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Koçer İ, Çelik E. In silico analysis of the different variable domain oriented single-chain variable fragment antibody-antigen complexes. J Biomol Struct Dyn 2024; 42:4699-4709. [PMID: 37288797 DOI: 10.1080/07391102.2023.2222191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 06/01/2023] [Indexed: 06/09/2023]
Abstract
Single-chain variable fragment (scFv) antibodies hold great potential as diagnostic tools and therapeutic agents, especially for tumor cells. Since these applications require their production with improved properties, the design strategy of scFvs is crucial for their active, soluble, and high yield expression with high affinity towards their antigens. The order of VL and VH domains is one of the important parameters that affect the expression and binding affinity properties of scFvs. In addition, the optimum order of VL and VH domains could change for each scFv. In the present study, we used computer simulation tools to evaluate the effect of variable domain orientation on structure, stability, interacting residues of scFvs, and binding free energies of scFv-antigen complexes. We selected anti-HER2 scFv, which is specific for human epidermal growth receptor 2 (HER2) overexpressed in breast cancer, and anti-IL-1β scFv against IL-1β which is an important inflammatory biomarker, as model scFvs. Molecular dynamics simulations of the scFv-antigen complexes for 100 ns resulted in stability and compactness for both scFv constructs. Interaction and binding free energies calculated by the Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) approach suggested that the relative binding energies of anti-HER2 scFv-VLVH and anti-HER2 scFv-VHVL constructs had similar binding affinity towards HER2, while a relatively more negative binding free energy obtained between anti-IL-1β scFv-VHVL and IL-1β pointed to a higher binding affinity. The in silico approach and the results obtained here could be applied as a guide for future experimental interaction studies for highly specific scFvs used as biotechnological tools.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- İlkay Koçer
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Institute of Science, Hacettepe University, Ankara, Turkey
| | - Eda Çelik
- Department of Chemical Engineering, Hacettepe University, Ankara, Turkey
- Institute of Science, Division of Bioengineering, Hacettepe University, Ankara, Turkey
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2
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Frota NF, Rebouças ADS, Fuzo CA, Lourenzoni MR. Alemtuzumab scFv fragments and CD52 interaction study through molecular dynamics simulation and binding free energy. J Mol Graph Model 2021; 107:107949. [PMID: 34089985 DOI: 10.1016/j.jmgm.2021.107949] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Specific antibody-antigen recognition is crucial for the immune response. Knowledge of molecular interaction details in the recognition process is fundamental for the rational design of antibodies with improved properties. We used state-of-the-art computer simulation tools to deepen the molecular-level understanding of the interactions between the monoclonal antibody Alemtuzumab and its antigen, the CD52 membrane receptor, of great biotechnological importance. Thus, we seek such responses by modeling the interaction of native and known mutants single-chain fragment variable (scFv) of Alemtuzumab with CD52 inserted in a membrane model to mimic the physiological conditions of antibody-antigen binding. Extensive molecular dynamics simulations of the interaction between Alemtuzumab's scFvs and CD52 promoted greater understanding of the structural and energetic bases, which can be translated into the biological action and affinity of this antibody. The quantification of the scFv-CD52 complexes binding free energy (ΔGbind) by Molecular Mechanics-Poisson-Boltzmann Surface Area (MM-PBSA) correlated with the experimental binding energies described before. Thus, the mutants D53K, K54D, and K56D resulted in less attractive ΔGbind, therefore lower scFv-CD52 affinity than the native scFv. On the other hand, K56D and K54D/K56D showed lower binding to CD52. These Results revealed that the model system mimicking an environment close to the physiological with the presence of the CD52 in a membrane model proved essential for this system's study. The present study allowed to unveil the molecular mechanisms involved in antigen-antibody interaction and the effects of mutations. Thus, these mechanisms may be explored in the Alemtuzumab variants' rational design with enhanced properties.
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Affiliation(s)
- Natália Fernandes Frota
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Alison de Sousa Rebouças
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil; Federal University of Ceara (UFC), Campus do Pici (Bloco 873), 60440-970, Fortaleza, Ceara Brazil
| | - Carlos Alessandro Fuzo
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marcos Roberto Lourenzoni
- Research Group on Protein Engineering and Health Solutions (GEPeSS), Fundação Oswaldo Cruz Ceará (Fiocruz-CE), São José, Precabura, 61760000, Eusébio, Ceara, Brazil.
