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Li R, Wilderotter S, Stoddard M, Van Egeren D, Chakravarty A, Joseph-McCarthy D. Computational identification of antibody-binding epitopes from mimotope datasets. Front Bioinform 2024; 4:1295972. [PMID: 38463209 PMCID: PMC10920257 DOI: 10.3389/fbinf.2024.1295972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: A fundamental challenge in computational vaccinology is that most B-cell epitopes are conformational and therefore hard to predict from sequence alone. Another significant challenge is that a great deal of the amino acid sequence of a viral surface protein might not in fact be antigenic. Thus, identifying the regions of a protein that are most promising for vaccine design based on the degree of surface exposure may not lead to a clinically relevant immune response. Methods: Linear peptides selected by phage display experiments that have high affinity to the monoclonal antibody of interest ("mimotopes") usually have similar physicochemical properties to the antigen epitope corresponding to that antibody. The sequences of these linear peptides can be used to find possible epitopes on the surface of the antigen structure or a homology model of the antigen in the absence of an antigen-antibody complex structure. Results and Discussion: Herein we describe two novel methods for mapping mimotopes to epitopes. The first is a novel algorithm named MimoTree that allows for gaps in the mimotopes and epitopes on the antigen. More specifically, a mimotope may have a gap that does not match to the epitope to allow it to adopt a conformation relevant for binding to an antibody, and residues may similarly be discontinuous in conformational epitopes. MimoTree is a fully automated epitope detection algorithm suitable for the identification of conformational as well as linear epitopes. The second is an ensemble approach, which combines the prediction results from MimoTree and two existing methods.
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Affiliation(s)
- Rang Li
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Sabrina Wilderotter
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | | | - Debra Van Egeren
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, United States
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Liang S, Zhang S, Bao Y, Zhang Y, Liu X, Yao H, Liu G. Combined Immunoinformatics to Design and Evaluate a Multi-Epitope Vaccine Candidate against Streptococcus suis Infection. Vaccines (Basel) 2024; 12:137. [PMID: 38400121 PMCID: PMC10892848 DOI: 10.3390/vaccines12020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Streptococcus suis (S. suis) is a zoonotic pathogen with multiple serotypes, and thus, multivalent vaccines generating cross-protection against S. suis infections are urgently needed to improve animal welfare and reduce antibiotic abuse. In this study, we established a systematic and comprehensive epitope prediction pipeline based on immunoinformatics. Ten candidate epitopes were ultimately selected for building the multi-epitope vaccine (MVSS) against S. suis infections. The ten epitopes of MVSS were all derived from highly conserved, immunogenic, and virulence-associated surface proteins in S. suis. In silico analyses revealed that MVSS was structurally stable and affixed with immune receptors, indicating that it would likely trigger strong immunological reactions in the host. Furthermore, mice models demonstrated that MVSS elicited high titer antibodies and diminished damages in S. suis serotype 2 and Chz infection, significantly reduced sequelae, induced cytokine transcription, and decreased organ bacterial burdens after triple vaccination. Meanwhile, anti-rMVSS serum inhibited five important S. suis serotypes in vitro, exerted beneficial protective effects against S. suis infections and significantly reduced histopathological damage in mice. Given the above, it is possible to develop MVSS as a universal subunit vaccine against multiple serotypes of S. suis infections.
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Affiliation(s)
- Song Liang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Shidan Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Yinli Bao
- Engineering Research Center for the Prevention and Control of Animal Original Zoonosis, Fujian Province University, College of Life Science, Longyan University, Longyan 364012, China
| | - Yumin Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyi Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangjin Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Animal Bacteriology, Ministry of Agriculture, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Sanya 572000, China
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Nagasawa N, Kimura R, Akagawa M, Shirai T, Sada M, Okayama K, Sato-Fujimoto Y, Saito M, Kondo M, Katayama K, Ryo A, Kuroda M, Kimura H. Molecular Evolutionary Analyses of the Spike Protein Gene and Spike Protein in the SARS-CoV-2 Omicron Subvariants. Microorganisms 2023; 11:2336. [PMID: 37764181 PMCID: PMC10537508 DOI: 10.3390/microorganisms11092336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
To better understand the evolution of the SARS-CoV-2 Omicron subvariants, we performed molecular evolutionary analyses of the spike (S) protein gene/S protein using advanced bioinformatics technologies. First, time-scaled phylogenetic analysis estimated that a common ancestor of the Wuhan, Alpha, Beta, Delta variants, and Omicron variants/subvariants diverged in May 2020. After that, a common ancestor of the Omicron variant generated various Omicron subvariants over one year. Furthermore, a chimeric virus between the BM.1.1.1 and BJ.1 subvariants, known as XBB, diverged in July 2021, leading to the emergence of the prevalent subvariants XBB.1.5 and XBB.1.16. Next, similarity plot (SimPlot) data estimated that the recombination point (breakpoint) corresponded to nucleotide position 1373. As a result, XBB.1.5 subvariants had the 5' nucleotide side from the breakpoint as a strain with a BJ.1 sequence and the 3' nucleotide side as a strain with a BM.1.1.1 sequence. Genome network data showed that Omicron subvariants were genetically linked with the common ancestors of the Wuhan and Delta variants, resulting in many amino acid mutations. Selective pressure analysis estimated that the prevalent subvariants, XBB.1.5 and XBB.1.16, had specific amino acid mutations, such as V445P, G446S, N460K, and F486P, located in the RBD when compared with the BA.4 and BA.5 subvariants. Moreover, some representative immunogenicity-associated amino acid mutations, including L452R, F486V, R493Q, and V490S, were also found in these subvariants. These substitutions were involved in the conformational epitopes, implying that these mutations affect immunogenicity and vaccine evasion. Furthermore, these mutations were identified as positive selection sites. These results suggest that the S gene/S protein Omicron subvariants rapidly evolved, and mutations observed in the conformational epitopes may reduce the effectiveness of the current vaccine, including bivalent vaccines such as mRNA vaccines containing the BA.4/BA.5 subvariants.
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Affiliation(s)
- Norika Nagasawa
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Ryusuke Kimura
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi-shi 371-8514, Gunma, Japan
| | - Mao Akagawa
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo-ku, Tokyo 113-8431, Japan;
| | - Tatsuya Shirai
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
| | - Mitsuru Sada
- Department of Respiratory Medicine, Kyourin University School of Medicine, 6-20-2, Shinkawa, Mitaka-shi 181-8611, Tokyo, Japan;
| | - Kaori Okayama
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
| | - Yuka Sato-Fujimoto
- Department of Medical Technology, Gunma Paz University School of Medical Science and Technology, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan;
| | - Makoto Saito
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Mayumi Kondo
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
| | - Kazuhiko Katayama
- Laboratory of Viral Infection Control, Ōmura Satoshi Memorial Institute, Graduate School of Infection Control Sciences, Kitasato University, 5-9-1, Shirogane, Minato-ku, Tokyo 108-8641, Japan;
| | - Akihide Ryo
- Department of Virology III, National Institute of Infectious Diseases, 4-7-1, Gakuen, Musashimurayama-shi 208-0011, Tokyo, Japan;
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku-ku, Tokyo 162-8640, Japan;
| | - Hirokazu Kimura
- Department of Health Science, Gunma Paz University Graduate School of Health Sciences, 1-7-1, Tonya-machi, Takasaki-shi 370-0006, Gunma, Japan; (N.N.); (K.O.)
