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An effective strategy for the humanization of antibody fragments under an accelerated timeline. Int J Biol Macromol 2022; 216:465-474. [PMID: 35803408 DOI: 10.1016/j.ijbiomac.2022.06.195] [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: 05/11/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 11/22/2022]
Abstract
The use of monoclonal antibodies (mAbs) in therapy is gradually advancing and discussions entail its safety, rentability and effectiveness. To this date, around a hundred mAbs have been approved by the FDA for the treatment of various diseases. Aiming for their large-scale production, recombinant DNA technology is mainly employed, and antibodies can be expressed in various eukaryotic and prokaryotic systems. Moreover, considering their heterologous origin and potential immunogenicity, various strategies have been developed for mAb humanization, considering that around 50 % of commercial mAbs are humanized. Hence, we introduce LimAb7, a mouse mAb capable of binding and neutralizing brown spider's Loxosceles intermedia dermonecrotic toxins in vivo/in vitro. This antibody has been produced in mouse and humanized scFv and diabody formats, however results indicated losses in antigen-binding affinity, stability, and neutralizing ability. Intending to develop evolved, stable, and neutralizing antibody fragments, we report for the first time the design of humanized antibody V-domains produced as Fab fragments, against spider venom toxins. Improvements in constructs were observed regarding their physicochemical stability, target binding and binding pattern maintenance. As their neutralizing features remain to be characterized, we believe this data sheds new light on antibody humanization by producing a parental molecule in different recombinant formats.
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2
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Jeong S, Widengren J, Lee JC. Fluorescent Probes for STED Optical Nanoscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 12:21. [PMID: 35009972 PMCID: PMC8746377 DOI: 10.3390/nano12010021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
Progress in developing fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, is inseparable from the advancement in optical fluorescence microscopy. Super-resolution microscopy, or optical nanoscopy, overcame the far-field optical resolution limit, known as Abbe's diffraction limit, by taking advantage of the photophysical properties of fluorescent probes. Therefore, fluorescent probes for super-resolution microscopy should meet the new requirements in the probes' photophysical and photochemical properties. STED optical nanoscopy achieves super-resolution by depleting excited fluorophores at the periphery of an excitation laser beam using a depletion beam with a hollow core. An ideal fluorescent probe for STED nanoscopy must meet specific photophysical and photochemical properties, including high photostability, depletability at the depletion wavelength, low adverse excitability, and biocompatibility. This review introduces the requirements of fluorescent probes for STED nanoscopy and discusses the recent progress in the development of fluorescent probes, such as fluorescent proteins, organic dyes, and fluorescent nanoparticles, for the STED nanoscopy. The strengths and the limitations of the fluorescent probes are analyzed in detail.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology (KTH), Stockholm 10691, Sweden;
| | - Jong-Chan Lee
- Department of New Biology, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea;
- New Biology Research Center, Daegu Gyeongbuk Institute of Science & Technology, Daegu 42988, Korea
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3
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Hasegawa H, Hsu A, Tinberg CE, Siegler KE, Nazarian AA, Tsai MM. Single amino acid substitution in LC-CDR1 induces Russell body phenotype that attenuates cellular protein synthesis through eIF2α phosphorylation and thereby downregulates IgG secretion despite operational secretory pathway traffic. MAbs 2017; 9:854-873. [PMID: 28379093 DOI: 10.1080/19420862.2017.1314875] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Amino acid sequence differences in the variable region of immunoglobulin (Ig) cause wide variations in secretion outputs. To address how a primary sequence difference comes to modulate Ig secretion, we investigated the biosynthetic process of 2 human IgG2κ monoclonal antibodies (mAbs) that differ only by one amino acid in the light chain complementarity-determining region 1 while showing ∼20-fold variance in secretion titer. Although poorly secreted, the lower-secreting mAb of the 2 was by no means defective in terms of its folding stability, antigen binding, and in vitro biologic activity. However, upon overexpression in HEK293 cells, the low-secreting mAb revealed a high propensity to aggregate into enlarged globular structures called Russell bodies (RBs) in the endoplasmic reticulum. While Golgi morphology was affected by the formation of RBs, secretory pathway membrane traffic remained operational in those cells. Importantly, cellular protein synthesis was severely suppressed in RB-positive cells through the phosphorylation of eIF2α. PERK-dependent signaling was implicated in this event, given the upregulation and nuclear accumulation of downstream effectors such as ATF4 and CHOP. These findings illustrated that the underlining process of poor Ig secretion in RB-positive cells was due to downregulation of Ig synthesis instead of a disruption or blockade of secretory pathway trafficking. Therefore, RB formation signifies an end of active Ig production at the protein translation level. Consequently, depending on how soon and how severely an antibody-expressing cell develops the RB phenotype, the productive window of Ig secretion can vary widely among the cells expressing different mAbs.