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Sandomenico A, Sivaccumar JP, Ruvo M. Evolution of Escherichia coli Expression System in Producing Antibody Recombinant Fragments. Int J Mol Sci 2020; 21:ijms21176324. [PMID: 32878291 PMCID: PMC7504322 DOI: 10.3390/ijms21176324] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/07/2023] Open
Abstract
Antibodies and antibody-derived molecules are continuously developed as both therapeutic agents and key reagents for advanced diagnostic investigations. Their application in these fields has indeed greatly expanded the demand of these molecules and the need for their production in high yield and purity. While full-length antibodies require mammalian expression systems due to the occurrence of functionally and structurally important glycosylations, most antibody fragments and antibody-like molecules are non-glycosylated and can be more conveniently prepared in E. coli-based expression platforms. We propose here an updated survey of the most effective and appropriate methods of preparation of antibody fragments that exploit E. coli as an expression background and review the pros and cons of the different platforms available today. Around 250 references accompany and complete the review together with some lists of the most important new antibody-like molecules that are on the market or are being developed as new biotherapeutics or diagnostic agents.
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Hortigüela MJ, Aumailley L, Srivastava A, Cunningham C, Anandakumar S, Robin S, Pandit A, Hu X, Wall JG. Engineering recombinant antibodies for polymer biofunctionalization. POLYM ADVAN TECHNOL 2015. [DOI: 10.1002/pat.3619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- María J. Hortigüela
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Lucie Aumailley
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Faculty of Medicine; Laval University and CHU de Quebec Research Center; Quebec Canada
| | - Akshay Srivastava
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Claire Cunningham
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Alimentary Glycoscience Research Cluster; National University of Ireland; Galway Ireland
| | - Soshee Anandakumar
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Sylvain Robin
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Transgene; Boulevard Gonthier d'Andernach; Parc d'Innovation 67405 Illkirch Graffenstaden France
| | - Abhay Pandit
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
| | - Xuejun Hu
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
- Medical College; Dalian University; Xuefu Avenue No.10, Dalian Economical and Technological Development Zone Liaoning 116622 China
| | - J. Gerard Wall
- Microbiology and the Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway; University Road, Galway; Ireland
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A novel multigene cloning method for the production of a motile ATPase. J Biotechnol 2015; 207:1-7. [PMID: 25956244 DOI: 10.1016/j.jbiotec.2015.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/10/2015] [Accepted: 04/15/2015] [Indexed: 11/22/2022]
Abstract
With the advent of nanotechnology, new functional modules (e.g., nanomotors, nanoprobes) have become essential in several medical fields. Generally, mechanical modulators systems are the principal components of most cutting-edge technologies in modern biomedical applications. However, the in vivo use of motile probes has raised many concerns due to their low sensitivity and non-biocompatibility. As an alternative, biological enzymatic engines have received increased attention. In particular, ATPases, which belong to a class of motile enzymes that catalyze chemical metabolic reactions, have emerged as a promising motor due to their improved biocompatibility and performance. However, ATPases usually suffer from lower functional activity and are difficult to express recombinantly in bacteria relative to their conventional and synthetic competitors. Here, we report a novel functional modified ATPase with both a simple purification protocol and enhanced motile activity. For this mutant ATPase, a new bacterial subcloning method was established. The ATPase-encoding sequence was redesigned so that the mutant ATPase could be easily produced in an Escherichia coli system. The modified thermophilic F1-ATPase (mTF1-ATPase) demonstrated 17.8unit/mg ATPase activity. We propose that derivatives of our ATPase may enable the development of novel in vitro and in vivo synthetic medical diagnostics, as well as therapeutics.