- Advanced Medical Science Research Center, Gunma Paz University Research Institute, 1338-4, Shibukawa, Shibukawa-shi 377-0008, Gunma, Japan; (R.K.); (T.S.)
- Department of Clinical Engineering, Gunma Paz University School of Medical Science and Technology, Takasaki-shi 370-0006, Gunma, Japan; (M.S.); (M.K.)
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Ahammer L, Unterhauser J, Eidelpes R, Meisenbichler C, Nothegger B, Covaciu CE, Cova V, Kamenik AS, Liedl KR, Breuker K, Eisendle K, Reider N, Letschka T, Tollinger M. Ascorbylation of a Reactive Cysteine in the Major Apple Allergen Mal d 1. Foods 2022; 11:2953. [PMID: 36230029 PMCID: PMC9562000 DOI: 10.3390/foods11192953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
The protein Mal d 1 is responsible for most allergic reactions to apples (Malus domestica) in the northern hemisphere. Mal d 1 contains a cysteine residue on its surface, with its reactive side chain thiol exposed to the surrounding food matrix. We show that, in vitro, this cysteine residue is prone to spontaneous chemical modification by ascorbic acid (vitamin C). Using NMR spectroscopy and mass spectrometry, we characterize the chemical structure of the cysteine adduct and provide a three-dimensional structural model of the modified apple allergen. The S-ascorbylated cysteine partially masks a major IgE antibody binding site on the surface of Mal d 1, which attenuates IgE binding in sera of apple-allergic patients. Our results illustrate, from a structural perspective, the role that chemical modifications of allergens with components of the natural food matrix can play.
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Affiliation(s)
- Linda Ahammer
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Jana Unterhauser
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Reiner Eidelpes
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Christina Meisenbichler
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Bettina Nothegger
- Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Claudia E. Covaciu
- Department of Dermatology, Venerology and Allergology, Central Teaching Hospital, 39100 Bolzano, Italy
| | - Valentina Cova
- Department of Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer, Italy
| | - Anna S. Kamenik
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Eisendle
- Department of Dermatology, Venerology and Allergology, Central Teaching Hospital, 39100 Bolzano, Italy
| | - Norbert Reider
- Department of Dermatology, Venerology and Allergology, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Letschka
- Department of Applied Genomics and Molecular Biology, Laimburg Research Centre, 39040 Auer, Italy
| | - Martin Tollinger
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria
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Hazebrouck S, Patil SU, Guillon B, Lahood N, Dreskin SC, Adel-Patient K, Bernard H. Immunodominant conformational and linear IgE epitopes lie in a single segment of Ara h 2. J Allergy Clin Immunol 2022; 150:131-139. [PMID: 35150723 PMCID: PMC10440805 DOI: 10.1016/j.jaci.2021.12.796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/16/2021] [Accepted: 12/27/2021] [Indexed: 11/21/2022]
Abstract
BACKGROUND Contribution of conformational epitopes to the IgE reactivity of peanut allergens Ara h 2 and Ara h 6 is at least as important as that of the linear epitopes. However, little is known about these conformational IgE-binding epitopes. OBJECTIVE We investigated the distribution of conformational epitopes on chimeric 2S-albumins. METHODS Recombinant chimeras were generated by exchanging structural segments between Ara h 2 and Ara h 6. Well-refolded chimeras, as verified by circular dichroism analysis, were then used to determine the epitope specificity of mAbs by performing competitive inhibition of IgG binding. Furthermore, we delineated the contribution of each segment to the overall IgE reactivity of both 2S-albumins by measuring the chimeras' IgE-binding capacity with sera from 21 patients allergic to peanut. We finally assessed chimeras' capacity to trigger mast cell degranulation. RESULTS Configuration of the conformational epitopes was preserved in the chimeras. Mouse IgG mAbs, raised against natural Ara h 6, and polyclonal human IgE antibodies recognized different conformational epitopes distributed all along Ara h 6. In contrast, we identified human IgG mAbs specific to different Ara h 2 linear or conformational epitopes located in all segments except the C-terminal one. The major conformational IgE-binding epitope of Ara h 2 was located in a segment located between residues 33 and 81 that also contains the major linear hydroxyproline-containing epitope. Accordingly, this segment is critical for the capacity of Ara h 2 to induce mast cell degranulation. CONCLUSIONS Chimeric 2S-albumins provide new insights on the conformational IgE-binding epitopes of Ara h 2 and Ara h 6. Proximity of the immunodominant linear and conformational IgE-binding epitopes probably contributes to the high allergenic potency of Ara h 2.
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Affiliation(s)
- Stéphane Hazebrouck
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France.
| | - Sarita U Patil
- Department of Medicine, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, the Food Allergy Center, Massachusetts General Hospital for Children, and Harvard Medical School, Boston, Mass
| | - Blanche Guillon
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
| | - Nicole Lahood
- Department of Medicine, Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, the Food Allergy Center, Massachusetts General Hospital for Children, and Harvard Medical School, Boston, Mass
| | - Stephen C Dreskin
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado-Denver, Aurora, Colo
| | - Karine Adel-Patient
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
| | - Hervé Bernard
- Université Paris Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Gif-sur-Yvette, France
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Wang EY, Dai Y, Rosen CE, Schmitt MM, Dong MX, Ferré EM, Liu F, Yang Y, González-Hernández JA, Meffre E, Hinchcliff M, Koumpouras F, Lionakis MS, Ring AM. High-throughput identification of autoantibodies that target the human exoproteome. Cell Rep Methods 2022; 2:100172. [PMID: 35360706 PMCID: PMC8967185 DOI: 10.1016/j.crmeth.2022.100172] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 12/11/2022]
Abstract
Autoantibodies that recognize extracellular proteins (the exoproteome) exert potent biological effects but are challenging to detect. Here, we developed rapid extracellular antigen profiling (REAP), a high-throughput technique for the comprehensive discovery of exoproteome-targeting autoantibodies. Patient samples are applied to a genetically barcoded yeast surface display library containing 2,688 human extracellular proteins. Antibody-coated yeast are isolated, and sequencing of barcodes is used to identify displayed antigens. To benchmark REAP's performance, we screened 77 patients with autoimmune polyglandular syndrome type 1 (APS-1). REAP sensitively and specifically detected both known and previously unidentified autoantibodies in APS-1. We further screened 106 patients with systemic lupus erythematosus (SLE) and identified numerous autoantibodies, several of which were associated with disease severity or specific clinical manifestations and exerted functional effects on cell signaling ex vivo. These findings demonstrate the utility of REAP to atlas the expansive landscape of exoproteome-targeting autoantibodies and their impacts on patient health outcomes.
