Chemistry, Stanford University, Stanford, California, United States of America
- Division of Translational Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail:
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30
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Seo MJ, Jeong KJ, Leysath CE, Ellington AD, Iverson BL, Georgiou G. Engineering antibody fragments to fold in the absence of disulfide bonds. Protein Sci 2009; 18:259-67. [PMID: 19177559 DOI: 10.1002/pro.31] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disulfide bonds play a critical role in the stabilization of the immunoglobulin beta-sandwich sandwich. Under reducing conditions, such as those that prevail in the cytoplasm, disulfide bonds do not normally form and as a result most antibodies expressed in that compartment (intrabodies) accumulate in a misfolded and inactive state. We have developed a simple method for the quantitative isolation of antibody fragments that retain full activity under reducing conditions from large mutant libraries. In E. coli, inactivation of the cysteine oxidoreductase DsbA abolishes protein oxidation in the periplasm, which leads to the accumulation of scFvs and other disulfide-containing proteins in a reduced form. Libraries of mutant scFvs were tethered onto the inner membrane of dsbA cells and mutants that could bind fluorescently labeled antigen in the reducing periplasm were screened by Anchored Periplasmic Expression (APEx; Harvey et al., Proc Natl Acad Sci USA 2004;101:9193-9198.). Using this approach, we isolated scFv antibody variants that are fully active when expressed in the cytoplasm or when the four Cys residues that normally form disulfides are substituted by Ser residues.
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Affiliation(s)
- Min Jeong Seo
- Department of Chemical Engineering, University of Texas, Austin, 78712, USA
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31
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Hu X, Kang S, Chen X, Shoemaker CB, Jin MM. Yeast surface two-hybrid for quantitative in vivo detection of protein-protein interactions via the secretory pathway. J Biol Chem 2009; 284:16369-16376. [PMID: 19369257 DOI: 10.1074/jbc.m109.001743] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A quantitative in vivo method for detecting protein-protein interactions will enhance our understanding of protein interaction networks and facilitate affinity maturation as well as designing new interaction pairs. We have developed a novel platform, dubbed "yeast surface two-hybrid (YS2H)," to enable a quantitative measurement of pairwise protein interactions via the secretory pathway by expressing one protein (bait) anchored to the cell wall and the other (prey) in soluble form. In YS2H, the prey is released either outside of the cells or remains on the cell surface by virtue of its binding to the bait. The strength of their interaction is measured by antibody binding to the epitope tag appended to the prey or direct readout of split green fluorescence protein (GFP) complementation. When two alpha-helices forming coiled coils were expressed as a pair of prey and bait, the amount of the prey in complex with the bait progressively decreased as the affinity changes from 100 pM to 10 microM. With GFP complementation assay, we were able to discriminate a 6-log difference in binding affinities in the range of 100 pM to 100 microM. The affinity estimated from the level of antibody binding to fusion tags was in good agreement with that measured in solution using a surface plasmon resonance technique. In contrast, the level of GFP complementation linearly increased with the on-rate of coiled coil interactions, likely because of the irreversible nature of GFP reconstitution. Furthermore, we demonstrate the use of YS2H in exploring the nature of antigen recognition by antibodies and activation allostery in integrins and in isolating heavy chain-only antibodies against botulinum neurotoxin.
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Affiliation(s)
- Xuebo Hu
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Sungkwon Kang
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Xiaoyue Chen
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853
| | - Charles B Shoemaker
- Department of Biomedical Sciences, Tufts Cummings School of Veterinary Medicine, North Grafton, Massachusetts 01536
| | - Moonsoo M Jin
- From the Department of Biomedical Engineering, Cornell University, Ithaca, New York 14853.
