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Kimura R, Noda D, Liu Z, Shi W, Akutsu R, Tagaya M. Biological Surface Layer Formation on Bioceramic Particles for Protein Adsorption. Biomimetics (Basel) 2024; 9:347. [PMID: 38921227 PMCID: PMC11201679 DOI: 10.3390/biomimetics9060347] [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: 05/13/2024] [Revised: 05/28/2024] [Accepted: 06/05/2024] [Indexed: 06/27/2024] Open
Abstract
In the biomedical fields of bone regenerative therapy, the immobilization of proteins on the bioceramic particles to maintain their highly ordered structures is significantly important. In this review, we comprehensively discussed the importance of the specific surface layer, which can be called "non-apatitic layer", affecting the immobilization of proteins on particles such as hydroxyapatite and amorphous silica. It was suggested that the water molecules and ions contained in the non-apatitic layer can determine and control the protein immobilization states. In amorphous silica particles, the direct interactions between proteins and silanol groups make it difficult to immobilize the proteins and maintain their highly ordered structures. Thus, the importance of the formation of a surface layer consisting of water molecules and ions (i.e., a non-apatitic layer) on the particle surfaces for immobilizing proteins and maintaining their highly ordered structures was suggested and described. In particular, chlorine-containing amorphous silica particles were also described, which can effectively form the surface layer of protein immobilization carriers. The design of the bio-interactive and bio-compatible surfaces for protein immobilization while maintaining the highly ordered structures will improve cell adhesion and tissue formation, thereby contributing to the construction of social infrastructures to support super-aged society.
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Affiliation(s)
| | | | | | | | | | - Motohiro Tagaya
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka 940-2188, Japan
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Yang Y, He X, Li F, He S, Liu M, Li M, Xia F, Su W, Liu G. Animal-derived food allergen: A review on the available crystal structure and new insights into structural epitope. Compr Rev Food Sci Food Saf 2024; 23:e13340. [PMID: 38778570 DOI: 10.1111/1541-4337.13340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 03/19/2024] [Indexed: 05/25/2024]
Abstract
Immunoglobulin E (IgE)-mediated food allergy is a rapidly growing public health problem. The interaction between allergens and IgE is at the core of the allergic response. One of the best ways to understand this interaction is through structural characterization. This review focuses on animal-derived food allergens, overviews allergen structures determined by X-ray crystallography, presents an update on IgE conformational epitopes, and explores the structural features of these epitopes. The structural determinants of allergenicity and cross-reactivity are also discussed. Animal-derived food allergens are classified into limited protein families according to structural features, with the calcium-binding protein and actin-binding protein families dominating. Progress in epitope characterization has provided useful information on the structural properties of the IgE recognition region. The data reveals that epitopes are located in relatively protruding areas with negative surface electrostatic potential. Ligand binding and disulfide bonds are two intrinsic characteristics that influence protein structure and impact allergenicity. Shared structures, local motifs, and shared epitopes are factors that lead to cross-reactivity. The structural properties of epitope regions and structural determinants of allergenicity and cross-reactivity may provide directions for the prevention, diagnosis, and treatment of food allergies. Experimentally determined structure, especially that of antigen-antibody complexes, remains limited, and the identification of epitopes continues to be a bottleneck in the study of animal-derived food allergens. A combination of traditional immunological techniques and emerging bioinformatics technology will revolutionize how protein interactions are characterized.
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Affiliation(s)
- Yang Yang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen, Fujian, China
| | - Xinrong He
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Fajie Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Shaogui He
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Xiamen, Fujian, China
| | - Meng Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- College of Marine Biology, Xiamen Ocean Vocational College, Xiamen, Fujian, China
| | - Mengsi Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
- School of Food Engineering, Zhangzhou Institute of Technology, Zhangzhou, Fujian, China
| | - Fei Xia
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Wenjin Su
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
| | - Guangming Liu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, Fujian, China
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3
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Kimura R, Chatani S, Inui M, Motozuka S, Liu Z, Tagaya M. Control of Biological Surface States on Chlorine-Doped Amorphous Silica Particles and Their Effective Absorptive Ability for Antibody Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8939-8949. [PMID: 38635896 DOI: 10.1021/acs.langmuir.4c00114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Amorphous silica particles (ASPs) have low biotoxicity and are used in foodstuffs; however, the adsorption states of proteins on their surfaces have not yet been clarified. If the adsorption states can be clarified and controlled, then a wide range of biological and medical applications can be expected. The conventional amorphous silica particles have the problem of protein adsorption due to the strong interaction with their dense silanol groups and denaturation. In this study, the surfaces of amorphous silica particles with a lower silanol group density were modified with a small amount of chlorine during the synthesis process to form a specific surface layer by adsorbing water molecules and ions in the biological fluid, thereby controlling the protein adsorption state. Specifically, the hydration state on the surface of the amorphous silica particles containing trace amounts of chlorine was evaluated, and the surface layer (especially the hydration state) for the adsorption of antibody proteins while maintaining their steric structures was evaluated and discussed. The results showed that the inclusion of trace amounts of chlorine increased the silanol groups and Si-Cl bonds in the topmost surface layer of the particles, thereby inducing the adsorption of ions and water molecules in the biological fluid. Then, it was found that a novel surface layer was formed by the effective adsorption of Na and phosphate ions, which would change the proportion of the components in the hydration layer. In particular, the proportion of the free water component increased by 21% with the doping of chlorine. Antibody proteins were effectively adsorbed on the particles doped with trace amounts of chlorine, and their steric adsorption states were evaluated. It was found that the proteins were clearly adsorbed and maintained the steric state of their secondary structure. In the immunoreactivity tests using streptavidin and biotin, biotin bound to the chlorine-doped particles showed efficient reactivity. In conclusion, this study is the first to discover the surface layer of the amorphous silica particles to maintain the steric structures of adsorbed proteins, which is expected to be used as a carrier particle for antibody test kits and immunochromatography.
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Affiliation(s)
- Reo Kimura
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka 940-2188, Japan
| | - Sunao Chatani
- Production Department, Ohara Quartz, Minato 1850, Wakayama, Wakayama 640-8404, Japan
| | - Masahiko Inui
- Production Department, Ohara Quartz, Minato 1850, Wakayama, Wakayama 640-8404, Japan
| | - Satoshi Motozuka
- Department of Materials Science and Engineering, Kyushu Institute of Technology, Sensuicho 1-1, Tobata-ku, Kitakyushu 804-8550, Japan
| | - Zizhen Liu
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka 940-2188, Japan
| | - Motohiro Tagaya
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, Kamitomioka 1603-1, Nagaoka 940-2188, Japan
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4
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Niemann M, Matern BM, Spierings E. Repeated local ellipsoid protrusion supplements HLA surface characterization. HLA 2024; 103:e15260. [PMID: 37853578 DOI: 10.1111/tan.15260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/11/2023] [Accepted: 10/05/2023] [Indexed: 10/20/2023]
Abstract
Allorecognition of donor HLA is a major risk factor for long-term kidney graft survival. Although several molecular matching algorithms have been proposed that compare physiochemical and structural features of the donors' and recipients' HLA proteins in order to predict their compatibility, the exact underlying mechanisms are still not fully understood. We hypothesized that the ElliPro approach of single ellipsoid fitting and protrusion ranking lacks sensitivity for the characteristic shape of HLA molecules and developed a prediction pipeline named Snowball that is fitting smaller ellipsoids iteratively to substructures. Aggregated protrusion ranks of locally fitted ellipsoids were calculated for 712 publicly available HLA structures and 78 predicted structures using AlphaFold 2. Amino-acid sequence and protrusion ranks were used to train deep neural network predictors to infer protrusion ranks for all known HLA sequences. Snowball protrusion ranks appear to be more sensitive than ElliPro scores in fine parts of the HLA such as the helix structures forming the HLA binding groove in particular when the ellipsoids are fitted to substructures considering atoms within a 15 Å radius. A cloud-based web service was implemented based on amino-acid matching considering both protein- and position-specific surface area and protrusion ranks extending the previously presented Snowflake prediction pipeline.
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Affiliation(s)
| | - Benedict M Matern
- Research and Development, PIRCHE AG, Berlin, Germany
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
| | - Eric Spierings
- Center for Translational Immunology, University Medical Center, Utrecht, Netherlands
- Central Diagnostic Laboratory, University Medical Center, Utrecht, Netherlands
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5
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Peissert F, Pedotti M, Corbellari R, Simonelli L, De Gasparo R, Tamagnini E, Plüss L, Elsayed A, Matasci M, De Luca R, Cassaniti I, Sammartino JC, Piralla A, Baldanti F, Neri D, Varani L. Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2300088. [PMID: 37829677 PMCID: PMC10566804 DOI: 10.1002/gch2.202300088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 10/14/2023]
Abstract
Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.
