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Éliás S, Wrzodek C, Deane CM, Tissot AC, Klostermann S, Ros F. Prediction of polyspecificity from antibody sequence data by machine learning. FRONTIERS IN BIOINFORMATICS 2024; 3:1286883. [PMID: 38651055 PMCID: PMC11033685 DOI: 10.3389/fbinf.2023.1286883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 04/25/2024] Open
Abstract
Antibodies are generated with great diversity in nature resulting in a set of molecules, each optimized to bind a specific target. Taking advantage of their diversity and specificity, antibodies make up for a large part of recently developed biologic drugs. For therapeutic use antibodies need to fulfill several criteria to be safe and efficient. Polyspecific antibodies can bind structurally unrelated molecules in addition to their main target, which can lead to side effects and decreased efficacy in a therapeutic setting, for example via reduction of effective drug levels. Therefore, we created a neural-network-based model to predict polyspecificity of antibodies using the heavy chain variable region sequence as input. We devised a strategy for enriching antibodies from an immunization campaign either for antigen-specific or polyspecific binding properties, followed by generation of a large sequencing data set for training and cross-validation of the model. We identified important physico-chemical features influencing polyspecificity by investigating the behaviour of this model. This work is a machine-learning-based approach to polyspecificity prediction and, besides increasing our understanding of polyspecificity, it might contribute to therapeutic antibody development.
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Affiliation(s)
- Szabolcs Éliás
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Clemens Wrzodek
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alain C. Tissot
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Stefan Klostermann
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Francesca Ros
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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2
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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3
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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4
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Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens. Proc Natl Acad Sci U S A 2020; 117:22341-22350. [PMID: 32855302 PMCID: PMC7486785 DOI: 10.1073/pnas.2005102117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conformational diversity and self-cross-reactivity of antigens have been correlated with evasion from neutralizing antibody responses. We utilized single cell B cell sequencing, biolayer interferometry and X-ray crystallography to trace mutation selection pathways where the antibody response must resolve cross-reactivity between foreign and self-proteins bearing near-identical contact surfaces, but differing in conformational flexibility. Recurring antibody mutation trajectories mediate long-range rearrangements of framework (FW) and complementarity determining regions (CDRs) that increase binding site conformational diversity. These antibody mutations decrease affinity for self-antigen 19-fold and increase foreign affinity 67-fold, to yield a more than 1,250-fold increase in binding discrimination. These results demonstrate how conformational diversity in antigen and antibody does not act as a barrier, as previously suggested, but rather facilitates high affinity and high discrimination between foreign and self.
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5
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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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Varese M, Guardiola S, García J, Giralt E. Enthalpy‐ versus Entropy‐Driven Molecular Recognition in the Era of Biologics. Chembiochem 2019; 20:2981-2986. [DOI: 10.1002/cbic.201900270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Monica Varese
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Salvador Guardiola
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
| | - Ernest Giralt
- Institute for Research in Biomedicine (IRB Barcelona)Barcelona Institute of Science and Technology (BIST) Baldiri Reixac, 10 08028 Barcelona Spain
- Department of Inorganic and Organic ChemistryUniversity of Barcelona Martí i Franquès 1–11 08028 Barcelona Spain
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7
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Osajima T, Hoshino T. Roles of the respective loops at complementarity determining region on the antigen-antibody recognition. Comput Biol Chem 2016; 64:368-383. [DOI: 10.1016/j.compbiolchem.2016.08.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 01/25/2023]
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8
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Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies. Structure 2016; 24:1346-1357. [PMID: 27477385 PMCID: PMC5250619 DOI: 10.1016/j.str.2016.06.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/07/2023]
Abstract
Antibody somatic hypermutation (SHM) and affinity maturation enhance antigen recognition by modifying antibody paratope structure to improve its complementarity with the target epitope. SHM-induced changes in paratope dynamics may also contribute to antibody maturation, but direct evidence of this is limited. Here, we examine two classes of HIV-1 broadly neutralizing antibodies (bNAbs) for SHM-induced changes in structure and dynamics, and delineate the effects of these changes on interactions with the HIV-1 envelope glycoprotein (Env). In combination with new and existing structures of unmutated and affinity matured antibody Fab fragments, we used hydrogen/deuterium exchange with mass spectrometry to directly measure Fab structural dynamics. Changes in antibody structure and dynamics were positioned to improve complementarity with Env, with changes in dynamics primarily observed at the paratope peripheries. We conclude that SHM optimizes paratope complementarity to conserved HIV-1 epitopes and restricts the mobility of paratope-peripheral residues to minimize clashes with variable features on HIV-1 Env.