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Affiliation(s)
- Eric Y. Wang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Connor E. Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monica M. Schmitt
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mei X. Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Elise M.N. Ferré
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Eric Meffre
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monique Hinchcliff
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Fotios Koumpouras
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michail S. Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy & Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron M. Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06510, USA
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7
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Tang H, Zhu R, Waldman M, Zhu Q. Structural determinants of the dominant conformational epitopes of phospholipase A2 receptor in primary membranous nephropathy. J Biol Chem 2022; 298:101605. [PMID: 35065076 DOI: 10.1016/j.jbc.2022.101605] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/27/2022] Open
Abstract
Anti-phospholipase A2 receptor autoantibody (PLA2R-Ab) plays a critical role in the pathogenesis of primary membranous nephropathy (PMN), an autoimmune kidney disease characterized by immune deposits in the glomerular subepithelial spaces and proteinuria. However, the mechanism of how PLA2R-Abs interact with the conformational epitope(s) of PLA2R has remained elusive. PLA2R is a single transmembrane helix receptor containing ten extracellular domains that begin with a CysR domain followed by a FnII and eight CTLD domains. Here, we examined the interactions of PLA2R-Ab with the full PLA2R protein, N-terminal domain truncations, and C-terminal domain deletions under either denaturing or physiological conditions. Our data demonstrate that the PLA2R-Abs against the dominant epitope (the N-terminal CysR-CTLD1 triple domain) possess weak cross-reactivities to the C-terminal domains beyond CTLD1. Moreover, both the CysR and CTLD1 domains are required to form a conformational epitope for PLA2R-Ab interaction, with FnII serving as a linker domain. Upon close examination, we also observed that patients with newly diagnosed PMN carry two populations of PLA2R-Abs in sera that react to the denatured CysR-CTLD3 (the PLA2R-Ab1) and denatured CysR-CTLD1 (the PLA2R-Ab2) domain complexes on Western blots, respectively. Furthermore, the PLA2R-Ab1 appeared at an earlier time point than PLA2R-Ab2 in patients, whereas the increased levels of PLA2R-Ab2 coincided with the worsening of proteinuria. In summary, our data support that an integrated folding of the three PLA2R N-terminal domains, CysR, FnII, and CTLD1, is a prerequisite to forming the PLA2R conformational epitope and that the dominant epitope-reactive PLA2R-Ab2 plays a critical role in PMN clinical progression.
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Ahn WS, Kim TS, Park YJ, Park YK, Kim HD, Kim J. Production, characterization, and epitope mapping of monoclonal antibodies of ribosomal protein S3 (rpS3). Anim Cells Syst (Seoul) 2021; 25:323-336. [PMID: 34745438 PMCID: PMC8567880 DOI: 10.1080/19768354.2021.1980100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Ribosomal protein S3 (rpS3), a member of 40S small ribosomal subunit, is a multifunctional protein with various extra-ribosomal functions including DNA repair endonuclease activity and is secreted from cancer cells. Therefore, antibodies with high specificity against rpS3 protein could be useful cancer biomarkers. In this study, polyclonal antibody (pAb) and monoclonal antibodies (mAbs) were raised against rpS3 protein and epitope mapping was performed for each antibody; the amino acid residues of rpS3 were scanned from amino acid 185 to 243 through peptide scanning to reveal the epitopes of each mAb. Results showed that pAb R2 has an epitope from amino acid 203 to 230, mAb M7 has an epitope from amino acid 213 to 221, and mAb M8 has an epitope from amino acid 197 to 219. Taken together, novel mAbs and pAb against rpS3 were raised and mapped against rpS3 with different specific epitopes.
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Affiliation(s)
- Woo-Sung Ahn
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Tae-Sung Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Yong Jun Park
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Young Kwang Park
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Hag Dong Kim
- HAEL Lab, Korea University, Seoul, Republic of Korea
| | - Joon Kim
- Laboratory of Biochemistry, Division of Life Sciences, Korea University, Seoul, Republic of Korea.,HAEL Lab, Korea University, Seoul, Republic of Korea
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9
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Nakatsuji M, Sugiura K, Suda K, Sakurai M, Ubatani M, Muroya H, Okubo R, Noguchi R, Kamata Y, Fukutomi Y, Ishibashi O, Nishimura S, Inui T. Structure-based prediction of the IgE epitopes of the major dog allergen Can f 1. FEBS J 2021; 289:1668-1679. [PMID: 34699686 DOI: 10.1111/febs.16252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/10/2021] [Accepted: 10/25/2021] [Indexed: 11/28/2022]
Abstract
Allergy to dogs has become increasingly prominent worldwide. Seven dog allergens have been identified, including Canis familiaris allergen 1-7 (Can f 1-7). Although Can f 1 is a major dog allergen sensitized to 50-75% of dog-allergic subjects, its IgE epitopes have not been identified. The structural analysis of an allergen is important to identify conformational epitopes. In this study, we generated a recombinant Can f 1 protein and determined its crystal structure using X-ray crystallography. Can f 1 had a typical lipocalin fold, which is composed of an eight-stranded β-barrel and α-helix, and has high similarity to Can f 2, Can f 4, and Can f 6 in overall structure. However, the localizations of surface charges on these proteins were quite different. Based on sequence alignment and tertiary structure, we predicted five critical residues (His86, Glu98, Arg111, Glu138, and Arg152) for the IgE epitopes. The relevance of these residues to IgE reactivity was assessed by generating Can f 1 mutants with these residues substituted for alanine. Although the effects of the mutation on IgE binding depended on the sera of dog-allergic patients, H86A and R152A mutants showed reduced IgE reactivity compared with wild-type Can f 1. These results suggest that Can f 1 residues His86 and Arg152 are candidates for the IgE conformational epitope.
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Affiliation(s)
- Masatoshi Nakatsuji
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Keisuke Sugiura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Keisuke Suda
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Michiko Sakurai
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Miki Ubatani
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Haruka Muroya
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Rina Okubo
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Ryo Noguchi
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Yoichi Kamata
- Department of Food and Nutrition, Senri Kinran University, Suita, Osaka, Japan
| | - Yuma Fukutomi
- Clinical Research Center for Allergy and Rheumatology, Sagamihara National Hospital, Sagamihara, Kanagawa, Japan
| | - Osamu Ishibashi
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Shigenori Nishimura
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
| | - Takashi Inui
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan
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10
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da Silva BM, Myung Y, Ascher DB, Pires DEV. epitope3D: a machine learning method for conformational B-cell epitope prediction. Brief Bioinform 2021; 23:6407730. [PMID: 34676398 DOI: 10.1093/bib/bbab423] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/25/2021] [Accepted: 09/14/2021] [Indexed: 11/13/2022] Open
Abstract
The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been developed over the past two decades to assist in epitope prediction; however, they have presented limited performance and generalization, particularly for the identification of conformational B-cell epitopes. Here, we present epitope3D, a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date. Our method uses the concept of graph-based signatures to model epitope and non-epitope regions as graphs and extract distance patterns that are used as evidence to train and test predictive models. We show epitope3D outperforms available alternative approaches, achieving Mathew's Correlation Coefficient and F1-scores of 0.55 and 0.57 on cross-validation and 0.45 and 0.36 during independent blind tests, respectively.