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Wang M, Zhang Y, Li B, Zhu J. Construction of scFv that bind both fibronectin-binding protein A and clumping factor A of Stapylococcus aureus. Res Vet Sci 2015; 100:109-14. [DOI: 10.1016/j.rvsc.2015.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 11/21/2014] [Accepted: 02/21/2015] [Indexed: 10/23/2022]
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Kavanagh O, Elliott CT, Campbell K. Progress in the development of immunoanalytical methods incorporating recombinant antibodies to small molecular weight biotoxins. Anal Bioanal Chem 2015; 407:2749-70. [PMID: 25716465 DOI: 10.1007/s00216-015-8502-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 01/08/2023]
Abstract
Rapid immunoanalytical screening of food and environmental samples for small molecular weight (hapten) biotoxin contaminations requires the production of antibody reagents that possess the requisite sensitivity and specificity. To date animal-derived polyclonal (pAb) and monoclonal (mAb) antibodies have provided the binding element of the majority of these assays but recombinant antibodies (rAb) isolated from in vitro combinatorial phage display libraries are an exciting alternative due to (1) circumventing the need for experimental animals, (2) speed of production in commonly used in vitro expression systems and (3) subsequent molecular enhancement of binder performance. Short chain variable fragments (scFv) have been the most commonly employed rAb reagents for hapten biotoxin detection over the last two decades but antibody binding fragments (Fab) and single domain antibodies (sdAb) are increasing in popularity due to increased expression efficiency of functional binders and superior resistance to solvents. rAb-based immunochromatographic assays and surface plasmon resonance (SPR) biosensors have been reported to detect sub-regulatory levels of fungal (mycotoxins), marine (phycotoxins) and aquatic biotoxins in a wide range of food and environmental matrices, however this technology has yet to surpass the performances of the equivalent mAb- and pAb-based formats. As such the full potential of rAb technology in hapten biotoxin detection has yet to be achieved, but in time the inherent advantages of engineered rAb are set to provide the next generation of ultra-high performing binder reagents for the rapid and specific detection of hapten biotoxins.
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Affiliation(s)
- Owen Kavanagh
- Institute for Global Food Security (IGFS), School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland, UK,
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Ayyar BV, Hearty S, O’Kennedy R. Facile domain rearrangement abrogates expression recalcitrance in a rabbit scFv. Appl Microbiol Biotechnol 2014; 99:2693-703. [DOI: 10.1007/s00253-014-6268-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 12/12/2022]
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Kim YP, Park D, Kim JJ, Choi WJ, Lee SH, Lee SY, Kim S, Chung JM, Jeon J, Lee BD, Shin JH, Lee YI, Cho H, Lee JM, Kang HC. Effective therapeutic approach for head and neck cancer by an engineered minibody targeting the EGFR receptor. PLoS One 2014; 9:e113442. [PMID: 25438047 PMCID: PMC4249956 DOI: 10.1371/journal.pone.0113442] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
Cetuximab, a chimeric monoclonal antibody developed for targeting the Epidermal Growth Factor Receptor (EGFR), has been intensively used to treat cancer patients with metastatic colorectal cancer and head and neck cancer. Intact immunoglobulin G (IgG) antibody like cetuximab, however, has some limitations such as high production cost and low penetration rate from vasculature into solid tumor mass due to its large size. In attempt to overcome these limitations, we engineered cetuximab to create single chain variable fragments (scFv-CH3; Minibody) that were expressed in bacterial system. Among three engineered minibodies, we found that MI061 minibody, which is composed of the variable heavy (VH) and light (VL) region joined by an 18-residue peptide linker, displays higher solubility and better extraction properties from bacterial lysate. In addition, we validated that purified MI061 significantly interferes ligand binding to EGFR and blocks EGFR's phosphorylation. By using a protein microarray composed of 16,368 unique human proteins covering around 2,400 plasma membrane associated proteins such as receptors and channels, we also demonstrated that MI061 only recognizes the EGFR but not other proteins as compared with cetuximab. These results indicated that engineered MI061 retains both binding specificity and affinity of cetuximab for EGFR. Although it had relatively short half-life in serum, it was shown to be highly significant anti-tumor effect by inhibiting ERK pathway in A431 xenograft model. Taken together, our present study provides compelling evidence that engineered minibody is more effective and promising agent for in vivo targeting of solid tumors.