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9
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Selzer L, Zlotnick A. Assembly and Release of Hepatitis B Virus. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a021394. [PMID: 26552701 DOI: 10.1101/cshperspect.a021394] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The hepatitis B virus (HBV) core protein is a dynamic and versatile protein that directs many viral processes. During capsid assembly, core protein allosteric changes ensure efficient formation of a stable capsid that assembles while packaging viral RNA-polymerase complex. Reverse transcription of the RNA genome as well as transport of the capsid to multiple cellular compartments are directed by dynamic phosphorylation and structural changes of core protein. Subsequently, interactions of the capsid with the surface proteins and/or host proteins trigger envelopment and release of the viral capsids or the transport to the nucleus. Held together by many weak protein-protein interactions, the viral capsid is an extraordinary metastable machine that is stable enough to persist in the cellular and extracellular environment but dissociates to allow release of the viral genome at the right time during infection.
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Affiliation(s)
- Lisa Selzer
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405
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10
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Awino JK, Zhao Y. Polymeric Nanoparticle Receptors as Synthetic Antibodies for Nonsteroidal Anti-Inflammatory Drugs (NSAIDs). ACS Biomater Sci Eng 2015; 1:425-430. [DOI: 10.1021/acsbiomaterials.5b00042] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph K. Awino
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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11
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Sun Y, Yang Y, Wang L, Lv L, Zhu J, Han W, Wang E, Guo X, Zhen Y. Highly sensitive detection of cancer antigen human epidermal growth factor receptor 2 using novel chicken egg yolk immunoglobulin. Biologicals 2015; 43:165-70. [PMID: 25841774 DOI: 10.1016/j.biologicals.2015.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/23/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) is an important biomarker that plays a crucial role in therapeutic decision-making for breast cancer patients. Ensuring the accuracy and reproducibility of HER2 assays by enzyme-linked immunosorbent assay (ELISA), western blot and immunohistochemistry (IHC) requires high sensitive and specific antibodies. Immunoglobulin Y (IgY) is a kind of avian antibody usually isolated from chicken egg yolks. Generation and use of IgY is of increasing interest in a wide variety of applications within the life sciences. In this study, IgY antibodies against two different truncated proteins of the extracellular domain (ECD) of human HER2 were produced, their sensitivity and specificity were evaluated. Specific IgYs were produced by hens immunized with the ECD proteins of human HER2 in long-standing immunization response and were isolated from yolks with a purity of 90% by water dilution, salt precipitations and ultrafiltration. The anti-HER2 IgYs were analytically validated for specificity by ELISA, western blot, immunocytochemistry and IHC. The IgYs bound desired targets in cells and fixed tissues and showed high affinity to HER2. The results demonstrated the viability of detection of HER2 with IgYs and showed promise for the using of IgYs in strict clinical validation.
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Affiliation(s)
- Yong Sun
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning Province, China
| | - Yiheng Yang
- Clinical Medicine of Seven-Year-Program, Dalian Medical University, Dalian, Liaoning Province, China
| | - Lifen Wang
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Li Lv
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Jie Zhu
- The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning Province, China
| | - Wenqi Han
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning Province, China
| | - Enxia Wang
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning Province, China
| | - Xin Guo
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning Province, China
| | - Yuhong Zhen
- College of Pharmacy, Dalian Medical University, Dalian, Liaoning Province, China.