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Affiliation(s)
- Bruna Moreira da Silva
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - YooChan Myung
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia.,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.,Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
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11
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Huang YL, Meyer D, Postel A, Tsai KJ, Liu HM, Yang CH, Huang YC, Berkley N, Deng MC, Wang FI, Becher P, Crooke H, Chang CY. Identification of a Common Conformational Epitope on the Glycoprotein E2 of Classical Swine Fever Virus and Border Disease Virus. Viruses 2021; 13:v13081655. [PMID: 34452520 PMCID: PMC8402670 DOI: 10.3390/v13081655] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/17/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Classical swine fever virus (CSFV) shares high structural and antigenic homology with bovine viral diarrhea virus (BVDV) and border disease virus (BDV). Because all three viruses can infect swine and elicit cross-reactive antibodies, it is necessary to differentiate among them with regard to serological diagnosis of classical swine fever. To understand the mechanism of cross-reactivity, it is important to define common or specific epitopes of these viruses. For this purpose, epitope mapping of six monoclonal antibodies (mAbs) was performed using recombinant expressed antigenic domains of CSFV and BDV E2 proteins. One CSFV-specific conformational epitope and one CSFV and BDV common epitope within domain B/C of E2 were identified. Site-directed mutagenesis confirmed that residues G725 and V738/I738 of the CSFV-specific epitope and P709/L709 and E713 of the second epitope are important for mAbs binding. Infection of CSFV in porcine cells was significantly reduced after pre-incubation of the cells with the domain B/C of E2 or after pre-incubation of CSFV with the mAbs detecting domain B/C. 3D structural modeling suggested that both epitopes are exposed on the surface of E2. Based on this, the identified epitopes represent a potential target for virus neutralization and might be involved in the early steps of CSFV infection.
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Affiliation(s)
- Yu-Liang Huang
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Denise Meyer
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (D.M.); (A.P.); (P.B.)
| | - Alexander Postel
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (D.M.); (A.P.); (P.B.)
| | - Kuo-Jung Tsai
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Hsin-Meng Liu
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Chia-Huei Yang
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Yu-Chun Huang
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Nicholas Berkley
- OIE Reference Laboratory for Classical Swine Fever, Animal and Plant Health Agency, New Haw KT15 3NB, Surrey, UK;
| | - Ming-Chung Deng
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
| | - Fun-In Wang
- School of Veterinary Medicine, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan;
| | - Paul Becher
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (D.M.); (A.P.); (P.B.)
| | - Helen Crooke
- OIE Reference Laboratory for Classical Swine Fever, Animal and Plant Health Agency, New Haw KT15 3NB, Surrey, UK;
- Correspondence: (H.C.); (C.-Y.C.); Tel.: +44-0-1932-357331 (H.C.); +886-2-2621-2111 (ext. 343) (C.-Y.C.)
| | - Chia-Yi Chang
- OIE Reference Laboratory for Classical Swine Fever, Animal Health Research Institute, Council of Agriculture, Executive Yuan, 376 Chung-Cheng Road, Tansui, New Taipei City 25158, Taiwan; (Y.-L.H.); (K.-J.T.); (H.-M.L.); (C.-H.Y.); (Y.-C.H.); (M.-C.D.)
- Correspondence: (H.C.); (C.-Y.C.); Tel.: +44-0-1932-357331 (H.C.); +886-2-2621-2111 (ext. 343) (C.-Y.C.)
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12
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Jiang X, Rao Q. Effect of Processing on Fish Protein Antigenicity and Allergenicity. Foods 2021; 10:969. [PMID: 33925068 DOI: 10.3390/foods10050969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/16/2021] [Accepted: 04/25/2021] [Indexed: 12/13/2022] Open
Abstract
Fish allergy is a life-long food allergy whose prevalence is affected by many demographic factors. Currently, there is no cure for fish allergy, which can only be managed by strict avoidance of fish in the diet. According to the WHO/IUIS Allergen Nomenclature Sub-Committee, 12 fish proteins are recognized as allergens. Different processing (thermal and non-thermal) techniques are applied to fish and fishery products to reduce microorganisms, extend shelf life, and alter organoleptic/nutritional properties. In this concise review, the development of a consistent terminology for studying food protein immunogenicity, antigenicity, and allergenicity is proposed. It also summarizes that food processing may lead to a decrease, no change, or even increase in fish antigenicity and allergenicity due to the change of protein solubility, protein denaturation, and the modification of linear or conformational epitopes. Recent studies investigated the effect of processing on fish antigenicity/allergenicity and were mainly conducted on commonly consumed fish species and major fish allergens using in vitro methods. Future research areas such as novel fish species/allergens and ex vivo/in vivo evaluation methods would convey a comprehensive view of the relationship between processing and fish allergy.
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13
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Khare S, Azevedo M, Parajuli P, Gokulan K. Conformational Changes of the Receptor Binding Domain of SARS-CoV-2 Spike Protein and Prediction of a B-Cell Antigenic Epitope Using Structural Data. Front Artif Intell 2021; 4:630955. [PMID: 33842877 PMCID: PMC8027118 DOI: 10.3389/frai.2021.630955] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/01/2021] [Indexed: 12/26/2022] Open
Abstract
COVID-19, the illness caused by the SARS-CoV-2 virus, is now a worldwide pandemic with mortality in hundreds of thousands as infections continue to increase. Containing the spread of this viral infection and decreasing the mortality rate is a major challenge. Identifying appropriate antigenic epitopes from the viral proteins is a very important task for vaccine production and the development of diagnostic kits and antibody therapy. A novel antigenic epitope would be specific to the SARS-CoV-2 virus and can distinguish infections caused by common cold viruses. In this study two approaches are employed to identify both continuous and conformational B-cell antigenic epitopes. To achieve this goal, we modeled a complete structure of the receptor binding domain (RBD) of the spike protein using recently deposited coordinates (6vxx, 6vsb, and 6w41) in the protein data bank. In addition, we also modeled the RBD-ACE2 receptor complex for SARS-CoV-2 using the SARS-CoV RBD-ACE2 complex (3D0J) as a reference model. Finally, structure based predicted antigenic epitopes were compared to the ACE2 binding region of RBD of SARS-CoV-2. The identified conformational epitopes show overlaps with the ACE2-receptor binding region of the RBD of SARS-CoV-2. Strategies defined in the current study identified novel antigenic epitope that is specific to the SARS-CoV-2 virus. Integrating such approach in the diagnosis can distinguish infections caused by common cold viruses from SARS-CoV-2 virus.
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Affiliation(s)
- Sangeeta Khare
- Division of Microbiology, National Center for Toxicological Research, United States-Food and Drug Administration, Jefferson, AR, United States
| | - Marli Azevedo
- Division of Microbiology, National Center for Toxicological Research, United States-Food and Drug Administration, Jefferson, AR, United States
| | - Pravin Parajuli
- Division of Microbiology, National Center for Toxicological Research, United States-Food and Drug Administration, Jefferson, AR, United States
| | - Kuppan Gokulan
- Division of Microbiology, National Center for Toxicological Research, United States-Food and Drug Administration, Jefferson, AR, United States
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14
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Chen YY, Li MS, Yun X, Xia F, Hu MJ, Jin T, Cao MJ, Lai D, Chen G, Liu GM. Site-Directed Mutations of Calcium-Binding Sites Contribute to Reducing the Immunoreactivity of the EF-Hand Sarcoplasmic Calcium-Binding Protein in Scylla paramamosain. J Agric Food Chem 2021; 69:428-436. [PMID: 33377774 DOI: 10.1021/acs.jafc.0c05733] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In order to reduce the immunoreactivity of sarcoplasmic calcium-binding protein (SCP), site-directed mutations were used to replace key amino acids in the conformational epitopes and calcium-binding sites. The mutant SCPs (mSCPs) were expressed in Escherichia coli, and their immunoreactivities were analyzed using iELISA and basophil activation assays. Furthermore, the structural changes of mSCPs were determined from the circular dichroism spectra. The iELISA results showed that mSCPs could effectively inhibit the binding of wild-type SCP (wtSCP) to sensitive serum, with inhibition rates that reached 90%. Moreover, mSCPs could downregulate the expression levels of CD63 and CD203c on the basophil surface. Compared with wtSCP, the peak values were significantly changed, and the calcium binding ability was impaired, which explained the decline in immunoreactivities of the mSCPs. All of the data confirmed that this approach was effective in reducing the immunoreactivity of SCP and could be applied to other shellfish allergens.
