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Lecerf M, Lacombe RV, Dimitrov JD. Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region. Front Immunol 2023; 14:1266668. [PMID: 38077343 PMCID: PMC10710144 DOI: 10.3389/fimmu.2023.1266668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
An antibody molecule that can bind to multiple distinct antigens is defined as polyreactive. In the present study, we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B-cell types of healthy humans. The data revealed several sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, and longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B-cell populations used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies and demonstrated that human antibodies can use multiple pathways for achieving antigen-binding promiscuity. These data reconcile some contradictions in the literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that the mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B-cell compartments. Finally, these data can be of use for efforts in the development and engineering of therapeutic antibodies.
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Affiliation(s)
| | | | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
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2
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Jaiswal D, Verma S, Nair DT, Salunke DM. Antibody multispecificity: A necessary evil? Mol Immunol 2022; 152:153-161. [DOI: 10.1016/j.molimm.2022.10.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
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3
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Blackler RJ, Müller-Loennies S, Pokorny-Lehrer B, Legg MSG, Brade L, Brade H, Kosma P, Evans SV. Antigen binding by conformational selection in near-germline antibodies. J Biol Chem 2022; 298:101901. [PMID: 35395245 PMCID: PMC9112003 DOI: 10.1016/j.jbc.2022.101901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/20/2023] Open
Abstract
Conformational flexibility in antibody-combining sites has been hypothesized to facilitate polyspecificity toward multiple unique epitopes and enable the limited germline repertoire to match an overwhelming diversity of potential antigens; however, elucidating the mechanisms of antigen recognition by flexible antibodies has been understandably challenging. Here, multiple liganded and unliganded crystal structures of the near-germline anticarbohydrate antibodies S25–2 and S25–39 are reported, which reveal an unprecedented diversity of complementarity-determining region H3 conformations in apparent equilibrium. These structures demonstrate that at least some germline or near-germline antibodies are flexible entities sensitive to their chemical environments, with conformational selection available as an evolved mechanism that preserves the inherited ability to recognize common pathogens while remaining adaptable to new threats.
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Affiliation(s)
- Ryan J Blackler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC, Canada
| | | | - Barbara Pokorny-Lehrer
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Max S G Legg
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC, Canada
| | - Lore Brade
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Helmut Brade
- Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Paul Kosma
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Stephen V Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria BC, Canada.
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4
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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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del Moral-Sánchez I, Sliepen K. Strategies for inducing effective neutralizing antibody responses against HIV-1. Expert Rev Vaccines 2019; 18:1127-1143. [PMID: 31791150 PMCID: PMC6961309 DOI: 10.1080/14760584.2019.1690458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Introduction: Despite intensive research efforts, there is still no effective prophylactic vaccine available against HIV-1. Currently, substantial efforts are devoted to the development of vaccines aimed at inducing broadly neutralizing antibodies (bNAbs), which are capable of neutralizing most HIV-1 strains. All bNAbs target the HIV-1 envelope glycoprotein (Env), but Env immunizations usually only induce neutralizing antibodies (NAbs) against the sequence-matched virus and not against other strains.Areas covered: We describe the different strategies that have been explored to improve the breadth and potency of anti-HIV-1 NAb responses. The discussed strategies include the application of engineered Env immunogens, optimization of (bNAb) epitopes, different cocktail and sequential vaccination strategies, nanoparticles and nucleic acid-based vaccines.Expert opinion: A combination of the strategies described in this review and future approaches are probably needed to develop an effective HIV-1 vaccine that can induce broad, potent and long-lasting NAb responses.
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Affiliation(s)
- Iván del Moral-Sánchez
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Kwinten Sliepen
- Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands,CONTACT Kwinten Sliepen Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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6
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Prigent J, Jarossay A, Planchais C, Eden C, Dufloo J, Kök A, Lorin V, Vratskikh O, Couderc T, Bruel T, Schwartz O, Seaman MS, Ohlenschläger O, Dimitrov JD, Mouquet H. Conformational Plasticity in Broadly Neutralizing HIV-1 Antibodies Triggers Polyreactivity. Cell Rep 2019; 23:2568-2581. [PMID: 29847789 PMCID: PMC5990490 DOI: 10.1016/j.celrep.2018.04.101] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/26/2018] [Accepted: 04/25/2018] [Indexed: 12/18/2022] Open
Abstract
Human high-affinity antibodies to pathogens often recognize unrelated ligands. The molecular origin and the role of this polyreactivity are largely unknown. Here, we report that HIV-1 broadly neutralizing antibodies (bNAbs) are frequently polyreactive, cross-reacting with non-HIV-1 molecules, including self-antigens. Mutating bNAb genes to increase HIV-1 binding and neutralization also results in de novo polyreactivity. Unliganded paratopes of polyreactive bNAbs with improved HIV-1 neutralization exhibit a conformational flexibility, which contributes to enhanced affinity of bNAbs to various HIV-1 envelope glycoproteins and non-HIV antigens. Binding adaptation of polyreactive bNAbs to the divergent ligands mainly involves hydrophophic interactions. Plasticity of bNAbs' paratopes may, therefore, facilitate accommodating divergent viral variants, but it simultaneously triggers promiscuous binding to non-HIV-1 antigens. Thus, a certain level of polyreactivity can be a mark of adaptable antibodies displaying optimal pathogens' recognition.