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Affiliation(s)
| | - Mattia Pedotti
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | | | - Luca Simonelli
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Raoul De Gasparo
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Elia Tamagnini
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Louis Plüss
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
| | | | | | | | - Irene Cassaniti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Jose’ Camilla Sammartino
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Antonio Piralla
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Fausto Baldanti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
- Department of Clinical Surgical Diagnostic and Pediatric SciencesUniversità degli Studi di PaviaPavia27100Italy
| | - Dario Neri
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
- Philogen SpALocalità Bellaria 35Sovicille (SI)53018Italy
| | - Luca Varani
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
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6
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Kowalczyk A, Gajda-Walczak A, Ruzycka-Ayoush M, Targonska A, Mosieniak G, Glogowski M, Szumera-Cieckiewicz A, Prochorec-Sobieszek M, Bamburowicz-Klimkowska M, Nowicka AM, Grudzinski IP. Parallel SPR and QCM-D Quantitative Analysis of CD9, CD63, and CD81 Tetraspanins: A Simple and Sensitive Way to Determine the Concentration of Extracellular Vesicles Isolated from Human Lung Cancer Cells. Anal Chem 2023. [PMID: 37307147 DOI: 10.1021/acs.analchem.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Tetraspanins, including CD9, CD63, and CD81, are transmembrane biomarkers that play a crucial role in regulating cancer cell proliferation, invasion, and metastasis, as well as plasma membrane dynamics and protein trafficking. In this study, we developed simple, fast, and sensitive immunosensors to determine the concentration of extracellular vesicles (EVs) isolated from human lung cancer cells using tetraspanins as biomarkers. We employed surface plasmon resonance (SPR) and quartz crystal microbalance with dissipation (QCM-D) as detectors. The monoclonal antibodies targeting CD9, CD63, and CD81 were oriented vertically in the receptor layer using either a protein A sensor chip (SPR) or a cysteamine layer that modified the gold crystal (QCM-D) without the use of amplifiers. The SPR studies demonstrated that the interaction of EVs with antibodies could be described by the two-state reaction model. Furthermore, the EVs' affinity to monoclonal antibodies against tetraspanins decreased in the following order: CD9, CD63, and CD81, as confirmed by the QCM-D studies. The results indicated that the developed immunosensors were characterized by high stability, a wide analytical range from 6.1 × 104 particles·mL-1 to 6.1 × 107 particles·mL-1, and a low detection limit (0.6-1.8) × 104 particles·mL-1. A very good agreement between the results obtained using the SPR and QCM-D detectors and nanoparticle tracking analysis demonstrated that the developed immunosensors could be successfully applied to clinical samples.
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Affiliation(s)
- Agata Kowalczyk
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Aleksandra Gajda-Walczak
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Monika Ruzycka-Ayoush
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
| | - Alicja Targonska
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura Street 3, PL-02-093 Warsaw, Poland
| | - Grazyna Mosieniak
- Laboratory of Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura Street 3, PL-02-093 Warsaw, Poland
| | - Maciej Glogowski
- Department of Lung Cancer and Chest Tumors, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Anna Szumera-Cieckiewicz
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Monika Prochorec-Sobieszek
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, Roentgena Street 5, PL-02-781 Warsaw, Poland
| | - Magdalena Bamburowicz-Klimkowska
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
| | - Anna M Nowicka
- Department of Inorganic and Analytical Chemistry, Faculty of Chemistry, University of Warsaw, Pasteura Street 1, PL-02-093 Warsaw, Poland
| | - Ireneusz P Grudzinski
- Department of Toxicology and Food Science, Faculty of Pharmacy, Medical University of Warsaw, Banacha Streer 1, PL-02-097 Warsaw, Poland
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7
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Bistaffa MJ, Camacho SA, Pazin WM, Constantino CJ, Oliveira ON, Aoki PH. Immunoassay platform with surface-enhanced resonance Raman scattering for detecting trace levels of SARS-CoV-2 spike protein. Talanta 2022; 244:123381. [PMID: 35364338 PMCID: PMC8928707 DOI: 10.1016/j.talanta.2022.123381] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/06/2022] [Accepted: 03/11/2022] [Indexed: 12/15/2022]
Abstract
The early diagnosis of Coronavirus disease (COVID-19) requires either an accurate detection of genetic material or a sensitive detection of viral proteins. In this work, we designed an immunoassay platform for detecting trace levels of SARS-CoV-2 spike (S) protein. It is based on surface-enhanced resonance Raman scattering (SERRS) of methylene blue (MB) adsorbed onto spherical gold nanoparticles (AuNPs) and coated with a 6 nm silica shell. The latter shell in the SERRS nanoprobe prevented aggregation and permitted functionalization with SARS-CoV-2 antibodies. Specificity of the immunoassay was achieved by combining this functionalization with antibody immobilization on the cover slides that served as the platform support. Different concentrations of SARS-CoV-2 antigen could be distinguished and the lack of influence of interferents was confirmed by treating SERRS data with the multidimensional projection technique Sammon's mapping. With SERRS using a laser line at 633 nm, the lowest concentration of spike protein detected was 10 pg/mL, achieving a limit of detection (LOD) of 0.046 ng/mL (0.60 pM). This value is comparable to the lowest concentrations in the plasma of COVID-19 patients at the onset of symptoms, thus indicating that the SERRS immunoassay platform may be employed for early diagnosis.
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8
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El-Awar N. HLA epitopes – Empirically defined as conformational amino acids sequences of the HLA antigen and are likely to be part of the binding sites of anti-HLA antibodies. Hum Immunol 2022; 83:204-218. [DOI: 10.1016/j.humimm.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/04/2021] [Accepted: 12/20/2021] [Indexed: 11/26/2022]
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9
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Wilson IA, Stanfield RL. 50 Years of structural immunology. J Biol Chem 2021; 296:100745. [PMID: 33957119 PMCID: PMC8163984 DOI: 10.1016/j.jbc.2021.100745] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/24/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022] Open
Abstract
Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.
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MESH Headings
- Adaptive Immunity
- Allergy and Immunology/history
- Animals
- Antibodies, Viral/chemistry
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Antibody Specificity
- Antigen Presentation
- Antigens, Viral/chemistry
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- COVID-19/immunology
- COVID-19/virology
- Crystallography/history
- Crystallography/methods
- History, 20th Century
- History, 21st Century
- Humans
- Immunity, Innate
- Protein Folding
- Protein Interaction Domains and Motifs
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Cytokine/chemistry
- Receptors, Cytokine/genetics
- Receptors, Cytokine/immunology
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- V(D)J Recombination
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Affiliation(s)
- Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA.
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, USA
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10
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Pomés A, Mueller GA, Chruszcz M. Structural Aspects of the Allergen-Antibody Interaction. Front Immunol 2020; 11:2067. [PMID: 32983155 PMCID: PMC7492603 DOI: 10.3389/fimmu.2020.02067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/29/2020] [Indexed: 12/23/2022] Open
Abstract
The development of allergic disease involves the production of IgE antibodies upon allergen exposure in a process called sensitization. IgE binds to receptors on the surface of mast cells and basophils, and subsequent allergen exposure leads to cross-linking of IgE antibodies and release of cell mediators that cause allergy symptoms. Although this process is quite well-understood, very little is known about the epitopes on the allergen recognized by IgE, despite the importance of the allergen-antibody interaction for the allergic response to occur. This review discusses efforts to analyze allergen-antibody interactions, from the original epitope mapping studies using linear peptides or recombinant allergen fragments, to more sophisticated technologies, such as X-ray crystallography and nuclear magnetic resonance. These state-of-the-art approaches, combined with site-directed mutagenesis, have led to the identification of conformational IgE epitopes. The first structures of an allergen (egg lysozyme) in complex with Fab fragments from IgG antibodies were determined in the 1980s. Since then, IgG has been used as surrogate for IgE, due to the difficulty of obtaining monoclonal IgE antibodies. Technical developments including phage display libraries have contributed to progress in epitope mapping thanks to the isolation of IgE antibody constructs from combinatorial libraries made from peripheral blood mononuclear cells of allergic donors. Most recently, single B cell antibody sequencing and human hybridomas are new breakthrough technologies for finally obtaining human IgE monoclonal antibodies, ideal for epitope mapping. The information on antigenic determinants will facilitate the design of hypoallergens for immunotherapy and the investigation of the fundamental mechanisms of the IgE response.
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Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, United States
| | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, United States
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11
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Abstract
Monoclonal antibodies recognize epitopes so specifically that altering a single residue can disrupt binding. In this issue of Science Signaling, Schüchner et al and Frohner et al report that flanking amino acids and an underappreciated posttranslational modification perturb epitope affinity for two groups of widely used monoclonal antibodies.