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Affiliation(s)
- Yi-Yu Chen
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Meng-Si Li
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Xiao Yun
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Fei Xia
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Meng-Jun Hu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Tengchuan Jin
- Hefei National Laboratory for Physical Sciences at Microscale, CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science & Technology of China, Hefei, Anhui 230026, China
| | - Min-Jie Cao
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
| | - Dong Lai
- The Second Affiliated Hospital of Xiamen Medical College, Xiamen, Fujian 361021, China
| | - Guixia Chen
- Women and Children's Hospital Affiliated to Xiamen University, Xiamen, Fujian 361003, China
| | - Guang-Ming Liu
- College of Food and Biological Engineering, Xiamen Key Laboratory of Marine Functional Food, Fujian Provincial Engineering Technology Research Center of Marine Functional Food, Jimei University, Xiamen, Fujian 361021, China
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15
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Jegatheeswaran S, Asnani A, Forman A, Hendel JL, Moore CJ, Nejatie A, Wang A, Wang JW, Auzanneau FI. Recognition of Dimeric Lewis X by Anti-Dimeric Le x Antibody SH2. Vaccines (Basel) 2020; 8:vaccines8030538. [PMID: 32957489 PMCID: PMC7563222 DOI: 10.3390/vaccines8030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The carbohydrate antigen dimeric Lewis X (DimLex), which accumulates in colonic and liver adenocarcinomas, is a valuable target to develop anti-cancer therapeutics. Using the native DimLex antigen as a vaccine would elicit an autoimmune response against the Lex antigen found on normal, healthy cells. Thus, we aim to study the immunogenic potential of DimLex and search internal epitopes displayed by DimLex that remain to be recognized by anti-DimLex monoclonal antibodies (mAbs) but no longer possess epitopes recognized by anti-Lex mAbs. In this context, we attempted to map the epitope recognized by anti-DimLex mAb SH2 by titrations and competitive inhibition experiments using oligosaccharide fragments of DimLex as well as Lex analogues. We compare our results with that reported for anti-Lex mAb SH1 and anti-polymeric Lex mAbs 1G5F6 and 291-2G3-A. While SH1 recognizes an epitope localized to the non-reducing end Lex trisaccharide, SH2, 1G5F6, and 291-2G3-A have greater affinity for DimLex conjugates than for Lex conjugates. We show, however, that the Lex trisaccharide is still an important recognition element for SH2, which (like 1G5F6 and 291-2G3-A) makes contacts with all three sugar units of Lex. In contrast to mAb SH1, anti-polymeric Lex mAbs make contact with the GlcNAc acetamido group, suggesting that epitopes extend further from the non-reducing end Lex. Results with SH2 show that this epitope is only recognized when DimLex is presented by glycoconjugates. We have reported that DimLex adopts two conformations around the β-d-GlcNAc-(1→3)-d-Gal bond connecting the Lex trisaccharides. We propose that only one of these conformations is recognized by SH2 and that this conformation is favored when the hexasaccharide is presented as part of a glycoconjugate such as DimLex-bovine serum albumin (DimLex-BSA). Proper presentation of the oligosaccharide candidate via conjugation to a protein or lipid is essential for the design of an anti-cancer vaccine or immunotherapeutic based on DimLex.
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Affiliation(s)
- Sinthuja Jegatheeswaran
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Immunology Department, University of Toronto, 1 King’s College Circle, Toronto, ON M5S-1A8, Canada
| | - Ari Asnani
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Universitas Jenderal Soedirman, Purwokerto, Jawa Tengah 53123, Indonesia
| | - Adam Forman
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S-3H6, Canada
| | - Jenifer L. Hendel
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Research and Development, Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14-3EB, UK
| | - Christopher J. Moore
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Quality Control, SteriMax Inc., 2770 Portland Dr, Oakville, ON L6H-6R4, Canada
| | - Ali Nejatie
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - An Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- SGS-CSTC Standards Technical Services Co., Ltd. 4/F, 4th Building, 889 Yishan Road, Xuhui District, Shanghai 200233, China
| | - Jo-Wen Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- IQVIA, QuintilesIMS, Clinical Research, 10188 Telesis Ct #400, San Diego, CA 92121, USA
| | - France-Isabelle Auzanneau
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Correspondence:
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16
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Opuni KFM, Koy C, Russ M, Reepmeyer M, Danquah BD, Weresow M, Alef A, Lorenz P, Thiesen HJ, Glocker MO. ITEM-THREE analysis of a monoclonal anti-malaria antibody reveals its assembled epitope on the pfMSP1 19 antigen. J Biol Chem 2020; 295:14987-14997. [PMID: 32848020 DOI: 10.1074/jbc.ra120.014802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/18/2020] [Indexed: 11/06/2022] Open
Abstract
Rapid diagnostic tests are first-line assays for diagnosing infectious diseases, such as malaria. To minimize false positive and false negative test results in population-screening assays, high-quality reagents and well-characterized antigens and antibodies are needed. An important property of antigen-antibody binding is recognition specificity, which best can be estimated by mapping an antibody's epitope on the respective antigen. We have cloned a malarial antigen-containing fusion protein, MBP-pfMSP119, in Escherichia coli, which then was structurally and functionally characterized before and after high pressure-assisted enzymatic digestion. We then used our previously developed method, intact transition epitope mapping-targeted high-energy rupture of extracted epitopes (ITEM-THREE), to map the area on the MBP-pfMSP119 antigen surface that is recognized by the anti-pfMSP119 antibody G17.12. We identified three epitope-carrying peptides, 386GRNISQHQCVKKQCPQNSGCFRHLDE411, 386GRNISQHQCVKKQCPQNSGCFRHLDEREE414, and 415CKCLLNYKQE424, from the GluC-derived peptide mixture. These peptides belong to an assembled (conformational) epitope on the MBP-pfMSP119 antigen whose identification was substantiated by positive and negative control experiments. In conclusion, our data help to establish a workflow to obtain high-quality control data for diagnostic assays, including the use of ITEM-THREE as a powerful analytical tool. Data are available via ProteomeXchange: PXD019717.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany; Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health, University of Ghana, Legon, Ghana
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Maren Reepmeyer
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany
| | | | | | - Peter Lorenz
- Institute for Immunology, University Medicine Rostock, Rostock, Germany
| | | | - Michael O Glocker
- Proteome Center Rostock, University Medicine Rostock and University of Rostock, Rostock, Germany.