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Affiliation(s)
- Young Pil Kim
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Dongsun Park
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Jae Jin Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Won-Jae Choi
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Sun Hee Lee
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
| | - Seo Yun Lee
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Soyeon Kim
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Jee Min Chung
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
| | - Jinseon Jeon
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
| | - Byoung Dae Lee
- Department of Neuroscience, Kyung Hee University School of Medicine, Seoul, South Korea
| | - Joo-Ho Shin
- Division of Pharmacology, Department of Molecular Cell Biology, Samsung Biomedical Research Institute, SungKyunKwan University School of Medicine, Suwon, South Korea
| | - Yun-il Lee
- Well Aging Research Center, Samsung Advanced Institute of Technology (SAIT), Suwon, South Korea
| | - Hyeseong Cho
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
- Department of Biochemistry, Ajou University School of Medicine, Suwon, South Korea
- * E-mail: (HC); (JL); (HCK)
| | - Jeong-Min Lee
- Department of Bio-Engineering, Life Science RD Center, Sinil Pharmaceutical Co., Seongnam, South Korea
- * E-mail: (HC); (JL); (HCK)
| | - Ho Chul Kang
- Department of Physiology, Ajou University School of Medicine, Suwon, South Korea
- Department of Biomedical Sciences, The Graduate School, Ajou University, Suwon, South Korea
- * E-mail: (HC); (JL); (HCK)
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Isolation and characterisation of a recombinant antibody fragment that binds NCAM1-expressing intervertebral disc cells. PLoS One 2013; 8:e83678. [PMID: 24349544 PMCID: PMC3862799 DOI: 10.1371/journal.pone.0083678] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/06/2013] [Indexed: 01/07/2023] Open
Abstract
Degeneration of the intervertebral discs (IVD) is a leading cause of neck and low back pain. Degeneration begins in the central nucleus pulposus region, leading to loss of IVD osmotic properties. Regeneration approaches include administration of matrix-mimicking scaffolds, cells and/or therapeutic factors. Cell-targeting strategies are likely to improve delivery due to the low cell numbers in the IVD. Single-chain antibody fragments (scFvs) that bind IVD cells were isolated for potential delivery of therapeutics to degenerated IVD. The most cell-distal domain of neural cell adhesion molecule 1 (NCAM1) was cloned and expressed in Escherichia coli. Phage display technology was used to isolate a human scFv against the recombinant domain by panning a scFv library on the immobilised protein. The isolated scFv bound cultured rat astrocytes, as well as bovine nucleus pulposus and annulus fibrosus cells in immunocytochemical studies. The scFv also labelled cells in bovine spinal cord and six-month and two-year old bovine IVD sections by immunohistochemistry. Antibody fragments can provide cell-binding moieties at improved cost, time, yield and functionalisation potential over whole antibodies. The described scFv has potential application in delivery of therapeutics to NCAM1-expressing cells in degenerated IVD.
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Hortigüela MJ, Wall JG. Improved detection of domoic acid using covalently immobilised antibody fragments. Mar Drugs 2013; 11:881-95. [PMID: 23493076 PMCID: PMC3705377 DOI: 10.3390/md11030881] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 01/13/2013] [Accepted: 02/21/2013] [Indexed: 12/16/2022] Open
Abstract
Antibody molecules, and antibody fragments in particular, have enormous potential in the development of biosensors for marine monitoring. Conventional immobilisation approaches used in immunoassays typically yield unstable and mostly incorrectly oriented antibodies, however, resulting in reduced detection sensitivities for already low concentration analytes. The 2H12 anti-domoic acid scFv antibody fragment was engineered with cysteine-containing linkers of two different lengths, distal to the antigen binding pocket, for covalent and correctly oriented immobilisation of the scFvs on functionalised solid supports. The Escherichia coli-produced, cysteine-engineered scFvs dimerised in solution and demonstrated similar efficiencies of covalent immobilisation on maleimide-activated plates and minimal non-covalent attachment. The covalently attached scFvs exhibited negligible leaching from the support under acidic conditions that removed almost 50% of the adsorbed wildtype fragment, and IC50s for domoic acid of 270 and 297 ng/mL compared with 1126 and 1482 ng/mL, respectively, for their non-covalently adsorbed counterparts. The expression and immobilisation approach will facilitate the development of stable, reusable biosensors with increased stability and detection sensitivity for marine neurotoxins.
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Affiliation(s)
| | - J. Gerard Wall
- Microbiology, NUI Galway, University Road, Galway, Ireland; E-Mail:
- Network of Excellence for Functional Biomaterials (NFB), NUI Galway, University Road, Galway, Ireland
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +353-91-495-808
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Hu X, Hortigüela MJ, Robin S, Lin H, Li Y, Moran AP, Wang W, Wall JG. Covalent and oriented immobilization of scFv antibody fragments via an engineered glycan moiety. Biomacromolecules 2012; 14:153-9. [PMID: 23215344 DOI: 10.1021/bm301518p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibody-derived fragments have enormous potential application in solid-phase assays such as biomarker detection and protein purification. Controlled orientation of the immobilized antibody molecules is a critical requirement for the sensitivity and efficacy of such assays. We present an approach for covalent, correctly oriented attachment of scFv antibody fragments on solid supports. Glycosylated scFvs were expressed in Escherichia coli and the C-terminal, binding pocket-distal glycan tag was oxidized for covalent attachment to amine-functionalized beads. The glycosylated scFvs could be immobilized at salt concentrations that precluded nonspecific adsorption of unglycosylated molecules and the covalently attached antibody fragments exhibited 4-fold higher functional activity than ionically adsorbed scFvs. The glyco-tethered scFvs were stable in NaCl concentrations that removed greater than 90% of adsorbed scFvs and they exhibited improved stability of antigen binding over both adsorbed scFvs and soluble, nonimmobilized scFvs in accelerated degradation tests. The simple expression and immobilization approach reported is likely to find broad application in in vitro antibody tests.