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Affiliation(s)
- Kevin A Janes
- Departments of Biomedical Engineering and Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
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12
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Abstract
In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an integral role in the armamentarium of immune defense against various pathogens. After an antigenic challenge, antibodies are secreted by differentiated B cells called plasma cells. Antibodies have two predominant roles that involve specific binding to antigens to launch an immune response, along with activation of other components of the immune system to fight pathogens. The ability of immunoglobulins to fight against innumerable and diverse pathogens lies in their intrinsic ability to discriminate between different antigens. Due to this specificity and high affinity for their antigens, antibodies have been a valuable and indispensable tool in research, diagnostics and therapy. Although seemingly a simple maneuver, the association between an antibody and its antigen, to make an antigen-antibody complex, is comprised of myriads of non-covalent interactions. Amino acid residues on the antigen binding site, the epitope, and on the antibody binding site, the paratope, intimately contribute to the energetics needed for the antigen-antibody complex stability. Structural biology methods to study antigen-antibody complexes are extremely valuable tools to visualize antigen-antibody interactions in detail; this helps to elucidate the basis of molecular recognition between an antibody and its specific antigen. The main scope of this chapter is to discuss the structure and function of different classes of antibodies and the various aspects of antigen-antibody interactions including antigen-antibody interfaces-with a special focus on paratopes, complementarity determining regions (CDRs) and other non-CDR residues important for antigen binding and recognition. Herein, we also discuss methods used to study antigen-antibody complexes, antigen recognition by antibodies, types of antigens in complexes, and how antigen-antibody complexes play a role in modern day medicine and human health. Understanding the molecular basis of antigen binding and recognition by antibodies helps to facilitate the production of better and more potent antibodies for immunotherapy, vaccines and various other applications.
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Affiliation(s)
- A Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
| | - Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC, 29208, USA.
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13
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Glesner J, Kapingidza AB, Godzwon M, Offermann LR, Mueller GA, DeRose EF, Wright P, Richardson CM, Woodfolk JA, Vailes LD, Wünschmann S, London RE, Chapman MD, Ohlin M, Chruszcz M, Pomés A. A Human IgE Antibody Binding Site on Der p 2 for the Design of a Recombinant Allergen for Immunotherapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:2545-2556. [PMID: 31554696 PMCID: PMC6810898 DOI: 10.4049/jimmunol.1900580] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 08/15/2019] [Indexed: 01/31/2023]
Abstract
Der p 2 is one of the most important allergens from the house dust mite Dermatophagoides pteronyssinus Identification of human IgE Ab binding epitopes can be used for rational design of allergens with reduced IgE reactivity for therapy. Antigenic analysis of Der p 2 was performed by site-directed mutagenesis based on the x-ray crystal structure of the allergen in complex with a Fab from the murine IgG mAb 7A1 that binds an epitope overlapping with human IgE binding sites. Conformational changes upon Ab binding were confirmed by nuclear magnetic resonance using a 7A1-single-chain variable fragment. In addition, a human IgE Ab construct that interferes with mAb 7A1 binding was isolated from a combinatorial phage-display library constructed from a mite-allergic patient and expressed as two recombinant forms (single-chain Fab in Pichia pastoris and Fab in Escherichia coli). These two IgE Ab constructs and the mAb 7A1 failed to recognize two Der p 2 epitope double mutants designed to abolish the allergen-Ab interaction while preserving the fold necessary to bind Abs at other sites of the allergen surface. A 10-100-fold reduction in binding of IgE from allergic subjects to the mutants additionally showed that the residues mutated were involved in IgE Ab binding. In summary, mutagenesis of a Der p 2 epitope defined by x-ray crystallography revealed an IgE Ab binding site that will be considered for the design of hypoallergens for immunotherapy.
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Affiliation(s)
- Jill Glesner
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | | | | | - Geoffrey A Mueller
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Eugene F DeRose
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | - Paul Wright
- University of Virginia, Charlottesville, VA 22903
| | | | | | - Lisa D Vailes
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903
| | | | - Robert E London
- National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709; and
| | | | | | | | - Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA 22903;
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14
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Ehlers AM, Blankestijn MA, Knulst AC, Klinge M, Otten HG. Can alternative epitope mapping approaches increase the impact of B-cell epitopes in food allergy diagnostics? Clin Exp Allergy 2018; 49:17-26. [PMID: 30294841 PMCID: PMC7380004 DOI: 10.1111/cea.13291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/14/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023]
Abstract
In vitro allergy diagnostics are currently based on the detection of specific IgE binding on intact allergens or a mixture thereof. This approach has drawbacks as it may yield false‐negative and/or false‐positive results. Thus, we reviewed the impact of known B‐cell epitopes of food allergens to predict transience or persistence, tolerance or allergy and the severity of an allergic reaction and to examine new epitope mapping strategies meant to improve serum‐based allergy diagnostics. Recent epitope mapping approaches have been worthwhile in epitope identification and may increase the specificity of allergy diagnostics by using epitopes predominately recognized by allergic patients in some cases. However, these approaches did not lead to discrimination between clinically relevant and irrelevant epitopes so far, since the polyclonal serum IgE‐binding epitope spectrum seems to be too individual, independent of the disease status of the patients. New epitope mapping strategies are necessary to overcome these obstacles. The use of patient‐derived monoclonal antibodies instead of patient sera for functional characterization of clinically relevant and irrelevant epitope combinations, distinguished by their ability to induce degranulation, might be a promising approach to gain more insight into the allergic reaction and to improve serum‐based allergy diagnostics.
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Affiliation(s)
- Anna M Ehlers
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Mark A Blankestijn
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Andre C Knulst
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,Department of Dermatology and Allergology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Henny G Otten
- Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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15
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Zhang H, Zhu X, Pascual G, Wadia JS, Keogh E, Hoozemans JJ, Siregar B, Inganäs H, Stoop EJM, Goudsmit J, Apetri A, Koudstaal W, Wilson IA. Structural Basis for Recognition of a Unique Epitope by a Human Anti-tau Antibody. Structure 2018; 26:1626-1634.e4. [PMID: 30318466 DOI: 10.1016/j.str.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/23/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023]
Abstract
Aggregation of the hyperphosphorylated protein tau into neurofibrillary tangles and neuropil threads is a hallmark of Alzheimer disease (AD). Identification and characterization of the epitopes recognized by anti-tau antibodies might shed light on the molecular mechanisms of AD pathogenesis. Here we report on the biochemical and structural characterization of a tau-specific monoclonal antibody CBTAU-24.1, which was isolated from the human memory B cell repertoire. Immunohistochemical staining with CBTAU-24.1 specifically detects pathological tau structures in AD brain samples. The crystal structure of CBTAU-24.1 Fab with a phosphorylated tau peptide revealed recognition of a unique epitope (Ser235-Leu243) in the tau proline-rich domain. Interestingly, the antibody can bind tau regardless of phosphorylation state of its epitope region and also recognizes both monomeric and paired helical filament tau irrespective of phosphorylation status. This human anti-tau antibody and its unique epitope may aid in development of diagnostics and/or therapeutic AD strategies.
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Affiliation(s)
- Heng Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Gabriel Pascual
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Jehangir S Wadia
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Elissa Keogh
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA
| | - Jeroen J Hoozemans
- Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands
| | - Berdien Siregar
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Hanna Inganäs
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Esther J M Stoop
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Jaap Goudsmit
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Adrian Apetri
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Wouter Koudstaal
- Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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16
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Abstract
With the increased global awareness and rise in food allergies, a multifold interest in food allergens is evident. The presence of undeclared food allergens results in expensive food recalls and increased risks of anaphylaxis for the sensitive individuals. Regardless of the allergenic food, the immunogen needs to be identified and detected before making any efforts to inactivate/eliminate it. In type I food allergies, protein immunogen cross-links immunoglobulin E, leading to basophil/mast cell degranulation, resulting in the symptoms that range from mild irritation to anaphylaxis. A portion/part of the protein, known as the epitope, can interact with either antibodies to elicit allergic reactions or T-cell receptors to initiate allergic sensitization. Antibody-recognized epitopes can be either a linear sequence of amino acids (linear epitope) or a three-dimensional motif (conformational epitope), while T-cell-receptor-recognized epitopes are exclusively linear peptides. Identifying and characterizing human-allergy-relevant epitopes are important for allergy diagnosis/prognosis, immunotherapy, and developing food processing methods that can reduce/eliminate immunogencity/immunoreactivity of the allergen.
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Affiliation(s)
- Changqi Liu
- School of Exercise and Nutritional Sciences, College of Health and Human Services , San Diego State University , 308 ENS Building, 5500 Campanile Drive , San Diego , California 92182-7251 , United States
| | - Shridhar K Sathe
- Department of Nutrition, Food & Exercise Sciences, College of Human Sciences , Florida State University , 402 SAN, 120 Convocation Way , Tallahassee , Florida 32306-1493 , United States
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17
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Epitope Mapping of Antibodies Using Bacterial Cell Surface Display of Gene Fragment Libraries. Methods Mol Biol 2018. [PMID: 29714017 DOI: 10.1007/978-1-4939-7841-0_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The unique property of specific high affinity binding to more or less any target of interest has made antibodies tremendously useful in numerous applications. Hence, knowledge of the precise binding site (epitope) of antibodies on the target protein is one of the most important features for understanding its performance and determining its reliability in immunoassays. Here, we describe an updated protocol for high-resolution method for mapping epitopes of antibodies based on bacterial surface expression of antigen fragments followed by antibody-based flow cytometric analysis. Epitopes are determined by DNA sequencing of the sorted antibody-binding cells followed by sequence alignment back to the antigen sequence. The method described here has been useful for the mapping of both monoclonal and polyclonal antibodies with varying sizes of epitopes.