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12
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Structural and electrostatic analysis of HLA B-cell epitopes: inference on immunogenicity and prediction of humoral alloresponses. Curr Opin Organ Transplant 2015; 19:420-7. [PMID: 24977436 DOI: 10.1097/mot.0000000000000108] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
PURPOSE OF REVIEW The immunogenic capacity of donor human leukocyte antigen (HLA) to induce humoral immune responses is not an intrinsic property of the mismatched alloantigen but depends on the HLA phenotype of the recipient. In recent years, advances in molecular sequence technology and information from X-ray crystallography have enabled structural comparison of donor and recipient HLA type providing an opportunity for a more rational approach for determining HLA compatibility. In this article, we review studies investigating the molecular basis of antibody-antigen interactions and present computational approaches to determine the complex physiochemical and structural properties of B-cell epitopes. RECENT FINDINGS The relative immunogenicity of individual HLA mismatches may be predicted from analysis of polymorphic amino acids at continuous and discontinuous HLA sequence positions. The use of alloantigen sequence information alone, however, provides limited insight into key determinants of B-cell epitope immunogenicity, such as the orientation, accessibility and physiochemical properties of amino acid side chains. Advances in computational molecular modelling techniques now enable assessment of HLA-alloantibody interactions at the atomic level. Recent evidence supports a strong link between HLA B-cell epitope surface electrostatic potential and their immunogenicity. SUMMARY Assessment of the surface electrostatic properties of HLA alloantigens and computational analyses of HLA-alloantibody interactions represent a promising area for future research into the molecular basis of HLA immunogenicity and antigenicity.
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Selzer L, Katen S, Zlotnick A. The hepatitis B virus core protein intradimer interface modulates capsid assembly and stability. Biochemistry 2014; 53:5496-504. [PMID: 25102363 PMCID: PMC4151697 DOI: 10.1021/bi500732b] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 08/05/2014] [Indexed: 12/19/2022]
Abstract
During the hepatitis B virus (HBV) life cycle, capsid assembly and disassembly must ensure correct packaging and release of the viral genome. Here we show that changes in the dynamics of the core protein play an important role in regulating these processes. The HBV capsid assembles from 120 copies of the core protein homodimer. Each monomer contains a conserved cysteine at position 61 that can form an intradimer disulfide that we use as a marker for dimer conformational states. We show that dimers in the context of capsids form intradimer disulfides relatively rapidly. Surprisingly, compared to reduced dimers, fully oxidized dimers assembled slower and into capsids that were morphologically similar but less stable. We hypothesize that oxidized protein adopts a geometry (or constellation of geometries) that is unfavorable for capsid assembly, resulting in weaker dimer-dimer interactions as well as slower assembly kinetics. Our results suggest that structural flexibility at the core protein intradimer interface is essential for regulating capsid assembly and stability. We further suggest that capsid destabilization by the C61-C61 disulfide has a regulatory function to support capsid disassembly and release of the viral genome.
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Affiliation(s)
- Lisa Selzer
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sarah
P. Katen
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
- Department
of Biology and Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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14
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Computational and statistical study on the molecular interaction between antigen and antibody. J Mol Graph Model 2014; 53:128-139. [DOI: 10.1016/j.jmgm.2014.07.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/07/2014] [Accepted: 07/09/2014] [Indexed: 01/04/2023]
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15
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Fryer JP, Lennon VA, Pittock SJ, Jenkins SM, Fallier-Becker P, Clardy SL, Horta E, Jedynak EA, Lucchinetti CF, Shuster EA, Weinshenker BG, Wingerchuk DM, McKeon A. AQP4 autoantibody assay performance in clinical laboratory service. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2014; 1:e11. [PMID: 25340055 PMCID: PMC4202686 DOI: 10.1212/nxi.0000000000000011] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 03/31/2014] [Indexed: 01/23/2023]
Abstract
Objective: To compare performance of contemporary aquaporin-4–immunoglobulin (Ig) G assays in clinical service. Methods: Sera from neurologic patients (4 groups) and controls were tested initially by service ELISA (recombinant human aquaporin-4, M1 isoform) and then by cell-based fluorescence assays: fixed (CBA, M1-aquaporin-4, observer-scored) and live (fluorescence-activated cell sorting [FACS], M1 and M23 aquaporin-4 isoforms). Group 1: all Mayo Clinic patients tested from January to May 2012; group 2: consecutive aquaporin-4-IgG–positive patients from September 2011 (Mayo and non-Mayo); group 3: suspected ELISA false-negatives from 2011 to 2013 (physician-reported, high likelihood of neuromyelitis optica spectrum disorders [NMOSDs] clinically); group 4: suspected ELISA false-positives (physician-reported, not NMOSD clinically). Results: Group 1 (n = 388): M1-FACS assay performed optimally (areas under the curves: M1 = 0.64; M23 = 0.57 [p = 0.02]). Group 2 (n = 30): NMOSD clinical diagnosis was confirmed by: M23-FACS, 24; M1-FACS, 23; M1-CBA, 20; and M1-ELISA, 18. Six results were suspected false-positive: M23-FACS, 2; M1-ELISA, 2; and M23-FACS, M1-FACS, and M1-CBA, 2. Group 3 (n = 31, suspected M1-ELISA false-negatives): results were positive for 5 sera: M1-FACS, 5; M23-FACS, 3; and M1-CBA, 2. Group 4 (n = 41, suspected M1-ELISA false-positives): all negative except 1 (positive only by M1-CBA). M1/M23-cotransfected cells expressing smaller membrane arrays of aquaporin-4 yielded fewer false- positive FACS results than M23-transfected cells. Conclusion: Aquaporin-4-transfected CBAs, particularly M1-FACS, perform optimally in aiding NMOSD serologic diagnosis. High-order arrays of M23-aquaporin-4 may yield false-positive results by binding IgG nonspecifically.