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Affiliation(s)
- Xuejun Hu
- Medical College, Dalian University, Xuefu Avenue No.10, Dalian Economical and Technological Development Zone, Liaoning 116622, China.
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Ahmad ZA, Yeap SK, Ali AM, Ho WY, Alitheen NBM, Hamid M. scFv antibody: principles and clinical application. Clin Dev Immunol 2012; 2012:980250. [PMID: 22474489 PMCID: PMC3312285 DOI: 10.1155/2012/980250] [Citation(s) in RCA: 469] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/07/2012] [Indexed: 01/16/2023]
Abstract
To date, generation of single-chain fragment variable (scFv) has become an established technique used to produce a completely functional antigen-binding fragment in bacterial systems. The advances in antibody engineering have now facilitated a more efficient and generally applicable method to produce Fv fragments. Basically, scFv antibodies produced from phage display can be genetically fused to the marker proteins, such as fluorescent proteins or alkaline phosphatase. These bifunctional proteins having both antigen-binding capacity and marker activity can be obtained from transformed bacteria and used for one-step immunodetection of biological agents. Alternatively, antibody fragments could also be applied in the construction of immunotoxins, therapeutic gene delivery, and anticancer intrabodies for therapeutic purposes. This paper provides an overview of the current studies on the principle, generation, and application of scFv. The potential of scFv in breast cancer research is also discussed in this paper.
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Affiliation(s)
- Zuhaida Asra Ahmad
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
| | - Swee Keong Yeap
- Institute of Bioscience, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
| | - Abdul Manaf Ali
- Faculty of Agriculture and Biotechnology, Universiti Sultan Zainal Abidin, Kampus Kota, Jalan Sultan Mahmud, 20400 Kuala Terengganu, Malaysia
| | - Wan Yong Ho
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
| | - Noorjahan Banu Mohamed Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
| | - Muhajir Hamid
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
- Department of Bioprocess Technology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, 43400 Serdang, Malaysia
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Hu X, O’Connor IB, Wall JG. Antibody Immobilization on Solid Surfaces: Methods and Applications. BIOLOGICAL INTERACTIONS WITH SURFACE CHARGE IN BIOMATERIALS 2011. [DOI: 10.1039/9781849733366-00090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The correct immobilization of the antibody component is one of the most critical steps in the development of immunoassays, immunosensors and immunochromatography matrices. Advances in hybridoma technology and protein engineering have allowed traditional limitations of polyreactivity of antibody preparations, poor device stability and random orientation of binding pockets to be largely overcome, resulting in stable, sensitive, highly specific and enormously diverse immunoplatforms with applications in diagnostics, environmental monitoring, and food and public safety. In this Chapter we introduce antibody structure and antibody-derived fragments, describe the most common methods of their immobilization and discuss ‘traditional’ applications of immobilized antibodies such as enzyme immunoassays and immunoaffinity chromatography, as well as exciting emerging uses in immunosensors, microarrays and nanomedicine.