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18
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McCoy AJ, Oeffner RD, Millán C, Sammito M, Usón I, Read RJ. Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement. Acta Crystallogr D Struct Biol 2018; 74:279-289. [PMID: 29652255 PMCID: PMC5892877 DOI: 10.1107/s2059798318001353] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 01/22/2018] [Indexed: 11/22/2022] Open
Abstract
Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.
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Affiliation(s)
- Airlie J. McCoy
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Robert D. Oeffner
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo Sammito
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, England
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19
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Sookrung N, Reamtong O, Poolphol R, Indrawattana N, Seesuay W, Saelim N, Tantilipikorn P, Bunnag C, Chaicumpa W, Tungtrongchitr A. Glutathione S-transferase (GST) of American Cockroach, Periplaneta americana: Classes, Isoforms, and Allergenicity. Sci Rep 2018; 8:484. [PMID: 29323160 PMCID: PMC5764987 DOI: 10.1038/s41598-017-18759-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/18/2017] [Indexed: 11/30/2022] Open
Abstract
Insect glutathione S-transferases (GSTs) play important roles in insecticide/drug resistance and stress response. Medically, GSTs of house dust mites (Dermatophagoides pteronyssinus and Blomia tropicalis) and German cockroach (Blattella germanica) are human allergens. In this study, classes, isoforms and B-cell and allergenic epitopes of GST of American cockroach, Periplaneta americana, the predominant species in the tropics and subtropics were investigated for the first time. Enzymatically active native and recombinant P. americana-GSTs bound to IgE in sera of all P. americana allergic patients that were tested. By gel-based proteomics and multiple sequence alignments, the native GST comprises three isoforms of delta and sigma classes. All isoforms interacted with serum IgE of the cockroach allergic subjects. Molecularly, the protein contains six B-cell epitopes; two epitopes located at β1-α1 and β4-α3 regions bound to patients’ serum IgE, indicating that they are allergenic. P. americana are ubiquitous and their GST can sensitize humans to allergic diseases; thus, the protein should be included in the allergen array for component resolved diagnosis (CRD) of allergic patients, either by skin prick test or specific IgE determination. The GST is suitable also as a target of environmental allergen detection and quantification for intervention of cockroach sensitization and allergic morbidity.
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Affiliation(s)
- Nitat Sookrung
- Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Rojana Poolphol
- Graduate Program in Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Department of Parasitology, Mahidol University, Bangkok, 10700, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Watee Seesuay
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Nawannaporn Saelim
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Department of Parasitology, Mahidol University, Bangkok, 10700, Thailand
| | - Pongsakorn Tantilipikorn
- Department of Oto-rhino-laryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chaweewan Bunnag
- Department of Oto-rhino-laryngology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Wanpen Chaicumpa
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.,Department of Parasitology, Mahidol University, Bangkok, 10700, Thailand
| | - Anchalee Tungtrongchitr
- Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand. .,Department of Parasitology, Mahidol University, Bangkok, 10700, Thailand.
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20
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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21
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Langley DB, Crossett B, Schofield P, Jackson J, Zeraati M, Maltby D, Christie M, Burnett D, Brink R, Goodnow C, Christ D. Structural basis of antigen recognition: crystal structure of duck egg lysozyme. Acta Crystallogr D Struct Biol 2017; 73:910-920. [PMID: 29095163 PMCID: PMC5683014 DOI: 10.1107/s2059798317013730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 09/25/2017] [Indexed: 11/13/2023] Open
Abstract
Duck egg lysozyme (DEL) is a widely used model antigen owing to its capacity to bind with differential affinity to anti-chicken egg lysozyme antibodies. However, no structures of DEL have so far been reported, and the situation had been complicated by the presence of multiple isoforms and conflicting reports of primary sequence. Here, the structures of two DEL isoforms from the eggs of the commonly used Pekin duck (Anas platyrhynchos) are reported. Using structural analyses in combination with mass spectrometry, non-ambiguous DEL primary sequences are reported. Furthermore, the structures and sequences determined here enable rationalization of the binding affinity of DEL for well documented landmark anti-lysozyme antibodies.
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Affiliation(s)
- David Brent Langley
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Ben Crossett
- The Mass Spectrometry Core Facility, The University of Sydney, The Hub, Charles Perkins Centre, Building D17, Camperdown, NSW 2006, Australia
| | - Peter Schofield
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Jenny Jackson
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Mahdi Zeraati
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - David Maltby
- The Mass Spectrometry Core Facility, The University of Sydney, The Hub, Charles Perkins Centre, Building D17, Camperdown, NSW 2006, Australia
| | - Mary Christie
- Molecular, Structural and Computational Division, Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Deborah Burnett
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
| | - Robert Brink
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Christopher Goodnow
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Daniel Christ
- Immunology Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, NSW 2010, Australia
- St Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
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22
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Yang D, Kroe-Barrett R, Singh S, Roberts CJ, Laue TM. IgG cooperativity - Is there allostery? Implications for antibody functions and therapeutic antibody development. MAbs 2017; 9:1231-1252. [PMID: 28812955 PMCID: PMC5680800 DOI: 10.1080/19420862.2017.1367074] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
A central dogma in immunology is that an antibody's in vivo functionality is mediated by 2 independent events: antigen binding by the variable (V) region, followed by effector activation by the constant (C) region. However, this view has recently been challenged by reports suggesting allostery exists between the 2 regions, triggered by conformational changes or configurational differences. The possibility of allosteric signals propagating through the IgG domains complicates our understanding of the antibody structure-function relationship, and challenges the current subclass selection process in therapeutic antibody design. Here we review the types of cooperativity in IgG molecules by examining evidence for and against allosteric cooperativity in both Fab and Fc domains and the characteristics of associative cooperativity in effector system activation. We investigate the origin and the mechanism of allostery with an emphasis on the C-region-mediated effects on both V and C region interactions, and discuss its implications in biological functions. While available research does not support the existence of antigen-induced conformational allosteric cooperativity in IgGs, there is substantial evidence for configurational allostery due to glycosylation and sequence variations.
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Affiliation(s)
- Danlin Yang
- a Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield , Connecticut , USA
| | - Rachel Kroe-Barrett
- a Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield , Connecticut , USA
| | - Sanjaya Singh
- b Janssen BioTherapeutics, Janssen Research & Development, LLC, Spring House , Pennsylvania , USA
| | - Christopher J Roberts
- c Department of Chemical and Biomolecular Engineering , University of Delaware , Newark , Delaware , USA
| | - Thomas M Laue
- d Department of Molecular, Cellular, and Biomedical Sciences , University of New Hampshire , Durham , New Hampshire , USA
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23
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Abstract
Sensitization to human leukocyte antigens (HLA) in organ transplant patients causes graft rejection, according to the humoral theory of transplantation. Sensitization is almost ubiquitous as anti-HLA antibodies are found in almost all sera of transplant recipients. Advances in testing assays and amino acid sequencing of HLA along with computer software contributed further to the understanding of antibody-antigen reactivity. It is commonly understood that antibodies bind to HLA antigens. With current knowledge of epitopes, it is more accurate to describe that antibodies bind to their target epitopes on the surface of HLA molecular chains. Epitopes are present on a single HLA (private epitope) or shared by multiple antigens (public epitope). The phenomenon of cross-reactivity in HLA testing, often explained as cross-reactive groups (CREGs) of antigens with antibody, can be clearly explained now by public epitopes. Since 2006, we defined and reported 194 HLA class I unique epitopes, including 56 cryptic epitopes on dissociated HLA class I heavy chains, 83 HLA class II epitopes, 60 epitopes on HLA-DRB1, 15 epitopes on HLA-DQB1, 3 epitopes on HLA-DQA1, 5 epitopes on HLA-DPB1, and 7 MICA epitopes. In this paper, we provide a summary of our findings.
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24
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Tasaniyananda N, Tungtrongchitr A, Seesuay W, Sakolvaree Y, Indrawattana N, Chaicumpa W, Sookrung N. A novel IgE-binding epitope of cat major allergen, Fel d 1. Biochem Biophys Res Commun 2016; 470:593-598. [PMID: 26797272 DOI: 10.1016/j.bbrc.2016.01.099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 01/16/2016] [Indexed: 11/25/2022]
Abstract
Information on the antigenic repertoire, especially the IgE-binding epitopes of an allergen is important for understanding the allergen induced immune response and cross-reactivity, as well as for generating the hypoallergenic variants for specific component resolved immunotherapy/diagnosis (CRIT and CRD). Data on the IgE-binding epitopes of cat allergens are scarce. In this study, a novel IgE-binding epitope of the cat major allergen, Fel d 1, was identified. Mouse monoclonal antibody (MAb) specific to the Fel d 1 was produced. Computerized intermolecular docking was used for determining the residues of the Fel d 1 bound by the specific MAb. The presumptive surface exposed residues of the Fel d 1 intrigued by the MAb are located on the chain 1. They are: L34 and T37 (helix 1); T39 (between helices 1 and 2); P40, E42 and E45 (helix 2); R61, K64, N65 and D68 (helix 3); and E73 and K76 (helix 4). The MAb competed efficiently with the cat allergic patients' serum IgE for Fel d 1 binding in the competitive IgE binding assay, indicating allergenicity of the MAb epitope. The newly identified allergenic epitope of the Fel d 1 is useful in a design of the CRIT and CRD for cat allergy.