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17
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Aso J, Kimura H, Ishii H, Saraya T, Kurai D, Matsushima Y, Nagasawa K, Ryo A, Takizawa H. Molecular Evolution of the Fusion Protein ( F) Gene in Human Respirovirus 3. Front Microbiol 2020; 10:3054. [PMID: 32010105 PMCID: PMC6974460 DOI: 10.3389/fmicb.2019.03054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
To elucidate the evolution of human respirovirus 3 (HRV3), we performed detailed genetic analyses of the F gene (full-length) detected from hundreds of HRV3 strains obtained from various geographic regions. First, we performed time-scaled evolutionary analyses using the Bayesian Markov chain Monte Carlo method. Then, we performed analyses of phylodynamics, similarity, phylogenetic distance, selective pressure, and conformational B-cell epitope with the F-protein structural analyses. Time-scaled phylogenetic tree showed that the common ancestor of HRV3 and bovine respirovirus 3 diverged over 300 years ago and subdivided it into three major clusters and four subclusters during the most recent 100 years. The overall evolutionary rate was approximately 10-3 substitutions/site/year. Indigenous similarity was seen in the present strains, and the mean phylogenetic distance were 0.033. Many negative selection sites were seen in the ectodomain. The conformational epitopes did not correspond to the neutralizing antibody binding sites. These results suggest that the HRV3 F gene is relatively conserved and restricted in this diversity to preserve the protein function, although these strains form many branches on the phylogenetic tree. Furthermore, HRV3 reinfection may be responsible for discordances between the conformational epitopes and the neutralizing antibody binding sites of the F protein. These findings contribute to a better understanding of HRV3 virology.
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Affiliation(s)
- Jumpei Aso
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Tokyo, Japan
| | - Hirokazu Kimura
- Department of Health Science, Graduate School of Health Science, Gunma Paz University, Gunma, Japan.,Department of Microbiology, School of Medicine, Yokohama City University, Kanagawa, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Tokyo, Japan
| | - Takeshi Saraya
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Tokyo, Japan
| | - Daisuke Kurai
- Department of General Medicine, Division of Infectious Diseases, School of Medicine, Kyorin University, Tokyo, Japan
| | - Yuki Matsushima
- Division of Virology, Kawasaki City Institute for Public Health, Kanagawa, Japan
| | - Koo Nagasawa
- Department of Pediatrics, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Akihide Ryo
- Department of Microbiology, School of Medicine, Yokohama City University, Kanagawa, Japan
| | - Hajime Takizawa
- Department of Respiratory Medicine, School of Medicine, Kyorin University, Tokyo, Japan
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18
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Abstract
Attention to therapeutic monoclonal antibodies has been dramatically increasing year by year. Their highly specific targeting of antigens can provide very effective medical treatment, and the advent of molecular-targeting medicine is allowing development of a new generation of therapeutic agents. However, there is one critical obstacle to overcome. Most of the established therapeutic monoclonal antibodies have specificity for the primary structures of target antigens, although all proteins harbor original native intact structures for their own specific functions. Stereo-specific monoclonal antibodies recognizing conformational structures of target antigens may thus offer a markedly more versatile approach. Their application may change the very concepts underlying use of therapeutic antibodies.
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Affiliation(s)
- Kanta Tsumoto
- Molecular Bioengineering Laboratory, Division of Chemistry for Materials, 1577 Kurima-Machiya-cho, Tsu, Mie 514-8507, Japan
| | - Yushi Isozaki
- Molecular Bioengineering Laboratory, Division of Chemistry for Materials, 1577 Kurima-Machiya-cho, Tsu, Mie 514-8507, Japan
| | - Hisanori Yagami
- Intelectual Property Office (IPO), Organization for the Promotion of Regional Innovation, 1577 Kurima-Machiya-cho, Tsu, Mie 514-8507, Japan
| | - Masahiro Tomita
- Molecular Bioengineering Laboratory, Division of Chemistry for Materials, 1577 Kurima-Machiya-cho, Tsu, Mie 514-8507, Japan
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19
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Sojar H, Baron S, Sullivan JT, Garrett M, van Haaren MM, Hoffman J, Overbaugh J, Doranz BJ, Hicar MD. Monoclonal Antibody 2C6 Targets a Cross-Clade Conformational Epitope in gp41 with Highly Active Antibody-Dependent Cell Cytotoxicity. J Virol 2019; 93:e00772-19. [PMID: 31217246 DOI: 10.1128/JVI.00772-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 06/13/2019] [Indexed: 12/11/2022] Open
Abstract
Previous studies in our laboratory characterized a panel of highly mutated HIV-specific conformational epitope-targeting antibodies (Abs) from a panel of HIV-infected long-term nonprogressors (LTNPs). Despite binding HIV envelope protein and having a high number of somatic amino acid mutations, these Abs had poor neutralizing activity. Because of the evidence of antigen-driven selection and the long CDR3 region (21 amino acids [aa]), we further characterized the epitope targeting of monoclonal Ab (MAb) 76-Q3-2C6 (2C6). We confirmed that 2C6 binds preferentially to trimeric envelope and recognizes the clades A, B, and C SOSIP trimers. 2C6 binds gp140 constructs of clades A, B, C, and D, suggesting a conserved binding site that we localized to the ectodomain of gp41. Ab competition with MAb 50-69 suggested this epitope localizes near aa 579 to 613 (referenced to HXB2 gp160). Peptide library scanning showed consistent binding in this region but to only a single peptide. Lack of overlapping peptide binding supported a nonlinear epitope structure. The significance of this site is supported by 2C6 having Ab-dependent cell cytotoxicity (ADCC) against envelope proteins from two clades. Using 2C6 and variants, alanine scanning mutagenesis identified three amino acids (aa 592, 595, and 596) in the overlapping region of the previously identified peptide. Additional amino acids at sites 524 and 579 were also identified, helping explain its conformational requirement. The fact that different amino acids were included in the epitope depending on the targeted protein supports the conclusion that 2C6 targets a native conformational epitope. When we mapped these amino acids on the trimerized structure, they spanned across oligomers, supporting the notion that the epitope targeted by 2C6 lies in a recessed pocket between two gp41 oligomers. A complete understanding of the epitope specificity of ADCC-mediating Abs is essential for developing effective immunization strategies that optimize protection by these Abs.IMPORTANCE This paper further defines the function and area of the HIV trimeric envelope protein targeted by the monoclonal antibody 2C6. 2C6 binding is influenced by amino acid mutations across two separate gp41 sections of the envelope trimer. This epitope is recognized on multiple clades (variant groups of circulating viruses) of gp41, gp140 trimers, and SOSIP trimers. For the clades tested, 2C6 has robust ADCC. As the target of 2C6 is available in the major clades of HIV and has robust ADCC activity, further definition and appreciation of targeting of antibodies similar to 2C6 during vaccine development should be considered.
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20
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Opuni KFM, Al-Majdoub M, Yefremova Y, El-Kased RF, Koy C, Glocker MO. Mass spectrometric epitope mapping. Mass Spectrom Rev 2018; 37:229-241. [PMID: 27403762 DOI: 10.1002/mas.21516] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/23/2016] [Indexed: 06/06/2023]
Abstract
Mass spectrometric epitope mapping has become a versatile method to precisely determine a soluble antigen's partial structure that directly interacts with an antibody in solution. Typical lengths of investigated antigens have increased up to several 100 amino acids while experimentally determined epitope peptides have decreased in length to on average 10-15 amino acids. Since the early 1990s more and more sophisticated methods have been developed and have forwarded a bouquet of suitable approaches for epitope mapping with immobilized, temporarily immobilized, and free-floating antibodies. While up to now monoclonal antibodies have been mostly used in epitope mapping experiments, the applicability of polyclonal antibodies has been proven. The antibody's resistance towards enzymatic proteolysis has been of key importance for the two mostly applied methods: epitope excision and epitope extraction. Sample consumption has dropped to low pmol amounts on both, the antigen and the antibody. While adequate in-solution sample handling has been most important for successful epitope mapping, mass spectrometric analysis has been found the most suitable read-out method from early on. The rapidity by which mass spectrometric epitope mapping nowadays is executed outperforms all alternative methods. Thus, it can be asserted that mass spectrometric epitope mapping has reached a state of maturity, which allows it to be used in any mass spectrometry laboratory. After 25 years of constant and steady improvements, its application to clinical samples, for example, for patient characterization and stratification, is anticipated in the near future. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:229-241, 2018.