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Affiliation(s)
- X. Hu
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
- Dalian University, Medical School Dalian Development Zone, Dalian China
| | - I. B. O’Connor
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
| | - J. G. Wall
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
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15
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Engineering of a fungal β-galactosidase to remove product inhibition by galactose. Appl Microbiol Biotechnol 2010; 87:1773-82. [DOI: 10.1007/s00253-010-2662-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 04/27/2010] [Accepted: 04/29/2010] [Indexed: 10/19/2022]
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Single-chain Fv antibody fragments retain binding properties of the monoclonal antibody raised against peptide P1 of the human prion protein. Appl Biochem Biotechnol 2009; 160:1808-21. [PMID: 19597999 DOI: 10.1007/s12010-009-8699-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2009] [Accepted: 06/19/2009] [Indexed: 10/20/2022]
Abstract
Prion diseases are incurable neurodegenerative diseases that affect both humans and animals. The infectious agent is a pathogenic form of the prion protein that accumulates in brain as amyloids. Currently, there is neither cure nor reliable preclinical diagnostics on the market available. The growing number of reports shows that passive immunisation is one of the most promising strategies for prion disease therapy, where antibodies against prions may prevent and even cure the infection. Since antibodies are large molecules and, thus, might not be suitable for the therapy, different antibody fragments are a good alternative. Therefore, we have designed and prepared single-chain antibody fragments (scFvs) derived from the PrP(Sc)-specific murine monoclonal antibody V5B2. Using a new expression vector pMD204, we produced scFvs in two opposing chain orientations in the periplasm of Escherichia coli. Both recombinant antibody fragments retained the specificity of the parent antibody and one of these exhibited binding properties comparable to the corresponding murine Fab fragments with the affinity in nM range. Our monovalent antibody fragments are of special interest in view of possible therapeutic reagents for prion diseases as well as for development of a new generation of diagnostics.
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Trigger factor from the psychrophilic bacterium Psychrobacter frigidicola is a monomeric chaperone. J Bacteriol 2008; 191:1162-8. [PMID: 19060145 DOI: 10.1128/jb.01137-08] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In eubacteria, trigger factor (TF) is the first chaperone to interact with newly synthesized polypeptides and assist their folding as they emerge from the ribosome. We report the first characterization of a TF from a psychrophilic organism. TF from Psychrobacter frigidicola (TF(Pf)) was cloned, produced in Escherichia coli, and purified. Strikingly, cross-linking and fluorescence anisotropy analyses revealed it to exist in solution as a monomer, unlike the well-characterized, dimeric E. coli TF (TF(Ec)). Moreover, TF(Pf) did not exhibit the downturn in reactivation of unfolded GAPDH (glyceraldehyde-3-phosphate dehydrogenase) that is observed with its E. coli counterpart, even at high TF/GAPDH molar ratios and revealed dramatically reduced retardation of membrane translocation by a model recombinant protein compared to the E. coli chaperone. TF(Pf) was also significantly more effective than TF(Ec) at increasing the yield of soluble and functional recombinant protein in a cell-free protein synthesis system, indicating that it is not dependent on downstream systems for its chaperoning activity. We propose that TF(Pf) differs from TF(Ec) in its quaternary structure and chaperone activity, and we discuss the potential significance of these differences in its native environment.
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O'Dwyer R, Razzaque R, Hu X, Hollingshead SK, Wall JG. Engineering of cysteine residues leads to improved production of a human dipeptidase enzyme in E. coli. Appl Biochem Biotechnol 2008; 159:178-90. [PMID: 18931951 DOI: 10.1007/s12010-008-8379-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 09/19/2008] [Indexed: 10/21/2022]
Abstract
Low yields, poor folding efficiencies and improper disulfide bridge formation limit large-scale production of cysteine-rich proteins in Escherichia coli. Human renal dipeptidase (MDP), the only human beta-lactamase known to date, is a homodimeric enzyme, which contains six cysteine residues per monomer. It hydrolyses penem and carbapenem beta-lactam antibiotics and can cleave dipeptides containing amino acids in both D: - and L: -configurations. In this study, MDP accumulated in inactive form in high molecular weight, disulfide-linked aggregates when produced in the E. coli periplasm. Mutagenesis of Cys361 that mediates dimer formation and Cys93 that is unpaired in the native MDP led to production of soluble recombinant enzyme, with no change in activity compared with the wild-type enzyme. The removal of unpaired or structurally inessential cysteine residues in this manner may allow functional production of many multiply disulfide-linked recombinant proteins in E. coli.