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Affiliation(s)
- Natt Tasaniyananda
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Anchalee Tungtrongchitr
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Watee Seesuay
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Yuwaporn Sakolvaree
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Nitat Sookrung
- Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
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25
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Yang Y, Xu Z, Zhang Z, Yang Z, Liu Y, Wang J, Cai T, Li S, Chen K, Shi J, Zhu W. Like-Charge Guanidinium Pairing between Ligand and Receptor: An Unusual Interaction for Drug Discovery and Design? J Phys Chem B 2015; 119:11988-97. [DOI: 10.1021/acs.jpcb.5b04130] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yang Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhijian Xu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- State
Key Laboratory of Medicinal Chemical Biology, Nankai University, 94
Weijin Road, Nankai District, Tianjin300071, China
| | - Zhengyan Zhang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Zhuo Yang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yingtao Liu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jinan Wang
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tingting Cai
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shujin Li
- College
of Chemistry, Chemical Engineering and Materials Science of Soochow
University, Soochow University, Suzhou, Jiangsu 215123, China
| | - Kaixian Chen
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiye Shi
- Informatics
Department, UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom
| | - Weiliang Zhu
- CAS
Key Laboratory of Receptor Research, Drug Discovery and Design Center,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
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26
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Kong L, Kadam RU, Giang E, Ruwona TB, Nieusma T, Culhane JC, Stanfield RL, Dawson PE, Wilson IA, Law M. Structure of Hepatitis C Virus Envelope Glycoprotein E1 Antigenic Site 314-324 in Complex with Antibody IGH526. J Mol Biol 2015; 427:2617-28. [PMID: 26135247 PMCID: PMC4523428 DOI: 10.1016/j.jmb.2015.06.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 01/19/2023]
Abstract
Hepatitis C virus (HCV) is a positive-strand RNA virus within the Flaviviridae family. The viral "spike" of HCV is formed by two envelope glycoproteins, E1 and E2, which together mediate viral entry by engaging host receptors and undergoing conformational changes to facilitate membrane fusion. While E2 can be readily produced in the absence of E1, E1 cannot be expressed without E2 and few reagents, including monoclonal antibodies (mAbs), are available for study of this essential HCV glycoprotein. A human mAb to E1, IGH526, was previously reported to cross-neutralize different HCV isolates, and therefore, we sought to further characterize the IGH526 neutralizing epitope to obtain information for vaccine design. We found that mAb IGH526 bound to a discontinuous epitope, but with a major component corresponding to E1 residues 314-324. The crystal structure of IGH526 Fab with this E1 glycopeptide at 1.75Å resolution revealed that the antibody binds to one face of an α-helical peptide. Single mutations on the helix substantially lowered IGH526 binding but did not affect neutralization, indicating either that multiple mutations are required or that additional regions are recognized by the antibody in the context of the membrane-associated envelope oligomer. Molecular dynamics simulations indicate that the free peptide is flexible in solution, suggesting that it requires stabilization for use as a candidate vaccine immunogen.
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Affiliation(s)
- Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rameshwar U Kadam
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erick Giang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tinashe B Ruwona
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Travis Nieusma
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jeffrey C Culhane
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Mansun Law
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.
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27
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Abstract
Peptide antibodies recognize epitopes with amino acid residues adjacent in sequence ("linear" epitopes). Such antibodies can be made to virtually any sequence and have been immensely important in all areas of molecular biology and diagnostics due to their versatility and to the rapid growth in protein sequence information. Today, peptide antibodies can be routinely and rapidly made to large numbers of peptides, including peptides with posttranslationally modified residues, and are used for immunoblotting, immunocytochemistry, immunohistochemistry, and immunoassays. In the future, peptide antibodies will continue to be immensely important for molecular biology, TCR- and MHC-like peptide antibodies may be produced routinely, peptide antibodies with predetermined conformational specificities may be designed, and peptide-based vaccines may become part of vaccination programs.
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Affiliation(s)
- Gunnar Houen
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark.
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28
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Templeton DM, Moehle K. Structural aspects of molecular recognition in the immune system. Part I: Acquired immunity (IUPAC Technical Report). PURE APPL CHEM 2014. [DOI: 10.1515/pac-2013-1020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Humoral immunity allows the body to mount a defense against pathogens and foreign substances, and to respond with memory to subsequent exposures. The molecular participants may also recognize self-structures, leading to attack on the body and autoimmune disease. The main players in humoral immunity are antibody-producing B lymphocytes, and several classes of T lymphocytes. This review deals with the molecular details of recognition of antigens by soluble antibodies, and of substances presented to receptors on the surfaces of T cells (TCRs). The prototype antibody consists of a dimer of dimers, two heavy (H) chains and two light (L) chains, with antigen recognition capacity lying in variable “head” regions of an H-L pair. Most crystallographic studies are done with this substructure, called a Fab fragment, bound in a soluble antigen complex. Homologous to this arrangement, the prototype TCR consists of two chains (α and β) that complex not soluble antigen, but usually a short peptide or other small molecule presented by proteins of the major histocompatibility complex. In each case a general background on the historical development of understanding the molecular recognition interface is given, followed by a number of examples of crystal structures from the recent literature that have allowed us to refine our understanding of the complex recognition process. Variations on the prototypical structures are also considered. The spectrum of recognition strategies involves interplay of lock-and-key with flexibility, varying degrees of entropic and enthalpic contributions, surface shaping by entrapped water molecules, and combinations of stabilizing hydrogen bonding, electrostatic interactions, salt bridging, and van der Waals forces. Preeminent in the recent literature are details of antibody binding to influenza A and human immunodeficiency viral antigens. Both viral antigens and attempts to understand autoimmunity are prominent in the recent TCR literature.
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29
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Choi YS, Yoon S, Kim KL, Yoo J, Song P, Kim M, Shin YE, Yang WJ, Noh JE, Cho HS, Kim S, Chung J, Ryu SH. Computational design of binding proteins to EGFR domain II. PLoS One 2014; 9:e92513. [PMID: 24710267 PMCID: PMC3977815 DOI: 10.1371/journal.pone.0092513] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/24/2014] [Indexed: 12/03/2022] Open
Abstract
We developed a process to produce novel interactions between two previously unrelated proteins. This process selects protein scaffolds and designs protein interfaces that bind to a surface patch of interest on a target protein. Scaffolds with shapes complementary to the target surface patch were screened using an exhaustive computational search of the human proteome and optimized by directed evolution using phage display. This method was applied to successfully design scaffolds that bind to epidermal growth factor receptor (EGFR) domain II, the interface of EGFR dimerization, with high reactivity toward the target surface patch of EGFR domain II. One potential application of these tailor-made protein interactions is the development of therapeutic agents against specific protein targets.
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Affiliation(s)
- Yoon Sup Choi
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- KT Institute of Convergence Technology, Seocho-gu, Seoul, Korea
| | - Soomin Yoon
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Kyung-Lock Kim
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Jiho Yoo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Parkyong Song
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Minsoo Kim
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Scripps Korea Antibody Institute, Chuncheon, Republic of Korea
| | - Young-Eun Shin
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Won Jun Yang
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
| | - Jung-eun Noh
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Hyun-soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Republic of Korea
| | - Sanguk Kim
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of IT Convergence Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Junho Chung
- Cancer Research Institute, Seoul National University School of Medicine, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University School of Medicine, Seoul, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
| | - Sung Ho Ryu
- School of Interdisciplinary Bioscience and Bioengineering (I-Bio), Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail: (SK); (JC); (SHR)
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30
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Volk AL, Hu FJ, Rockberg J. Epitope mapping of monoclonal and polyclonal antibodies using bacterial cell surface display. Methods Mol Biol 2014; 1131:485-500. [PMID: 24515484 DOI: 10.1007/978-1-62703-992-5_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The unique property of specific high-affinity binding to more or less any target of interest has made antibodies tremendously useful in numerous applications. Hence knowledge of the precise binding site (epitope) of antibodies on the target protein is one of the most important features for understanding its performance and determining its reliability in immunoassays. Here, we describe a high-resolution method for mapping epitopes of antibodies based on bacterial surface expression of antigen fragments followed by antibody-based flow cytometric sorting. Epitopes are determined by DNA sequencing of the sorted antibody-binding cells followed by sequence alignment back to the antigen sequence. The method described here has been useful for the mapping of both monoclonal and polyclonal antibodies with varying sizes of epitopes.