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Affiliation(s)
- Haruki Hasegawa
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Ann Hsu
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Christine E Tinberg
- a Department of Therapeutic Discovery , Amgen Inc. , South San Francisco , CA , USA
| | - Karen E Siegler
- c Department of Cardiometabolic Disorders , Amgen Inc. , South San Francisco , CA , USA
| | - Aaron A Nazarian
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
| | - Mei-Mei Tsai
- b Department of Therapeutic Discovery , Amgen Inc. , Thousand Oaks , CA , USA
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Kawakami Y, Kinoshita M, Mori Y, Okochi S, Hirano S, Shimoda I, Kanzaki K, Suzuki-Yamamoto T, Kimoto M, Sugahara M, Hori T, Saino H, Miyano M, Yamamoto S, Takahashi Y. The Y54(L)W mutation of anti-leukotriene C 4single-chain antibody increases affinity to leukotriene E 4. J Biochem 2017; 161:79-86. [DOI: 10.1093/jb/mvw055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 08/11/2016] [Indexed: 11/14/2022] Open
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5
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Vermeire T, Vermaere S, Schepens B, Saelens X, Van Gucht S, Martens L, Vandermarliere E. Scop3D: three-dimensional visualization of sequence conservation. Proteomics 2015; 15:1448-52. [PMID: 25641949 DOI: 10.1002/pmic.201400354] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 12/02/2014] [Accepted: 01/28/2015] [Indexed: 02/04/2023]
Abstract
The integration of a protein's structure with its known sequence variation provides insight on how that protein evolves, for instance in terms of (changing) function or immunogenicity. Yet, collating the corresponding sequence variants into a multiple sequence alignment, calculating each position's conservation, and mapping this information back onto a relevant structure is not straightforward. We therefore built the Sequence Conservation on Protein 3D structure (scop3D) tool to perform these tasks automatically. The output consists of two modified PDB files in which the B-values for each position are replaced by the percentage sequence conservation, or the information entropy for each position, respectively. Furthermore, text files with absolute and relative amino acid occurrences for each position are also provided, along with snapshots of the protein from six distinct directions in space. The visualization provided by scop3D can for instance be used as an aid in vaccine development or to identify antigenic hotspots, which we here demonstrate based on an analysis of the fusion proteins of human respiratory syncytial virus and mumps virus.