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32
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Chen J, Zhou J, Sanders CK, Nolan JP, Cai H. A surface display yeast two-hybrid screening system for high-throughput protein interactome mapping. Anal Biochem 2009; 390:29-37. [PMID: 19298787 DOI: 10.1016/j.ab.2009.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 03/04/2009] [Accepted: 03/11/2009] [Indexed: 10/21/2022]
Abstract
Despite the wide acceptance of yeast two-hybrid (Y2H) system for protein-protein interaction analysis and discovery, conventional Y2H assays are not well suited for high-throughput screening of the protein interaction network ("interactome") on a genomic scale due to several limitations, including labor-intensive agar plating and colony selection methods associated with the use of nutrient selection markers, complicated reporter analysis methods associated with the use of LacZ enzyme reporters, and incompatibility of the liquid handling robots. We recently reported a robust liquid culture Y2H system based on quantitative analysis of yeast-enhanced green fluorescent protein (yEGFP) reporters that greatly increased the analysis throughput and compatibility with liquid handling robots. To further advance its utility in high-throughput complementary DNA (cDNA) library screening, we report the development of a novel surface display Y2H (sdY2H) library screening system with uniquely integrated surface display hemagglutination (sdHA) antigen and yEGFP reporters. By introduction of a surface reporter sdHA into the yEGFP-based Y2H system, positive Y2H targets are quickly isolated from library cells by a simple magnetic separation without a large plating effort. Moreover, the simultaneous scoring of multiple reporters, including sdHA, yEGFP, and conventional nutrient markers, greatly increased the specificity of the Y2H assay. The feasibility of the sdY2H assay on large cDNA library screening was demonstrated by the successful recovery of positive P53/T interaction pairs at a target-to-background ratio of 1:1,000,000. Together with the massive parallel DNA sequencing technology, it may provide a powerful proteomic tool for high-throughput interactome mapping on a genomic scale.
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Affiliation(s)
- Jun Chen
- Biosciences Division, National Flow Cytometry Resource, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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33
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Presta LG. Molecular engineering and design of therapeutic antibodies. Curr Opin Immunol 2009; 20:460-70. [PMID: 18656541 DOI: 10.1016/j.coi.2008.06.012] [Citation(s) in RCA: 365] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2008] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 10/21/2022]
Abstract
Since the first murine monoclonal antibody was approved for human therapeutic use over a decade ago, the realization that monoclonal antibody therapeutics could be engineered to improve their efficacy has inspired an astonishing array of novel antibody constructs. Early focus was on reducing the immunogenicity of rodent antibodies via humanization and generation of antibodies in transgenic mice; as those techniques were being established and then provided marketed therapeutic antibodies, the focus expanded to include engineering for enhanced effector functions, control of half-life, tumor and tissue accessibility, augmented biophysical characteristics such as stability, and more efficient (and less costly) production. Over the past two years significant progress in designing antibodies with improved pharmacokinetic properties, via modified interaction with the neonatal Fc receptor (FcRn), has been achieved. Likewise, the ability to alter the communication of a therapeutic antibody with the immune system has been advanced, using both manipulation of the immunoglobulin protein sequence and its glycosylation. Although clinical evaluation of these engineered modifications has yet to be reported, results in primates are encouraging.
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34
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mazor Y, Van Blarcom T, Iverson BL, Georgiou G. E-clonal antibodies: selection of full-length IgG antibodies using bacterial periplasmic display. Nat Protoc 2008; 3:1766-77. [DOI: 10.1038/nprot.2008.176] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Link AJ, Jeong KJ, Georgiou G. Beyond toothpicks: new methods for isolating mutant bacteria. Nat Rev Microbiol 2007; 5:680-8. [PMID: 17676054 DOI: 10.1038/nrmicro1715] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Over the past 50 years genetic analysis in microbiology has relied predominantly on selections and plate assays using chromogenic enzyme substrates - for example, X-gal assays for the detection of beta-galactosidase activity. Recent advances in fluorescent assays and high throughput screening technologies have paved the way for the rapid isolation of mutants that confer complex phenotypes and for the quantitative analysis of the evolution of new traits in bacterial populations. This Review highlights the power of novel single-cell screening technologies and their applications to genetics, evolution and the biotechnological uses of bacteria.
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Affiliation(s)
- A James Link
- Department of Chemical Engineering, University of Texas, 1 University Station, Austin, Texas 78712, USA
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