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Affiliation(s)
- Anna-Luisa Volk
- School of Biotechnology, AlbaNova University Center, KTH - Royal Institute of Technology, Stockholm, Sweden
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31
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Kong L, Giang E, Nieusma T, Kadam RU, Cogburn KE, Hua Y, Dai X, Stanfield RL, Burton DR, Ward AB, Wilson IA, Law M. Hepatitis C virus E2 envelope glycoprotein core structure. Science 2013; 342:1090-4. [PMID: 24288331 DOI: 10.1126/science.1243876] [Citation(s) in RCA: 311] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hepatitis C virus (HCV), a Hepacivirus, is a major cause of viral hepatitis, liver cirrhosis, and hepatocellular carcinoma. HCV envelope glycoproteins E1 and E2 mediate fusion and entry into host cells and are the primary targets of the humoral immune response. The crystal structure of the E2 core bound to broadly neutralizing antibody AR3C at 2.65 angstroms reveals a compact architecture composed of a central immunoglobulin-fold β sandwich flanked by two additional protein layers. The CD81 receptor binding site was identified by electron microscopy and site-directed mutagenesis and overlaps with the AR3C epitope. The x-ray and electron microscopy E2 structures differ markedly from predictions of an extended, three-domain, class II fusion protein fold and therefore provide valuable information for HCV drug and vaccine design.
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Affiliation(s)
- Leopold Kong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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33
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Shokri A, Ramezani M, Fattahi A, Kass SR. Electrostatically defying cation-cation clusters: can likes attract in a low-polarity environment? J Phys Chem A 2013; 117:9252-8. [PMID: 24011262 DOI: 10.1021/jp405063h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Like-charge ion pairing is commonly observed in protein structures and plays a significant role in biochemical processes. Density functional calculations combined with the conductor-like polarizable continuum model were employed to study the formation possibilities of doubly charged noncovalently linked complexes of a series of model compounds and amino acids in the gas phase and in solution. Hydrogen bond interactions were found to offset the Coulombic repulsion such that cation-cation clusters are minima on the potential energy surfaces and neither counterions nor solvent molecules are needed to hold them together. In the gas phase the dissociation energies are exothermic, and the separation barriers span from 1.7 to 15.6 kcal mol(-1). Liquid-phase computations indicate that the separation enthalpies of the cation-cation complexes become endothermic in water and nonpolar solvents with dielectric constants of ≥7 (i.e., the value for THF). These results reveal that electrostatically defying noncovalent complexes of like-charged ions can overcome their Coulombic repulsion even in low-polarity environments.
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Affiliation(s)
- Alireza Shokri
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota55455, United States
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34
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El-Awar N, Nguyen A, Almeshari K, Alawami M, Alzayer F, Alharbi M, Sasaki N, Terasaki PI. HLA class II DQA and DQB epitopes: recognition of the likely binding sites of HLA-DQ alloantibodies eluted from recombinant HLA-DQ single antigen cell lines. Hum Immunol 2013; 74:1141-52. [PMID: 23756161 DOI: 10.1016/j.humimm.2013.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 04/29/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Donor-specific antibodies (DSA) in sera of sensitized transplant patients are often produced against the specific epitopes on mismatched HLA antigens. In this study, we selected sera from 30 kidney transplant patients with DSA and AMR to define DQ epitopes. Using adsorption and elution assays, we identified 18 antibody reaction patterns to define 6 new epitopes and to confirm 12 previously defined epitopes. In one patient case, one mismatched antigen produced 3 different antibodies and, in another, antibodies were produced against the alpha and beta chains of the same antigen. For some sera, a single epitope can explain reactions for 27 of the 29 DQ beads in the single antigen panel. Several studies highlighted the prevalence of anti-DQ antibodies. In 2011, Almeshari et al. observed DQ DSA in 34/46 (74%) of rejection episodes - 44 patients had DSA and 20 lost their graft due to AMR. Other studies have shown a high prevalence of anti-DQ antibodies and an association with adverse effects on the graft. We conclude that analysis of the epitopes of the DQ antibodies using Adsorption/Elution and testing on single antigen DQ beads helps to better understand the specificities and cross-reactions of DQ antibodies in transplant patients.
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35
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Hoppe S, Bier FF, Nickisch-Rosenegk MV. Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PLoS One 2013; 8:e65837. [PMID: 23734261 PMCID: PMC3667084 DOI: 10.1371/journal.pone.0065837] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/30/2013] [Indexed: 01/03/2023] Open
Abstract
Campylobacter jejuni remains one of the major gut pathogens of our time. Its zoonotic nature and wide-spread distribution in industrialized countries calls for a quick and reliable diagnostic tool. Antibody-based detection presents a suitable means to identify pathogenic bacteria. However, the knowledge about immunodominant targets is limited. Thus, an approach is presented, which allows for the rapid screening of numerous cDNA derived expression clones to identify novel antigens. The deeper understanding of immunodominant proteins assists in the design of diagnostic tools and furthers the insight into the bacterium's pathogenicity as well as revealing potential candidates for vaccination. We have successfully screened 1536 clones of an expression library to identify 22 proteins that have not been described as immunodominant before. After subcloning the corresponding 22 genes and expression of full-length proteins, we investigated the immunodominant character by microarrays and ELISA. Subsequently, seven proteins were selected for epitope mapping. For cj0669 and cj0920c linear epitopes were identified. For cj0669, specificity assays revealed a specific linear epitope site. Consequently, an eleven amino acid residue sequence TLIKELKRLGI was analyzed via alanine scan, which revealed the glycine residue to be significant for binding of the antibody. The innovative approach presented herein of generating cDNAs of prokaryotes in combination with a microarray platform rendering time-consuming purification steps obsolete has helped to illuminate novel immunodominant proteins of C.jejuni. The findings of a specific linear epitope pave the way for a plethora of future research and the potential use in diagnostic applications such as serological screenings. Moreover, the current approach is easily adaptable to other highly relevant bacteria making it a formidable tool for the future discovery of antigens and potential biomarkers. Consequently, it is desirable to simplify the identification of structural epitopes, as this would extend the spectrum of novel epitopes to be detected.
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Affiliation(s)
- Sebastian Hoppe
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
| | - Frank F. Bier
- Fraunhofer Institute for Biomedical Engineering, Am Muehlenberg, Potsdam, Germany
- University Potsdam, Institute of Biochemistry and Biology, Potsdam, Germany
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36
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Mukamoto M, Maeda H, Kohda T, Nozaki C, Takahashi M, Kozaki S. Characterization of neutralizing mouse-human chimeric and shuffling antibodies against botulinum neurotoxin A. Microbiol Immunol 2012; 56:748-55. [DOI: 10.1111/j.1348-0421.2012.00503.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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37
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Kirchdoerfer RN, Herrin BR, Han BW, Turnbough CL, Cooper MD, Wilson IA. Variable lymphocyte receptor recognition of the immunodominant glycoprotein of Bacillus anthracis spores. Structure 2012; 20:479-86. [PMID: 22405006 DOI: 10.1016/j.str.2012.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Revised: 01/06/2012] [Accepted: 01/10/2012] [Indexed: 11/28/2022]
Abstract
Variable lymphocyte receptors (VLRs) are the adaptive immune receptors of jawless fish, which evolved adaptive immunity independent of other vertebrates. In lieu of the immunoglobulin fold-based T and B cell receptors, lymphocyte-like cells of jawless fish express VLRs (VLRA, VLRB, or VLRC) composed of leucine-rich repeats and are similar to toll-like receptors (TLRs) in structure, but antibodies (VLRB) and T cell receptors (VLRA and VLRC) in function. Here, we present the structural and biochemical characterization of VLR4, a VLRB, in complex with BclA, the immunodominant glycoprotein of Bacillus anthracis spores. Using a combination of crystallography, mutagenesis, and binding studies, we delineate the mode of antigen recognition and binding between VLR4 and BclA, examine commonalities in VLRB recognition of antigens, and demonstrate the potential of VLR4 as a diagnostic tool for the identification of B. anthracis spores.
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Affiliation(s)
- Robert N Kirchdoerfer
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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38
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Marseglia A, Castellazzi AM, Valsecchi C, Licari A, Piva G, Rossi F, Fiorentini L, Marseglia GL. Outcome of oral provocation test in egg-sensitive children receiving semi-fat hard cheese Grana Padano PDO (protected designation of origin) containing, or not, lysozyme. Eur J Nutr 2012; 52:877-83. [PMID: 22692502 DOI: 10.1007/s00394-012-0394-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 05/29/2012] [Indexed: 11/25/2022]
Abstract
PURPOSE Lysozyme, obtained from egg white, is a potential food allergen used in the dairy industry to prevent late blowing of the loaf caused by the outgrowth of clostridial spores (Cl. butyricum and Cl. tyrobutyricum) during cheese aging. The aim of this study was to evaluate the possible correlation between egg protein allergy in pediatric age and sensitization to egg lysozyme, used for the preparation of Grana Padano cheese. METHODS The tolerability of Grana Padano cheese has been evaluated in pediatric patients allergic to egg proteins through an oral provocation test with increasing amounts of cheese containing, or not, lysozyme at 12 and 24 months of aging. RESULTS When lysozyme-sensitized children received 12-months aged and lysozyme-containing cheese, several immediate and late adverse reactions such as itching, abdominal pain, vomiting, nausea, dermatitis, rhinitis, bronchial asthma, urticaria, and angioedema were seen in 5 out of 21 subjects; only 1 out of 21 children showed an adverse reaction after challenge with 24-months-ripened lysozyme-containing cheese. CONCLUSIONS There is a possible relationship between the severity of allergic reactions and the lysozyme-specific IgE level in blood. In particular vomiting, hypotension, and abdominal pain were present when IgE level was higher than 7 kU/L. A ripening time of 24 months may reduce allergy problems when lysozyme-containing cheese is given to sensitized subjects, probably due to the hydrolysis of antigenic epitopes during aging.