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Affiliation(s)
- J P Fryer
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - V A Lennon
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - S J Pittock
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - S M Jenkins
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - P Fallier-Becker
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - S L Clardy
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - E Horta
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - E A Jedynak
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - C F Lucchinetti
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - E A Shuster
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - B G Weinshenker
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - D M Wingerchuk
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
| | - A McKeon
- Departments of Laboratory Medicine and Pathology (J.P.F., V.A.L., S.J.P., E.H., E.A.J., A.M.), Neurology (V.A.L., S.J.P., S.L.C., C.F.L., B.G.W., A.M.), Immunology (V.A.L.), and Health Sciences Research (S.M.J.), College of Medicine, Mayo Clinic, Rochester, MN; Institute of Pathology and Neuropathology (P. F.-B.), University of Tubingen, Germany; Department of Neurology (E.A.S.), College of Medicine, Mayo Clinic, Jacksonville, FL; and Department of Neurology (D.M.W.), College of Medicine, Mayo Clinic, Scottsdale, AZ
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16
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Backbone flexibility of CDR3 and immune recognition of antigens. J Mol Biol 2013; 426:1583-99. [PMID: 24380763 DOI: 10.1016/j.jmb.2013.12.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/03/2013] [Accepted: 12/19/2013] [Indexed: 11/22/2022]
Abstract
Conformational entropy is an important component of protein-protein interactions; however, there is no reliable method for computing this parameter. We have developed a statistical measure of residual backbone entropy in folded proteins by using the ϕ-ψ distributions of the 20 amino acids in common secondary structures. The backbone entropy patterns of amino acids within helix, sheet or coil form clusters that recapitulate the branching and hydrogen bonding properties of the side chains in the secondary structure type. The same types of residues in coil and sheet have identical backbone entropies, while helix residues have much smaller conformational entropies. We estimated the backbone entropy change for immunoglobulin complementarity-determining regions (CDRs) from the crystal structures of 34 low-affinity T-cell receptors and 40 high-affinity Fabs as a result of the formation of protein complexes. Surprisingly, we discovered that the computed backbone entropy loss of only the CDR3, but not all CDRs, correlated significantly with the kinetic and affinity constants of the 74 selected complexes. Consequently, we propose a simple algorithm to introduce proline mutations that restrict the conformational flexibility of CDRs and enhance the kinetics and affinity of immunoglobulin interactions. Combining the proline mutations with rationally designed mutants from a previous study led to 2400-fold increase in the affinity of the A6 T-cell receptor for Tax-HLAA2. However, this mutational scheme failed to induce significant binding changes in the already-high-affinity C225-Fab/huEGFR interface. Our results will serve as a roadmap to formulate more effective target functions to design immune complexes with improved biological functions.