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Affiliation(s)
- Tessa Vermeire
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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6
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Safarnejad MR, Jouzani GS, Tabatabaie M, Twyman RM, Schillberg S. Antibody-mediated resistance against plant pathogens. Biotechnol Adv 2011; 29:961-71. [DOI: 10.1016/j.biotechadv.2011.08.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Revised: 08/12/2011] [Accepted: 08/12/2011] [Indexed: 02/06/2023]
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7
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Kachko A, Kochneva G, Sivolobova G, Grazhdantseva A, Lupan T, Zubkova I, Wells F, Merchlinsky M, Williams O, Watanabe H, Ivanova A, Shvalov A, Loktev V, Netesov S, Major ME. New neutralizing antibody epitopes in hepatitis C virus envelope glycoproteins are revealed by dissecting peptide recognition profiles. Vaccine 2011; 30:69-77. [PMID: 22041300 DOI: 10.1016/j.vaccine.2011.10.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 08/22/2011] [Accepted: 10/18/2011] [Indexed: 02/07/2023]
Abstract
One of the greatest challenges to HCV vaccine development is the induction of effective immune responses using recombinant proteins or vectors. In order to better understand which vaccine-induced antibodies contribute to neutralization of HCV the quality of polyclonal anti-E1E2 antibody responses in immunized mice and chimpanzees was assessed at the level of epitope recognition using peptide scanning and neutralization of chimeric 1a/2a, 1b/2a and 2a HCVcc after blocking or affinity elution of specific antibodies. Mice and chimpanzees were immunized with genotype 1a (H77) HCV gpE1E2; all samples contained cross-neutralizing antibody against HCVcc. By functionally dissecting the polyclonal immune responses we identified three new regions important for neutralization within E1 (aa264-318) and E2 (aa448-483 and aa496-515) of the HCV glycoproteins, the third of which (aa496-515) is highly conserved (85-95%) amongst genotypes. Antibodies to aa496-515 were isolated by affinity binding and elution from the serum of a vaccinated chimpanzee and found to specifically neutralize chimeric 1a/2a, 1b/2a and 2a HCVcc. IC50 titres (IgG ng/mL) for the aa496-515 eluate were calculated as 142.1, 239.37 and 487.62 against 1a/2a, 1b/2a and 2a HCVcc, respectively. Further analysis demonstrated that although antibody to this new, conserved neutralization epitope is efficiently induced with recombinant proteins in mice and chimpanzees; it is poorly induced during natural infection in patients and chimpanzees (7 out of 68 samples positive) suggesting the epitope is poorly presented to the immune system in the context of the viral particle. These findings have important implications for the development of HCV vaccines and strategies designed to protect against heterologous viruses. The data also suggest that recombinant or synthetic antigens may be more efficient at inducing neutralizing antibodies to certain epitopes and that screening virally infected patients may not be the best approach for finding new cross-reactive epitopes.
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Affiliation(s)
- Alla Kachko
- Laboratory of Hepatitis Viruses, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA.
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8
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Blackler RJ, Müller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV. A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Biochemistry 2011; 50:3357-68. [DOI: 10.1021/bi101886v] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan J. Blackler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Sven Müller-Loennies
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Cory L. Brooks
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Dylan W. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
| | - Lore Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, A-1190 Vienna, Austria
| | - Helmut Brade
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Parkallee 22, D-23845 Borstel, Germany
| | - Stephen V. Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3P6, Canada
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9
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Al-Rubeai M. Production of Antibody Fab Fragments in Escherichia coli. ANTIBODY EXPRESSION AND PRODUCTION 2011. [PMCID: PMC7121915 DOI: 10.1007/978-94-007-1257-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A phage-display library is the most broadly used platform for preparation of recombinant human monoclonal antibody Fab fragments. Panning is effective for the selection of immunoglobulin genes from naïve and immune libraries. However, it is possible to bypass the phage display system if human peripheral lymphocytes are obtained from seropositive patients with infectious diseases as a source of immunoglobulin genes. Direct screening of bacterial colonies producing Fab fragments by colony blotting using filter membranes is practical for the isolation of human Fab fragments to major antigens of pathogens. An oligoclonal culture can also be used, and is a partial application of Epstein-Barr virus transformation of peripheral lymphocytes. Using these procedures, neutralizing antibody Fab fragments to various antigens can be obtained with a sufficient level of cloning efficacy. Chain shuffling and site-directed mutagenesis are also useful ways to improve the quality of the cloned antibody Fab fragments.