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Affiliation(s)
- A Marseglia
- Dipartimento di Scienze Clinico-Chirurgiche, Diagnostiche e Pediatriche, Sezione di Scienze Pediatriche, Fondazione IRCCS Policlinico San Matteo, Università degli Studi di Pavia, Piazzale Golgi 9, 27100, Pavia, Italy
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39
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Lee I, Luo X, Huang J, Cui XT, Yun M. Detection of cardiac biomarkers using single polyaniline nanowire-based conductometric biosensors. BIOSENSORS-BASEL 2012; 2:205-20. [PMID: 25585711 PMCID: PMC4263570 DOI: 10.3390/bios2020205] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 04/20/2012] [Accepted: 04/25/2012] [Indexed: 12/04/2022]
Abstract
The detection of myoglobin (Myo), cardiac troponin I (cTnI), creatine kinase-MB (CK-MB), and b-type natriuretic peptide (BNP) plays a vital role in diagnosing cardiovascular diseases. Here we present single site-specific polyaniline (PANI) nanowire biosensors that can detect cardiac biomarkers such as Myo, cTnI, CK-MB, and BNP with ultra-high sensitivity and good specificity. Using single PANI nanowire-based biosensors integrated with microfluidic channels, very low concentrations of Myo (100 pg/mL), cTnI (250 fg/mL), CK-MB (150 fg/mL), and BNP (50 fg/mL) were detected. The single PANI nanowire-based biosensors displayed linear sensing profiles for concentrations ranging from hundreds (fg/mL) to tens (ng/mL). In addition, devices showed a fast (few minutes) response satisfying respective reference conditions for Myo, cTnI, CK-MB, and BNP diagnosis of heart failure and for determining the stage of the disease. This single PANI nanowire-based biosensor demonstrated superior biosensing reliability with the feasibility of label free detection and improved processing cost efficiency due to good biocompatibility of PANI to monoclonal antibodies (mAbs). Therefore, this development of single PANI nanowire-based biosensors can be applied to other biosensors for cancer or other diseases.
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Affiliation(s)
- Innam Lee
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Xiliang Luo
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Jiyong Huang
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA.
| | - Xinyan Tracy Cui
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Minhee Yun
- Department of Electrical and Computer Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA.
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40
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Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint. Structure 2012; 20:259-69. [DOI: 10.1016/j.str.2011.11.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 11/22/2011] [Accepted: 11/22/2011] [Indexed: 11/18/2022]
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41
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Stanfield RL, Julien JP, Pejchal R, Gach JS, Zwick MB, Wilson IA. Structure-based design of a protein immunogen that displays an HIV-1 gp41 neutralizing epitope. J Mol Biol 2011; 414:460-76. [PMID: 22033480 PMCID: PMC3245871 DOI: 10.1016/j.jmb.2011.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Revised: 10/03/2011] [Accepted: 10/10/2011] [Indexed: 01/21/2023]
Abstract
Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, we identified an unrelated protein, interleukin (IL)-22, with a surface-exposed region that is structurally homologous in its backbone to the gp41 Z13e1 epitope. By grafting the gp41 Z13e1 epitope sequence onto the structurally homologous region in IL-22, we engineered a novel protein (Z13-IL22-2) that contains the MPER epitope sequence for use as a potential immunogen and as a reagent for the detection of Z13e1-like antibodies. The Z13-IL22-2 protein binds Fab Z13e1 with a K(d) of 73 nM. The crystal structure of Z13-IL22-2 in complex with Fab Z13e1 shows that the epitope region is faithfully replicated in the Fab-bound scaffold protein; however, isothermal calorimetry studies indicate that Fab binding to Z13-IL22-2 is not a lock-and-key event, leaving open the question of whether conformational changes upon binding occur in the Fab, in Z13-IL-22, or in both.
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Affiliation(s)
- Robyn L Stanfield
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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42
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Kirchdoerfer RN, Garner AL, Flack CE, Mee JM, Horswill AR, Janda KD, Kaufmann GF, Wilson IA. Structural basis for ligand recognition and discrimination of a quorum-quenching antibody. J Biol Chem 2011; 286:17351-8. [PMID: 21454495 PMCID: PMC3089576 DOI: 10.1074/jbc.m111.231258] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 03/13/2011] [Indexed: 11/06/2022] Open
Abstract
In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using "quorum sensing," which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 Å resolution to determine its mechanism of ligand recognition. A key Glu(H95) provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11·AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.
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Affiliation(s)
| | | | - Caralyn E. Flack
- the Department of Microbiology, University of Iowa, Iowa City, Iowa 52242
| | | | | | - Kim D. Janda
- Chemistry and Immunology & Microbial Science
- The Skaggs Institute for Chemical Biology
- Worm Institute for Research and Medicine, The Scripps Research Institute, La Jolla, California 92037 and
| | | | - Ian A. Wilson
- From the Departments of Molecular Biology and
- The Skaggs Institute for Chemical Biology
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Xia L, Willison LN, Porter L, Robotham JM, Teuber SS, Sathe SK, Roux KH. Mapping of a conformational epitope on the cashew allergen Ana o 2: a discontinuous large subunit epitope dependent upon homologous or heterologous small subunit association. Mol Immunol 2010; 47:1808-16. [PMID: 20362338 DOI: 10.1016/j.molimm.2010.01.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 01/19/2010] [Accepted: 01/22/2010] [Indexed: 01/05/2023]
Abstract
The 11S globulins are members of the cupin protein superfamily and represent an important class of tree nut allergens for which a number of linear epitopes have been mapped. However, specific conformational epitopes for these allergens have yet to be described. We have recently reported a cashew Ana o 2 conformational epitope defined by murine mAb 2B5 and competitively inhibited by a subset of patient IgE antibodies. The 2B5 epitope appears to reside on the large (acidic) subunit, is dependent upon small (basic) subunit association for expression, and is highly susceptible to denaturation. Here we fine map the epitope using a combination of recombinant chimeric cashew Ana o 2-soybean Gly m 6 chimeras, deletion and point mutations, molecular modeling, and electron microscopy of 2B5-Ana o 2 immune complexes. Key residues appear confined to a 24 amino acid segment near the N-terminus of the large subunit peptide, a portion of which makes direct contact with the small subunit. These data provide an explanation for both the small subunit dependence and the structurally labile nature of the epitope.
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Affiliation(s)
- Lixin Xia
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4295, USA
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44
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Yokota A, Tsumoto K, Shiroishi M, Nakanishi T, Kondo H, Kumagai I. Contribution of asparagine residues to the stabilization of a proteinaceous antigen-antibody complex, HyHEL-10-hen egg white lysozyme. J Biol Chem 2010; 285:7686-96. [PMID: 20038580 PMCID: PMC2844214 DOI: 10.1074/jbc.m109.089623] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 12/10/2009] [Indexed: 11/06/2022] Open
Abstract
Many germ line antibodies have asparagine residues at specific sites to achieve specific antigen recognition. To study the role of asparagine residues in the stabilization of antigen-antibody complexes, we examined the interaction between hen egg white lysozyme (HEL) and the corresponding HyHEL-10 variable domain fragment (Fv). We introduced Ala and Asp substitutions into the Fv side chains of L-Asn-31, L-Asn-32, and L-Asn-92, which interact directly with residues in HEL via hydrogen bonding in the wild-type Fv-HEL complex, and we investigated the interactions between these mutant antibodies and HEL. Isothermal titration calorimetric analysis showed that all the mutations decreased the negative enthalpy change and decreased the association constants of the interaction. Structural analyses showed that the effects of the mutations on the structure of the complex could be compensated for by conformational changes and/or by gains in other interactions. Consequently, the contribution of two hydrogen bonds was minor, and their abolition by mutation resulted in only a slight decrease in the affinity of the antibody for its antigen. By comparison, the other two hydrogen bonds buried at the interfacial area had large enthalpic advantage, despite entropic loss that was perhaps due to stiffening of the interface by the bonds, and were crucial to the strength of the interaction. Deletion of these strong hydrogen bonds could not be compensated for by other structural changes. Our results suggest that asparagine can provide the two functional groups for strong hydrogen bond formation, and their contribution to the antigen-antibody interaction can be attributed to their limited flexibility and accessibility at the complex interface.