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Affiliation(s)
- Kwabena F M Opuni
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Mahmoud Al-Majdoub
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Yelena Yefremova
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Reham F El-Kased
- Microbiology and Immunology Faculty of Pharmacy, The British University in Egypt, Cairo, Egypt
| | - Cornelia Koy
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
| | - Michael O Glocker
- Proteome Center Rostock, University Medicine and Natural Science Faculty, University of Rostock, Rostock, Germany
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21
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Tian X, Qiu H, Zhou Z, Wang S, Fan Y, Li X, Chu R, Li H, Zhou R, Wang H. Identification of a Critical and Conformational Neutralizing Epitope in Human Adenovirus Type 4 Hexon. J Virol 2018; 92:e01643-17. [PMID: 29093098 DOI: 10.1128/JVI.01643-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023] Open
Abstract
Human adenovirus type 4 (HAdV-4) is an epidemic virus that contributes to serious acute respiratory disease (ARD) in both pediatric and adult patients. However, no licensed drug or vaccine is currently available to the civilian population. The identification of neutralizing epitopes of HAdV-4 should allow the development of a novel antiviral vaccine and a novel gene transfer vector, and an effective neutralizing monoclonal antibody (MAb) will be useful in developing appropriate antiviral drugs. In this study, we report that MAb MN4b shows strong neutralizing activity against HAdV-4. MN4b recognizes a conformational epitope (418AGSEK422) within hypervariable region 7 (HVR7). Mutations within this site permitted HAdV-4 mutants to escape neutralization by MN4b and to resist neutralization by animal and human anti-HAdV-4 sera. A recombinant virus, rAd3-A4R7-1, containing the identified neutralizing epitope in the HVR7 region of HAdV-3 hexon, successfully induced antiserum that inhibited HAdV-4 infection. These results indicate that a small surface loop of HAdV-4 hexon is a critical neutralization epitope for this virus. The generation of MN4b and the identification of this neutralizing epitope may be useful in developing therapeutic treatment, a subunit vaccine, and a novel vector that can escape preexisting neutralization for HAdV-4. IMPORTANCE Neutralizing antibodies are considered good tools for the prevention of human adenovirus type 4 (HAdV-4) infections. The identification of the epitopes recognized by such neutralizing antibodies is important for the generation of recombinant antiviral vaccines. However, until now, no neutralizing epitope has been reported for HAdV-4. Here, we developed a serotype-specific neutralizing MAb directed against HAdV-4, MN4b. We provide evidence that MN4b recognizes a conformational epitope within HVR7 of HAdV-4 hexon. Antisera generated to this conformational epitope displayed on HAdV-3 hexon inhibited infection of AD293 cells by HAdV-4. Our findings are very important for the development of therapeutic treatment, a subunit vaccine, and a novel vector for HAdV-4.
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22
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Guan J, Bywaters SM, Brendle SA, Ashley RE, Makhov AM, Conway JF, Christensen ND, Hafenstein S. High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16. Viruses 2017; 9:v9120374. [PMID: 29211035 PMCID: PMC5744149 DOI: 10.3390/v9120374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/13/2017] [Accepted: 11/18/2017] [Indexed: 01/14/2023] Open
Abstract
Cancers attributable to human papillomavirus (HPV) place a huge burden on the health of both men and women. The current commercial vaccines are genotype specific and provide little therapeutic benefit to patients with existing HPV infections. Identifying the conformational epitopes on the virus capsid supports the development of improved recombinant vaccines to maximize long-term protection against multiple types of HPV. Fragments of antibody (Fab) digested from the neutralizing monoclonal antibodies H16.V5 (V5) and H16.U4 (U4) were bound to HPV16 capsids and the structures of the two virus-Fab complexes were solved to near atomic resolution using cryo-electron microscopy. The structures reveal virus conformational changes, the Fab-binding mode to the capsid, the residues comprising the epitope and indicate a potential interaction of U4 with the minor structural protein, L2. Competition enzyme-linked immunosorbent assay (ELISA) showed V5 outcompetes U4 when added sequentially, demonstrating a steric interference even though the footprints do not overlap. Combined with our previously reported immunological and structural results, we propose that the virus may initiate host entry through an interaction between the icosahedral five-fold vertex of the capsid and receptors on the host cell. The highly detailed epitopes identified for the two antibodies provide a framework for continuing biochemical, genetic and biophysical studies.
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Affiliation(s)
- Jian Guan
- Department of Medicine, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Stephanie M Bywaters
- Department of Pathology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Sarah A Brendle
- Department of Pathology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Robert E Ashley
- Department of Medicine, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Alexander M Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 5th Ave, Pittsburgh, PA 15260, USA.
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 5th Ave, Pittsburgh, PA 15260, USA.
| | - Neil D Christensen
- Department of Pathology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
| | - Susan Hafenstein
- Department of Medicine, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, Millennium Science Complex, University Park, State College, PA 16802, USA.
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23
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Levin M, Rotthus S, Wendel S, Najafi N, Källström E, Focke-Tejkl M, Valenta R, Flicker S, Ohlin M. Multiple independent IgE epitopes on the highly allergenic grass pollen allergen Phl p 5. Clin Exp Allergy 2015; 44:1409-19. [PMID: 25262820 PMCID: PMC4278554 DOI: 10.1111/cea.12423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2014] [Revised: 07/06/2014] [Accepted: 08/15/2014] [Indexed: 11/30/2022]
Abstract
Background Group 5 allergens are small proteins that consist of two domains. They belong to the most potent respiratory allergens. Objective To determine the binding sites and to study allergic patients' IgE recognition of the group 5 allergen (Phl p 5) from timothy grass pollen using human monoclonal IgE antibodies that have been isolated from grass pollen allergic patients. Methods Using recombinant isoallergens, fragments, mutants and synthetic peptides of Phl p 5, as well as peptide-specific antibodies, the interaction of recombinant human monoclonal IgE and Phl p 5 was studied using direct binding and blocking assays. Cross-reactivity of monoclonal IgE with group 5 allergens in several grasses was studied and inhibition experiments with patients' polyclonal IgE were performed. Results Monoclonal human IgE showed extensive cross-reactivity with group 5 allergens in several grasses. Despite its small size of 29 kDa, four independent epitope clusters on isoallergen Phl p 5.0101, two in each domain, were recognized by human IgE. Isoallergen Phl p 5.0201 carried two of these epitopes. Inhibition studies with allergic patients' polyclonal IgE suggest the presence of additional IgE epitopes on Phl p 5. Conclusions & Clinical Relevance Our results reveal the presence of a large number of independent IgE epitopes on the Phl p 5 allergen explaining the high allergenic activity of this protein and its ability to induce severe allergic symptoms. High-density IgE recognition may be a general feature of many potent allergens and form a basis for the development of improved diagnostic and therapeutic procedures in allergic disease.