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Affiliation(s)
- Ronan O'Dwyer
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, National Technology Park, Limerick, Ireland
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Chang HJ, Choi SW, Chun HS. Expression of functional single-chain variable domain fragment antibody (scFv) against mycotoxin zearalenone in Pichia pastoris. Biotechnol Lett 2008; 30:1801-6. [DOI: 10.1007/s10529-008-9770-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 05/15/2008] [Accepted: 05/30/2008] [Indexed: 11/24/2022]
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20
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Gasser B, Saloheimo M, Rinas U, Dragosits M, Rodríguez-Carmona E, Baumann K, Giuliani M, Parrilli E, Branduardi P, Lang C, Porro D, Ferrer P, Tutino ML, Mattanovich D, Villaverde A. Protein folding and conformational stress in microbial cells producing recombinant proteins: a host comparative overview. Microb Cell Fact 2008; 7:11. [PMID: 18394160 PMCID: PMC2322954 DOI: 10.1186/1475-2859-7-11] [Citation(s) in RCA: 232] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/04/2008] [Indexed: 11/17/2022] Open
Abstract
Different species of microorganisms including yeasts, filamentous fungi and bacteria have been used in the past 25 years for the controlled production of foreign proteins of scientific, pharmacological or industrial interest. A major obstacle for protein production processes and a limit to overall success has been the abundance of misfolded polypeptides, which fail to reach their native conformation. The presence of misfolded or folding-reluctant protein species causes considerable stress in host cells. The characterization of such adverse conditions and the elicited cell responses have permitted to better understand the physiology and molecular biology of conformational stress. Therefore, microbial cell factories for recombinant protein production are depicted here as a source of knowledge that has considerably helped to picture the extremely rich landscape of in vivo protein folding, and the main cellular players of this complex process are described for the most important cell factories used for biotechnological purposes.
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Affiliation(s)
- Brigitte Gasser
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | | | - Ursula Rinas
- Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Martin Dragosits
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Escarlata Rodríguez-Carmona
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Kristin Baumann
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Giuliani
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Ermenegilda Parrilli
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Paola Branduardi
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Christine Lang
- Technical University Berlin, Faculty III, Institute for Microbiology and Genetics, Berlin, Germany
| | - Danilo Porro
- University of Milano-Bicocca, Department of Biotechnology and Bioscience, Milan, Italy
| | - Pau Ferrer
- Autonomous University of Barcelona, Department of Chemical Engineering, Barcelona, Spain
| | - Maria Luisa Tutino
- University of Naples Federico II, School of Biotechnological Sciences, Naples, Italy
| | - Diethard Mattanovich
- University of Natural Resources and Applied Life Sciences Vienna, Department of Biotechnology, Vienna, Austria
| | - Antonio Villaverde
- Autonomous University of Barcelona, Institute for Biotechnology and Biomedicine, Department of Genetics and Microbiology, and CIBER-BBN Network in Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
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Höfer N, Kolaj O, Li H, Cherezov V, Gillilan R, Wall JG, Caffrey M. Crystallization and preliminary X-ray diffraction analysis of a soluble domain of the putative zinc transporter CzrB from Thermus thermophilus. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:673-7. [PMID: 17671365 PMCID: PMC2335163 DOI: 10.1107/s1744309107032277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 07/02/2007] [Indexed: 11/11/2022]
Abstract
CzrB is a putative zinc transporter from Thermus thermophilus. The protein is proposed to consist of a hexahelical transmembrane domain with a cytosolic extramembranal C-terminus. The latter 92-residue fragment may be expressed free and may function independently of the full-length integral membrane protein. A 6xHis-tagged form of the water-soluble fragment has been overexpressed in Escherichia coli and diffraction-quality crystals of the tagged and tag-free variants have been grown. Preliminary X-ray analyses of tag-free fragment crystals with (2.2 A resolution) and without zinc ions (1.7 A resolution) reveal that the former has at least two zinc ions bound per monomer.
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Affiliation(s)
- Nicole Höfer
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Olga Kolaj
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Hui Li
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Vadim Cherezov
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Richard Gillilan
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14850, USA
| | - J. Gerard Wall
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
| | - Martin Caffrey
- Department of Chemical and Environmental Sciences and Materials and Surface Science Institute, University of Limerick, Limerick, Ireland
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
- Biochemistry, Biophysics and Chemistry, The Ohio State University, Columbus, OH 43210, USA
- Correspondence e-mail:
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Hu X, O'Hara L, White S, Magner E, Kane M, Wall JG. Optimisation of production of a domoic acid-binding scFv antibody fragment in Escherichia coli using molecular chaperones and functional immobilisation on a mesoporous silicate support. Protein Expr Purif 2007; 52:194-201. [PMID: 17005419 DOI: 10.1016/j.pep.2006.08.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 08/14/2006] [Accepted: 08/15/2006] [Indexed: 11/28/2022]
Abstract
Domoic acid is a potent neurotoxin that can lead to amnesic shellfish poisoning in humans through ingestion of contaminated shellfish. We have produced and purified an anti-domoic acid single-chain Fragment variable (scFv) antibody fragment from the Escherichia coli periplasm. Yields of functional protein were increased by up to 100-fold upon co-production of E. coli DnaKJE molecular chaperones but co-overproduction of GroESL led to a reduction in solubility of the scFv. Co-production of the peptidyl-prolyl isomerase trigger factor resulted in accumulation of unprocessed scFv in the E. coli cytoplasm. This was due to an apparent bottleneck in translocation of the cytoplasmic membrane by the recombinant polypeptide. Co-expression of the E. coli disulfide bond isomerase dsbC increased scFv yields by delaying lysis of the host bacterial cells though this effect was not synergistic with molecular chaperone co-production. Meanwhile, use of a cold-shock promoter for protein production led to accumulation of greater amounts of scFv polypeptide which was predominantly in insoluble form and could not be rescued by chaperones. Purification of the scFv was achieved using an optimised metal affinity chromatography procedure and the purified protein bound domoic acid when immobilised on a mesoporous silicate support. The work outlines the potential benefit of applying a molecular chaperone/folding catalyst screening approach to improve antibody fragment production for applications such as sensor development.