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Affiliation(s)
- Julie Prigent
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Annaëlle Jarossay
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France
| | - Cyril Planchais
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Caroline Eden
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jérémy Dufloo
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | - Ayrin Kök
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Valérie Lorin
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Oxana Vratskikh
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France
| | - Thérèse Couderc
- Biology of Infection Unit, INSERM U1117, Department of Cell Biology and Infection, Institut Pasteur, Paris 75015, France
| | - Timothée Bruel
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | - Olivier Schwartz
- Virus & Immunity Unit, Department of Virology, Institut Pasteur, Paris 75015, France; CNRS URA3015, Paris 75015, France
| | | | | | - Jordan D Dimitrov
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; INSERM, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France; Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris 75006, France.
| | - Hugo Mouquet
- Laboratory of Humoral Response to Pathogens, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1222, Paris 75015, France.
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7
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Antibody specificity and promiscuity. Biochem J 2019; 476:433-447. [PMID: 30723137 DOI: 10.1042/bcj20180670] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 12/16/2022]
Abstract
The immune system is capable of making antibodies against anything that is foreign, yet it does not react against components of self. In that sense, a fundamental requirement of the body's immune defense is specificity. Remarkably, this ability to specifically attack foreign antigens is directed even against antigens that have not been encountered a priori by the immune system. The specificity of an antibody for the foreign antigen evolves through an iterative process of somatic mutations followed by selection. There is, however, accumulating evidence that the antibodies are often functionally promiscuous or multi-specific which can lead to their binding to more than one antigen. An important cause of antibody cross-reactivity is molecular mimicry. Molecular mimicry has been implicated in the generation of autoimmune response. When foreign antigen shares similarity with the component of self, the antibodies generated could result in an autoimmune response. The focus of this review is to capture the contrast between specificity and promiscuity and the structural mechanisms employed by the antibodies to accomplish promiscuity, at the molecular level. The conundrum between the specificity of the immune system for foreign antigens on the one hand and the multi-reactivity of the antibody on the other has been addressed. Antibody specificity in the context of the rapid evolution of the antigenic determinants and molecular mimicry displayed by antigens are also discussed.
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8
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Salunke DM, Nair DT. Macromolecular structures: Quality assessment and biological interpretation. IUBMB Life 2017; 69:563-571. [DOI: 10.1002/iub.1640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Dinakar M. Salunke
- International Centre for Genetic Engineering and Biotechnology; Aruna Asaf Ali Marg; New Delhi India
| | - Deepak T. Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster; 3rd Milestone, Faridabad-Gurgaon Expressway Faridabad Haryana India
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9
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Weichenberger CX, Pozharski E, Rupp B. Twilight reloaded: the peptide experience. Acta Crystallogr D Struct Biol 2017; 73:211-222. [PMID: 28291756 PMCID: PMC5349433 DOI: 10.1107/s205979831601620x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 10/12/2016] [Indexed: 01/20/2024] Open
Abstract
The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.
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Affiliation(s)
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Bernhard Rupp
- k.k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084, USA
- Department of Genetic Epidemiology, Medical University Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck, Austria
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10
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Rupp B, Wlodawer A, Minor W, Helliwell JR, Jaskolski M. Correcting the record of structural publications requires joint effort of the community and journal editors. FEBS J 2016; 283:4452-4457. [PMID: 27229767 DOI: 10.1111/febs.13765] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/13/2016] [Accepted: 05/25/2016] [Indexed: 01/04/2023]
Abstract
Seriously flawed and even fictional models of biomolecular crystal structures, although rare, still persist in the record of structural repositories and databases. The ensuing problems of database contamination and persistence of publications based on incorrect structure models must be effectively addressed. The burden cannot be simply left to the critical voices who take the effort to contribute dissenting comments that are mostly ignored. The entire structural biology community, and particularly the journal editors who exercise significant power in this respect, must engage in a constructive dialog lest structural biology lose its credibility as an evidence-based empirical science.
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Affiliation(s)
- Bernhard Rupp
- k.-k. Hofkristallamt, Vista, CA, USA.,Department of Genetic Epidemiology, Medical University of Innsbruck, Austria
| | - Alexander Wlodawer
- Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, USA
| | - Wladek Minor
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | | | - Mariusz Jaskolski
- Department of Crystallography, Faculty of Chemistry, Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Adam Mickiewicz University, Poznan, Poland
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Salunke DM, Khan T, Gaur V, Tapryal S, Kaur K. Response to Comment on Three X-ray Crystal Structure Papers. THE JOURNAL OF IMMUNOLOGY 2016; 196:524-8. [PMID: 26747566 DOI: 10.4049/jimmunol.1501474] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
| | - Tarique Khan
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, TX 75390
| | - Vineet Gaur
- International Institute of Molecular and Cell Biology; Warsaw 02-109, Poland
| | - Suman Tapryal
- Department of Biotechnology, Central University of Rajasthan, Bandarsindri-305817, India; and
| | - Kanwaljeet Kaur
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
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12
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Stanfield R, Pozharski E, Rupp B. Comment on Three X-ray Crystal Structure Papers. THE JOURNAL OF IMMUNOLOGY 2016; 196:521-4. [PMID: 26747564 DOI: 10.4049/jimmunol.1501343] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | - Edwin Pozharski
- School of Medicine, University of Maryland, Baltimore, MD 21201;
| | - Bernhard Rupp
- Medical University of Innsbruck, A 6020 Innsbruck, Austria; and Department of Forensic Crystallography, k.-k. Hofkristallamt, Vista, CA 92084
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