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Affiliation(s)
- M Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
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24
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Xin L, Jinyan G, Shengfa H, Yuanyuan W, Hongbing C. Identification of conformational antigenic epitopes and dominant amino acids of buffalo β-lactoglobulin. J Food Sci 2014; 79:T748-56. [PMID: 24689774 DOI: 10.1111/1750-3841.12409] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 01/22/2014] [Indexed: 11/29/2022]
Abstract
Major allergen β-lactoglobulin exists in many mammalian types of milk except human breast. Buffalo milk also contains this major allergen but the detailed information on its epitopes is not available. The aim of this work was to map and characterize its conformational antigenic epitopes. Sixty mimotopes of buffalo β-lactoglobulin were produced by biopanning of phage display peptide library and then 2 mimotopes, specific for sera from rabbit 1 and 2, respectively, were predicted to be conformational epitope candidates by the use of DNAStar and web tool of MIMOX. On the basis of bioinformation analysis, 5 conserved amino acid residues PL-ENK were identified in 2 conformational epitope sequences and 7 conformational epitopes were derived from 2 mimotopes by molecular modeling. The result showed that these conformational epitopes were located in the 2 regions on buffalo β-lactoglobulin and composed of 5 hydrophilic and 2 hydrophobic amino acids.
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Affiliation(s)
- Li Xin
- State Key Laboratory of Food Science and Technology, Nanchang Univ, Nanchang, 330047, China; School of life sciences and food engineering Nanchang Univ, Nanchang, 330047, China
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25
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Abstract
Random phage display library is used to map conformational as well as linear epitopes. These libraries are available in varying lengths and with circularization. We provide here a protocol conveying our experience using a commercially available peptide phage display library, which in our hands provides good results.
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26
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Dougall AM, Skwarczynski M, Khoshnejad M, Chandrudu S, Daly NL, Toth I, Loukas A. Lipid core peptide targeting the cathepsin D hemoglobinase of Schistosoma mansoni as a component of a schistosomiasis vaccine. Hum Vaccin Immunother 2013; 10:399-409. [PMID: 24231271 DOI: 10.4161/hv.27057] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The self-adjuvanting lipid core peptide (LCP) system offers a safe alternative vaccine delivery strategy, eliminating the need for additional adjuvants such as CpG Alum. In this study, we adopted the LCP as a scaffold for an epitope located on the surface of the cathepsin D hemoglobinase (Sm-CatD) of the human blood fluke Schistosoma mansoni. Sm-CatD plays a pivotal role in digestion of the fluke's bloodmeal and has been shown to be efficacious as a subunit vaccine in a murine model of human schistosomiasis. Using molecular modeling we showed that S. mansoni cathepsin D possesses a predicted surface exposed α-helix (A₂₆₃K) that corresponds to an immunodominant helix and target of enzyme-neutralizing antibodies against Necator americanus APR-1 (Na-APR-1), the orthologous protease and vaccine antigen from blood-feeding hookworms. The A₂₆₃K epitope was engineered as two peptide variants, one of which was flanked at both termini with a coil maintaining sequence, thereby promoting the helical characteristics of the native A₂₆₃K epitope. Some of the peptides were fused to a self-adjuvanting lipid core scaffold to generate LCPs. Mice were vaccinated with unadjuvanted peptides, peptides formulated with Freund's adjuvants, or LCPs. Antibodies generated to LCPs recognized native Sm-CatD within a soluble adult schistosome extract, and almost completely abolished its enzymatic activity in vitro. Using immunohistochemistry we showed that anti-LCP antibodies bound to the native Sm-CatD protein in the esophagus and anterior regions of the gastrodermis of adult flukes. Vaccines offer an alternative control strategy in the fight against schistosomiasis, and further development of LCPs containing multiple epitopes from this and other vaccine antigens should become a research priority.
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Affiliation(s)
- Annette M Dougall
- Australian Institute of Tropical Health and Medicine; Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Cairns, QLD Australia
| | - Mariusz Skwarczynski
- Australian Institute of Tropical Health and Medicine; Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Cairns, QLD Australia; The University of Queensland; School of Chemistry and Molecular Biosciences; St. Lucia; QLD Australia; The University of Queensland; School of Pharmacy; Wooloongabba, QLD Australia
| | - Makan Khoshnejad
- The University of Queensland; School of Chemistry and Molecular Biosciences; St. Lucia; QLD Australia
| | - Saranya Chandrudu
- The University of Queensland; School of Chemistry and Molecular Biosciences; St. Lucia; QLD Australia
| | - Norelle L Daly
- Australian Institute of Tropical Health and Medicine; Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Cairns, QLD Australia
| | - Istvan Toth
- Australian Institute of Tropical Health and Medicine; Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Cairns, QLD Australia; The University of Queensland; School of Chemistry and Molecular Biosciences; St. Lucia; QLD Australia; The University of Queensland; School of Pharmacy; Wooloongabba, QLD Australia
| | - Alex Loukas
- Australian Institute of Tropical Health and Medicine; Centre for Biodiscovery and Molecular Development of Therapeutics; James Cook University; Cairns, QLD Australia
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27
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Su HP, Golden JW, Gittis AG, Hooper JW, Garboczi DN. Structural basis for the binding of the neutralizing antibody, 7D11, to the poxvirus L1 protein. Virology 2007; 368:331-41. [PMID: 17688903 PMCID: PMC2100026 DOI: 10.1016/j.virol.2007.06.042] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 06/04/2007] [Accepted: 06/27/2007] [Indexed: 01/07/2023]
Abstract
Medical countermeasures to prevent or treat smallpox are needed due to the potential use of poxviruses as biological weapons. Safety concerns with the currently available smallpox vaccine indicate a need for research on alternative poxvirus vaccine strategies. Molecular vaccines involving the use of proteins and/or genes and recombinant antibodies are among the strategies under current investigation. The poxvirus L1 protein, encoded by the L1R open reading frame, is the target of neutralizing antibodies and has been successfully used as a component of both protein subunit and DNA vaccines. L1-specific monoclonal antibodies (e.g., mouse monoclonal antibody mAb-7D11, mAb-10F5) with potent neutralizing activity bind L1 in a conformation-specific manner. This suggests that proper folding of the L1 protein used in molecular vaccines will affect the production of neutralizing antibodies and protection. Here, we co-crystallized the Fab fragment of mAb-7D11 with the L1 protein. The crystal structure of the complex between Fab-7D11 and L1 reveals the basis for the conformation-specific binding as recognition of a discontinuous epitope containing two loops that are held together by a disulfide bond. The structure of this important conformational epitope of L1 will contribute to the development of molecular poxvirus vaccines and also provides a novel target for anti-poxvirus drugs. In addition, the sequence and structure of Fab-7D11 will contribute to the development of L1-targeted immunotherapeutics.
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Affiliation(s)
- Hua-Poo Su
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA
| | - Joseph W. Golden
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - Apostolos G. Gittis
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA
| | - Jay W. Hooper
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702
| | - David N. Garboczi
- Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 12441 Parklawn Drive, Rockville, MD 20852, USA
- *Corresponding author. Mailing address. 12441 Parklawn Drive, Rockville, Maryland 20852, USA. Phone: 301-496-4773. Fax: 301-402-0284. E-mail:
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