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Affiliation(s)
- Mohamed Al-Rubeai
- Dept. Chemical & Biochemical, Engineering, University College, Dublin, Belfield, Dublin 4, Ireland
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10
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Naumann JM, Küttner G, Bureik M. Expression and Secretion of a CB4-1 scFv–GFP Fusion Protein by Fission Yeast. Appl Biochem Biotechnol 2010; 163:80-9. [DOI: 10.1007/s12010-010-9018-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Accepted: 06/17/2010] [Indexed: 11/28/2022]
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11
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Mandrika I, Prusis P, Bergström J, Yahorava S, Wikberg JES. Improving the affinity of antigens for mutated antibodies by use of statistical molecular design. J Pept Sci 2008; 14:786-96. [DOI: 10.1002/psc.999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Tao YL, Cheng XJ, Fu YF, Tsukamoto H, Yoshihara E, Tachibana H. Modification of a human monoclonal antibody Fab fragment specific for Plasmodium falciparum 19-kDa C-terminal merozoite surface protein 1 by site-directed mutagenesis. Parasitol Res 2008; 103:429-33. [PMID: 18446371 DOI: 10.1007/s00436-008-0994-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
Abstract
We recently produced human monoclonal antibody Fab fragments specific for the 19-kDa C-terminal merozoite surface protein 1 of Plasmodium falciparum in a bacterial expression system. The effect of single amino acid modifications in the third complementarity-determining regions of the heavy and light chains on affinity was examined in one of the Fab fragments, Pf25. Recombination polymerase chain reaction was used to modify Tyr(92) or Ile(97) in the light chain and Val(101) or Trp(107) in the heavy chain. No effective replacements for Tyr(92) and Val(101) were found, but possible substitutions of Ile(97) with Gly, Leu, Glu, Ala and Ser, and of Trp(107) with Arg and Ser were demonstrated. Of these modified Fab fragments, the affinities of Fabs with Ile(97)-Leu and Trp(107)-Ser mutations were slightly higher than that of the original Fab. The effects of these modifications on the antigen-antibody interaction are discussed.
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Affiliation(s)
- Yan-Lin Tao
- Department of Medical Microbiology and Parasitology, Fudan University School of Medicine, Shanghai, 200032, China
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13
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Gach JS, Quendler H, Strobach S, Katinger H, Kunert R. Structural analysis and in vivo administration of an anti-idiotypic antibody against mAb 2F5. Mol Immunol 2007; 45:1027-34. [PMID: 17804071 DOI: 10.1016/j.molimm.2007.07.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Revised: 07/24/2007] [Accepted: 07/26/2007] [Indexed: 01/19/2023]
Abstract
Anti-idiotypic antibody (Ab2) 3H6 is directed against the human monoclonal antibody 2F5, which is one of a few neutralising antibodies against HIV-1. Since the binding epitope of 2F5 is cryptic and no neutralising immune response could be elicited by several potential vaccines comprising this region, Ab2/3H6 represents a potent vaccine candidate for active immunisation. Here we describe the molecular features of Ab2/3H6 after changing the antigen binding specificity by single point mutations in the complementarity-determining region 3 of the Ab2/3H6 heavy chain. The resulting Ab2/3H6 mutants were compared in several experimental settings to the wild type Ab2/3H6 Fab fragment. Moreover, we report about an immunisation study with Ab2/3H6 Fab variants, which elicited a specific 2F5-like humoral immune response in BALB/c mice.
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Affiliation(s)
- Johannes S Gach
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
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14
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Mandrika I, Prusis P, Yahorava S, Tars K, Wikberg JES. QSAR of multiple mutated antibodies. J Mol Recognit 2007; 20:97-102. [PMID: 17421049 DOI: 10.1002/jmr.817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this study was to develop predictive quantitative structure-activity relationship (QSAR) modeling for antibody-peptide interactions. A small single chain antibody library was designed and manufactured around the murine anti-p24 (HIV-1) monoclonal antibody CB4-1 by use of statistical molecular design (SMD) principles and site directed mutagenesis, and its affinity for a p24 derived antigen was determined by fluorescence polarization. A satisfactory QSAR model (Q(2) = 0.74, R(2) = 0.88) was derived by correlating the affinity data to physicochemical property scales of the amino acids varied in the library. The model explains most of the antibody-antigen interactions of the studied set, and provides insights into the molecular mechanism involved in antigen binding.