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Affiliation(s)
- Xuejun Hu
- Department of Chemical and Environmental Sciences, University of Limerick, Plassey Technology Park, Limerick, Ireland
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23
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Bardwell JC. Disulfide Bond Formation Enzymes. MOLECULAR MACHINES INVOLVED IN PROTEIN TRANSPORT ACROSS CELLULAR MEMBRANES 2007. [DOI: 10.1016/s1874-6047(07)25005-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Hu X, Spada S, White S, Hudson S, Magner E, Wall JG. Adsorption and Activity of a Domoic Acid Binding Antibody Fragment on Mesoporous Silicates. J Phys Chem B 2006; 110:18703-9. [PMID: 16970501 DOI: 10.1021/jp062423e] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The adsorption of an anti-domoic acid single-chain Fv (scFv) antibody fragment onto a range of mesoporous silicate supports was investigated. The scFv fragment adsorbed to all materials investigated, and pI had an apparently large effect on coating, with the greatest-and fastest-adsorption found on the most negatively charged silicates. Maximal coating levels attainable did not reflect the pore diameters of the materials. The immobilized antibody was functional on all materials and bound its antigen, a naturally occurring neurotoxin produced by shellfish, in a rapidly saturating manner that suggested the antibody adsorbed in a multilayer on the mesoporous particles. The antigen:antibody ratio decreased from 1:1.3 to <1:10 with increasing concentration of immobilized antibody, and the immobilized scFv exhibited no detectable reduction in domoic acid binding over a 42-day incubation period.
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Affiliation(s)
- Xuejun Hu
- Department of Chemical and Environmental Sciences, and Materials and Surface Science Institute, University of Limerick, Plassey Technology Park, Limerick, Ireland
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Finlay WJJ, Shaw I, Reilly JP, Kane M. Generation of high-affinity chicken single-chain Fv antibody fragments for measurement of the Pseudonitzschia pungens toxin domoic acid. Appl Environ Microbiol 2006; 72:3343-9. [PMID: 16672476 PMCID: PMC1472335 DOI: 10.1128/aem.72.5.3343-3349.2006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibody-based assay systems are now accepted by regulatory authorities for detection of the toxins produced by phytoplankton that accumulate in shellfish tissues. However, the generation of suitable antibodies for sensitive assay development remains a major challenge. We have examined the potential of using the chicken immune system to generate high-affinity, high-specificity recombinant antibody fragments against phytotoxins. Following immunization of the chicken with domoic acid-bovine serum albumin, a single-chain antibody variable region (scFv) gene library was generated from single V(H) and V(L) genes isolated from the immune cells in the spleen and bone marrow. scFvs reacting with domoic acid were isolated by phage display and affinity matured by light chain shuffling, resulting in an approximate 10-fold increase in sensitivity. The isolated scFvs were effectively expressed in Escherichia coli and readily purified by affinity chromatography. They were then used to develop a convenient and sensitive indirect competitive enzyme-linked immunosorbent assay for domoic acid, with a 50% effective dose of 156 ng/ml, which could be used reliably with shellfish extracts. This study demonstrates that chickens provide a valuable model system for the simplified, rapid generation of high-affinity recombinant antibody fragments with specificity for small toxin molecules.
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Affiliation(s)
- William J J Finlay
- National Diagnostics Centre, National University of Ireland, Galway, Ireland
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