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Affiliation(s)
- Akiko Yokota
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579
- the Protein Design Research Group, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566
| | - Kouhei Tsumoto
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579
- the Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277-8562, and
| | - Mitsunori Shiroishi
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579
| | - Takeshi Nakanishi
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579
| | - Hidemasa Kondo
- the Functional Protein Research Group, Research Institute of Genome-based Biofactory, National Institute of Advanced Industrial Science and Technology, 2-17-2-1 Tsukisamu-Higashi, Toyohira, Sapporo 062-8517, Japan
| | - Izumi Kumagai
- From the Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aoba-yama 6-6-11, Sendai 980-8579
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45
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Irving MB, Craig L, Menendez A, Gangadhar BP, Montero M, van Houten NE, Scott JK. Exploring peptide mimics for the production of antibodies against discontinuous protein epitopes. Mol Immunol 2009; 47:1137-48. [PMID: 20031219 DOI: 10.1016/j.molimm.2009.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Revised: 10/12/2009] [Accepted: 10/15/2009] [Indexed: 11/30/2022]
Abstract
Peptide "mimics" (mimotopes) of linear protein epitopes and carbohydrate epitopes have been successfully used as immunogens to elicit cross-reactive antibodies against their cognate epitopes; however, immunogenic mimicry has been difficult to achieve for discontinuous protein epitopes. To explore this, we developed from phage-displayed peptide libraries optimized peptide mimics for three well-characterized discontinuous epitopes on hen egg lysozyme and horse cytochrome c. The peptides competed with their cognate antigens for antibody binding, displayed affinities in the nM range, and shared critical binding residues with their native epitopes. Yet, while immunogenic, none of the peptides elicited antibodies that cross-reacted with their cognate antigens. We analyzed the 3-D structure of the site within each discontinuous epitope that shared critical binding residues with its peptide mimic, and observed that in each case it formed a ridge-like patch on the epitope; in no case did it cover most or all of the epitope. Thus, the peptides' lack of immunogenic mimicry could be attributed to their inability to recapitulate the topological features of their cognate epitopes. Our results suggest that direct peptide immunizations are not a practical strategy for generating targeted antibody responses against discontinuous epitopes.
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Affiliation(s)
- Melita B Irving
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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46
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Pomés A. Relevant B cell epitopes in allergic disease. Int Arch Allergy Immunol 2009; 152:1-11. [PMID: 19940500 DOI: 10.1159/000260078] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The 3-dimensional structure of an allergen defines the accessible parts on the surface of the molecule or epitopes that interact with antibodies. Mapping the antigenic determinants for IgE antibody binding has been pursued through strategies based on the use of overlapping synthetic peptides, recombinant allergenic fragments or unfolded allergens. These approaches led to the identification of mostly linear epitopes and are useful for food allergens that undergo digestion or food processing. For inhaled allergens, conformational epitopes appear to be the primary targets of IgE responses. Knowledge of the molecular structure of allergens alone and in complex with antibodies that interfere with IgE antibody binding is important to understand the immune recognition of B cell-antigenic determinants on allergens and the design of recombinant allergens for immunotherapy. Starting with the molecular cloning and expression of allergens, and with the advent of X-ray crystallography and nuclear magnetic resonance techniques, we have been able to visualize conformational epitopes on allergens.
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Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, Va., USA.
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47
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Comparison of the results obtained by ELISA and surface plasmon resonance for the determination of antibody affinity. J Immunol Methods 2009; 352:13-22. [PMID: 19854197 DOI: 10.1016/j.jim.2009.10.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 09/22/2009] [Accepted: 10/08/2009] [Indexed: 11/22/2022]
Abstract
The aim of this study was to compare the affinity values obtained for a monoclonal antibody/antigen complex using two different techniques, surface plasmon resonance (SPR) and an enzyme linked immunosorbent assay (ELISA) approach recently described by Bobrovnik S.A. and by Stevens F.J. These two techniques can be used in particular to determine the equilibrium dissociation constant, K(D), of the complex in solution or on a surface. Bobrovnik's method gives two K(D) values that differ by a factor of 100, demonstrating that two populations of complexes are present in solution. In an initial step, one protein binds relatively weakly to the other (high K(D)) and this is followed by a conformational change in the most flexible portion of the antigen, which increases the affinity (low K(D)). Only the higher of the two K(D) values can be detected when complex formation in solution is investigated using SPR, because the interaction measured concerns the fibronectin/antibody complexes of lowest affinity. In contrast, when measuring association at the sensor surface, SPR gives an average result between the two K(D) values because complexes corresponding to both affinities can form in this situation. The constants that characterise the kinetics of the fibronectin-antibody interaction obtained by SPR and ELISA are therefore different, because the methods do not allow the same phenomena to be observed. However they are consistent and complementary.
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48
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El-Awar N, Terasaki PI, Nguyen A, Sasaki N, Morales-Buenrostro LE, Saji H, Maruya E, Poli F. Epitopes of human leukocyte antigen class I antibodies found in sera of normal healthy males and cord blood. Hum Immunol 2009; 70:844-53. [DOI: 10.1016/j.humimm.2009.06.020] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2008] [Revised: 06/20/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
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49
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Xu WX, He YP, Tang HP, Jia XF, Ji CN, Gu SH, Sun XX, Xie Y. Minimal motif mapping of a known epitope on human zona pellucida protein-4 using a peptide biosynthesis strategy. J Reprod Immunol 2009; 81:9-16. [PMID: 19539378 DOI: 10.1016/j.jri.2009.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 04/07/2009] [Accepted: 04/13/2009] [Indexed: 10/20/2022]
Abstract
An important step in the development of a human zona pellucida (huZP) peptide vaccine is to define the minimal amino acid motif for a mapped B cell epitope peptide within huZP4. Identification of this minimal motif is necessary to remove an overlapping T cell epitope that induces a pathogenic T cell response. Here we describe motif (PLTLEL(314-319)) mapping of an 18mer B cell epitope peptide(308-325) on huZP4 protein (previously known as huZP1/ZPB protein), achieved using a set of 22 biosynthetic 8mer peptides fused with truncated glutathione S-transferase (GST) or truncated streptavidin protein, and detected using rabbit anti-porcine zona pellucida (pZP) IgG. The immunogenicity of the B cell epitope peptide was evaluated in rabbits using expressed B cell epitope peptide fused with truncated streptavidin as the antigen. This construct elicited high titer antibody to the 18mer B cell epitope peptide, with reactivity to native human ZP, the biosynthetic 18mer peptide and the 18mer peptide GST fusion protein.
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Affiliation(s)
- Wan-Xiang Xu
- Shanghai Institute of Planned Parenthood Research, Shanghai 200032, China.
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50
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Duquesnoy RJ, Marrari M. Correlations between Terasaki's HLA class I epitopes and HLAMatchmaker-defined eplets on HLA-A, -B and -C antigens. ACTA ACUST UNITED AC 2009; 74:117-33. [PMID: 19497041 DOI: 10.1111/j.1399-0039.2009.01271.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the determination of human leukocyte antigen (HLA) antibody specificity has traditionally been directed toward HLA antigens, there is now increasing attention to structurally defined HLA epitopes. An understanding of the HLA epitope repertoire is important to acceptable mismatching for sensitized patients and to a new epitope-based matching algorithm aimed to reduce antibody-mediated rejection. There are two strategies to determine the HLA epitope repertoire. Terasaki's group has used an empirical method to analyze the reactivity of single allele Luminex panels with mouse monoclonal antibodies (mAbs) and absorbed/eluted alloantibodies with a computer program based on shared residues in the amino acid sequences of reactive alleles. HLAMatchmaker is a theoretical algorithm that predicts HLA epitopes on the HLA molecular surface from stereochemical modeling of epitope-paratope interfaces of antigen-antibody complexes. Our epitope repertoire is based on so-called 'eplets' representing 3-A patches of at least one polymorphic residue on the molecular surface. A comparative analysis has shown that 81/103 Terasaki's HLA class I epitopes are equivalent to individual eplets (n = 50) or pairs of eplets (n = 31) separated far enough to serve as potential contact sites for two complementarity-determining regions of antibody. An additional 12 Terasaki's epitopes (TerEps) correspond to eplets with permissible residue combinations that do not seem to affect epitope specificity. We could not identify corresponding eplets for the remaining 10 TerEps, including 8 that might be considered xeno-epitopes defined by mouse mAbs. Conversely, HLAMatchmaker has 38 additional eplets in well-exposed surface positions that do not have equivalent TerEps, and for many of them, we have found specific antibodies. These findings strengthen the concept that eplets are essential basic units of HLA epitopes and that they provide a better understanding of HLA immunogenicity (i.e. ability to induce an antibody response) and antigenicity (i.e. reactivity with specific antibody).
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Affiliation(s)
- R J Duquesnoy
- Division of Transplantation Pathology, Thomas E. Starzl Transplantation Institute, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA.
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