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Affiliation(s)
- Ilona Mandrika
- Department of Pharmaceutical Pharmacology, Uppsala University, SE-751 24 Uppasala, Sweden
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15
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Hilpert K, Winkler DFH, Hancock REW. Cellulose-bound Peptide Arrays: Preparation and Applications. Biotechnol Genet Eng Rev 2007; 24:31-106. [DOI: 10.1080/02648725.2007.10648093] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Otte L, Knaute T, Schneider-Mergener J, Kramer A. Molecular basis for the binding polyspecificity of an anti-cholera toxin peptide 3 monoclonal antibody. J Mol Recognit 2006; 19:49-59. [PMID: 16273596 DOI: 10.1002/jmr.757] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The onset of autoimmune diseases is proposed to involve binding promiscuity of antibodies (Abs) and T-cells, an often reported yet poorly understood phenomenon. Here, we attempt to approach two questions: first, is binding promiscuity a general feature of monoclonal antibodies (mAbs) and second, what is the molecular basis for polyspecificity? To this end, the anti-cholera toxin peptide 3 (CTP3) mAb TE33 was investigated for polyspecific binding properties. Screening of phage display libraries identified two epitope-unrelated peptides that specifically bound TE33 with affinities similar to or 100-fold higher than the wild-type epitope. Substitutional analyses revealed distinct key residue patterns recognized by the antibody suggesting a unique binding mode for each peptide. A database query with one of the consensus motifs and a subsequent binding study uncovered 45 peptides (derived from heterologous proteins) that bound TE33. To better understand the structural basis of the observed polyspecificity we modeled the new cyclic epitope in complex with TE33. The interactions between this peptide and TE33 suggested by our model are substantially different from the interactions observed in the X-ray structure of the wild-type epitope complex. However, the overall binding conformation of the peptides is similar. Together, our results support the theory of a general polyspecific potential of mAbs.
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Affiliation(s)
- Livia Otte
- Institut für Medizinische Immunologie, Charité-Universitätsmedizin Berlin, Berlin, Germany
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Raes J, Van de Peer Y. Functional divergence of proteins through frameshift mutations. Trends Genet 2005; 21:428-31. [PMID: 15951050 DOI: 10.1016/j.tig.2005.05.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2004] [Revised: 04/21/2005] [Accepted: 05/26/2005] [Indexed: 11/21/2022]
Abstract
Frameshift mutations are generally considered to be deleterious and of little importance for the evolution of novel gene functions. However, by screening an exhaustive set of vertebrate gene families, we found that, when a second transcript encoding the original gene product compensates for this mutation, frameshift mutations can be retained for millions of years and enable new gene functions to be acquired.
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Affiliation(s)
- Jeroen Raes
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology (VIB), Ghent University, Technologiepark 927, B-9052 Ghent, Belgium
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18
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Tachibana H, Matsumoto N, Cheng XJ, Tsukamoto H, Yoshihara E. Improved affinity of a human anti-Entamoeba histolytica Gal/GalNAc lectin Fab fragment by a single amino acid modification of the light chain. CLINICAL AND DIAGNOSTIC LABORATORY IMMUNOLOGY 2005; 11:1085-8. [PMID: 15539510 PMCID: PMC524788 DOI: 10.1128/cdli.11.6.1085-1088.2004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We previously produced, in Escherichia coli, a human monoclonal antibody Fab fragment, CP33, specific for the galactose- and N-acetyl-D-galactosamine-inhibitable lectin of Entamoeba histolytica. To prepare antibodies with a higher affinity to the lectin, recombination PCR was used to exchange Ser91 and Arg96 in the third complementarity-determining region of the light chain with other amino acids. The screening of 200 clones of each exchange by an indirect fluorescent antibody test showed that 14 clones for Ser91 and nine clones for Arg96 reacted strongly with E. histolytica trophozoites. Sequence analyses revealed that the substituted amino acids at Ser91 were Ala in five clones, Gly in three clones, Pro in two clones, and Val in two clones, while the amino acid at position 96 was substituted with Leu in three clones. The remaining eight clones exhibited no amino acid change at position 91 or 96. These mutant Fab fragments were purified and subjected to a surface plasmon resonance assay to measure the affinity of these proteins to the cysteine-rich domain of lectin. Pro or Gly substitution for Ser91 caused an increased affinity of the Fab, but substitution with Ala or Val did not. The replacement of Arg96 with Leu did not affect affinity. These results demonstrate that modification of antibody genes by recombination PCR is a useful method for affinity maturation and that amino acid substitution at position 91 yields Fabs with increased affinity for the lectin.