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17
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Two-in-One antibodies with dual action Fabs. Curr Opin Chem Biol 2013; 17:400-5. [DOI: 10.1016/j.cbpa.2013.04.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/27/2013] [Accepted: 04/15/2013] [Indexed: 11/22/2022]
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18
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Willis JR, Briney BS, DeLuca SL, Crowe JE, Meiler J. Human germline antibody gene segments encode polyspecific antibodies. PLoS Comput Biol 2013; 9:e1003045. [PMID: 23637590 PMCID: PMC3636087 DOI: 10.1371/journal.pcbi.1003045] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 03/15/2013] [Indexed: 11/25/2022] Open
Abstract
Structural flexibility in germline gene-encoded antibodies allows promiscuous binding to diverse antigens. The binding affinity and specificity for a particular epitope typically increase as antibody genes acquire somatic mutations in antigen-stimulated B cells. In this work, we investigated whether germline gene-encoded antibodies are optimal for polyspecificity by determining the basis for recognition of diverse antigens by antibodies encoded by three VH gene segments. Panels of somatically mutated antibodies encoded by a common VH gene, but each binding to a different antigen, were computationally redesigned to predict antibodies that could engage multiple antigens at once. The Rosetta multi-state design process predicted antibody sequences for the entire heavy chain variable region, including framework, CDR1, and CDR2 mutations. The predicted sequences matched the germline gene sequences to a remarkable degree, revealing by computational design the residues that are predicted to enable polyspecificity, i.e., binding of many unrelated antigens with a common sequence. The process thereby reverses antibody maturation in silico. In contrast, when designing antibodies to bind a single antigen, a sequence similar to that of the mature antibody sequence was returned, mimicking natural antibody maturation in silico. We demonstrated that the Rosetta computational design algorithm captures important aspects of antibody/antigen recognition. While the hypervariable region CDR3 often mediates much of the specificity of mature antibodies, we identified key positions in the VH gene encoding CDR1, CDR2, and the immunoglobulin framework that are critical contributors for polyspecificity in germline antibodies. Computational design of antibodies capable of binding multiple antigens may allow the rational design of antibodies that retain polyspecificity for diverse epitope binding.
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Affiliation(s)
- Jordan R. Willis
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Bryan S. Briney
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Samuel L. DeLuca
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
| | - James E. Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Institute for Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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19
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Frese K, Eisenmann M, Ostendorp R, Brocks B, Pabst S. An automated immunoassay for early specificity profiling of antibodies. MAbs 2013; 5:279-87. [PMID: 23412646 DOI: 10.4161/mabs.23539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Antibody-based therapeutics are of great value for the treatment of human diseases. In addition to functional activity, affinity or physico-chemical properties, antibody specificity is considered to be one of the most crucial attributes for safety and efficacy. Consequently, appropriate studies are required before entering clinical trials. High content protein arrays are widely applied to assess antibody specificity, but this commercial solution can only be applied to final therapeutic antibody candidates because such arrays are expensive and their throughput is limited. A flexible, high-throughput and economical assay that allows specificity testing of IgG or Fab molecules during early discovery is described here. The 384-well microtiter plate assay contains a comprehensive panel of 32 test proteins and uses electrochemiluminescence as readout. The Protein Panel Profiling ( 3P) was used to analyze marketed therapeutic antibodies that all showed highly specific binding profiles. Subsequently, 3P was applied to antibody candidates from early discovery and the results compared well with those obtained with a commercially available high content protein chip. Our results suggest that 3P can be applied as an additional filter for lead selection, allowing the identification of favorable antibody candidates in early discovery and thereby increasing the speed and possibility of success in drug development.