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Affiliation(s)
- Hiroshi Tachibana
- Department of Infectious Diseases, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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Olsen RJ, Mazlo J, Koepsell SA, McKeithan TW, Hinrichs SH. Minimal structural elements of an inhibitory anti-ATF1/CREB single-chain antibody fragment (scFv41.4). HYBRIDOMA AND HYBRIDOMICS 2003; 22:65-77. [PMID: 12831531 DOI: 10.1089/153685903321947987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Antibody variable domains represent potential structural models for the rational design of therapeutic molecules that bind cellular proteins with high affinity and specificity. The Activating Transcription Factor 1 (ATF1)/Cyclic AMP Response Element Binding Protein (CREB) family of transcription factors are particularly relevant targets due to their strong association with melanoma and clear cell sarcoma. Biochemical and structural investigations were performed to optimize a single-chain antibody fragment (scFv), scFv41.4, that disrupts the binding of ATF1/CREB to cyclic-AMP response elements (CRE) in vitro and inhibits transcriptional activation in cells. Molecular modeling and ligand docking simulations suggested that scFv41.4 could function as a disulfide-deficient single domain scFv. Functional studies verified that deletion of the light chain did not result in reduced inhibitory activity. The isolated heavy chain was predicted to assume a relaxed structural conformation that maintained a functional antigen binding pocket. The minimal structural elements necessary for intracellular function were further analyzed by selective deletion of CDR1 and CDR2. V(H)-CDR1 and V(H)-CDR3 were shown to play a key role in antigen binding activity, but V(H)-CDR2 was dispensable. Thus, scFv41.4 represents a unique molecule with potential for use in the design of peptidomimetic derivatives having therapeutic application to human cancer.
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Affiliation(s)
- R J Olsen
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198-6495, USA
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Marchalonis JJ, Adelman MK, Robey IF, Schluter SF, Edmundson AB. Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humans. J Mol Recognit 2001; 14:110-21. [PMID: 11301481 DOI: 10.1002/jmr.527] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This review considers definitions of the specificity of antibodies including the development of recent concepts of recognition polyspecificity and epitope promiscuity. Using sets of homologous and unrelated peptides derived from the sequences of immunoglobulin and T cell receptor chains we offer operational definitions of cross-reactivity by investigating correlations of either identities in amino acid sequence, or in hydrophobicity/hydrophilicity profiles with degree of binding in enzyme-linked immunosorbent assays. Polyreactivity, or polyspecificity, are terms used to denote binding of a monoclonal antibody or purified antibody preparation to large complex molecules that are structurally unrelated, such as thyroglobulin and DNA. As a first approximation, there is a linear correlation between degree of sequence identity or hydrophobicity/hydrophilicity and antigenic cross-binding. However, catastrophic interchanges of amino acids can occur where changing of one amino acid out of 16 in a synthetic peptide essentially eliminates binding to certain antibodies. An operational definition of epitope promiscuity for peptides is the case where two peptides show little or no identity in amino acid sequence but bind strongly to the same antibody as shown by either direct binding or competitive inhibition. Analysis of antibodies of humans and sharks, the two most divergent species in evolution to express antibodies and the combinatorial immune response, indicates that the capacity for both exquisite specificity and epitope recognition promiscuity are essential conserved features of individual vertebrate antibodies.
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Affiliation(s)
- J J Marchalonis
- Microbiology and Immunology, College of Medicine, University of Arizona, Tucson, Arizona, USA.
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