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Affiliation(s)
- Katrin Frese
- Protein Sciences Department, MorphoSys AG, Martinsried/Planegg, Germany
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20
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Sykes KF, Legutki JB, Stafford P. Immunosignaturing: a critical review. Trends Biotechnol 2013; 31:45-51. [DOI: 10.1016/j.tibtech.2012.10.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Revised: 10/26/2012] [Accepted: 10/29/2012] [Indexed: 01/08/2023]
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21
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Kroening K, Johnston SA, Legutki JB. Autoreactive antibodies raised by self derived de novo peptides can identify unrelated antigens on protein microarrays. Are autoantibodies really autoantibodies? Exp Mol Pathol 2012; 92:304-11. [DOI: 10.1016/j.yexmp.2012.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 03/01/2012] [Indexed: 10/28/2022]
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22
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Fernandes RA, Shore DA, Vuong MT, Yu C, Zhu X, Pereira-Lopes S, Brouwer H, Fennelly JA, Jessup CM, Evans EJ, Wilson IA, Davis SJ. T cell receptors are structures capable of initiating signaling in the absence of large conformational rearrangements. J Biol Chem 2012; 287:13324-35. [PMID: 22262845 PMCID: PMC3339974 DOI: 10.1074/jbc.m111.332783] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/10/2012] [Indexed: 12/18/2022] Open
Abstract
Native and non-native ligands of the T cell receptor (TCR), including antibodies, have been proposed to induce signaling in T cells via intra- or intersubunit conformational rearrangements within the extracellular regions of TCR complexes. We have investigated whether any signatures can be found for such postulated structural changes during TCR triggering induced by antibodies, using crystallographic and mutagenesis-based approaches. The crystal structure of murine CD3ε complexed with the mitogenic anti-CD3ε antibody 2C11 enabled the first direct structural comparisons of antibody-liganded and unliganded forms of CD3ε from a single species, which revealed that antibody binding does not induce any substantial rearrangements within CD3ε. Saturation mutagenesis of surface-exposed CD3ε residues, coupled with assays of antibody-induced signaling by the mutated complexes, suggests a new configuration for the complex within which CD3ε is highly exposed and reveals that no large new CD3ε interfaces are required to form during antibody-induced signaling. The TCR complex therefore appears to be a structure that is capable of initiating intracellular signaling in T cells without substantial structural rearrangements within or between the component subunits. Our findings raise the possibility that signaling by native ligands might also be initiated in the absence of large structural rearrangements in the receptor.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- CD3 Complex/chemistry
- CD3 Complex/genetics
- CD3 Complex/immunology
- Crystallography, X-Ray
- Dimerization
- Epitopes, T-Lymphocyte/immunology
- Humans
- Immunoglobulin Fab Fragments/immunology
- Jurkat Cells
- Mice
- Mutagenesis, Site-Directed
- Protein Conformation
- Protein Structure, Tertiary
- Receptors, Antigen, T-Cell/chemistry
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Signal Transduction/immunology
- Structure-Activity Relationship
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Affiliation(s)
- Ricardo A. Fernandes
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - David A. Shore
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Mai T. Vuong
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Chao Yu
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Xueyong Zhu
- the Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Selma Pereira-Lopes
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Heather Brouwer
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Janet A. Fennelly
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Claire M. Jessup
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Edward J. Evans
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
| | - Ian A. Wilson
- the Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037
| | - Simon J. Davis
- From the Nuffield Department of Clinical Medicine and Medical Research Council Human Immunology Unit, The University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom and
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23
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Haidar JN, Yuan QA, Zeng L, Snavely M, Luna X, Zhang H, Zhu W, Ludwig DL, Zhu Z. A universal combinatorial design of antibody framework to graft distinct CDR sequences: a bioinformatics approach. Proteins 2011; 80:896-912. [PMID: 22180101 DOI: 10.1002/prot.23246] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 10/15/2011] [Accepted: 11/04/2011] [Indexed: 12/20/2022]
Abstract
Antibody (Ab) humanization is crucial to generate clinically relevant biologics from hybridoma-derived monoclonal antibodies (mAbs). In this study, we integrated antibody structural information from the Protein Data Bank with known back-to-mouse mutational data to build a universal consensus of framework positions (10 heavy and 7 light) critical for the preservation of the functional conformation of the Complimentarity Determining Region of antibodies. On the basis of FR consensus, we describe here a universal combinatorial library suitable for humanizing exogenous antibodies by CDR-grafting. The six CDRs of the murine anti-human EGFR Fab M225 were grafted onto a distinct (low FR sequence similarity to M225) human FR sequence that incorporates at the 17 FR consensus positions the permutations of the naturally observed amino acid diversities. Ten clones were selected from the combinatorial library expressing phage-displayed humanized M225 Fabs. Surprisingly, 2 of the 10 clones were found to bind EGFR with stronger affinity than M225. Cell-based assays demonstrated that the 10 selected clones retained epitope specificity by blocking EGFR phosphorylation and thus hindering cellular proliferation. Our results suggest that there is a universal and structurally rigid near-CDR set of FR positions that cooperatively support the binding conformation of CDRs.
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Affiliation(s)
- Jaafar N Haidar
- Department of Antibody Technology, ImClone Systems, a Wholly-Owned Subsidiary of Eli Lilly and Company, Alexandria Center for Life Sciences, New York, New York 10016, USA.
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24
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Bostrom J, Haber L, Koenig P, Kelley RF, Fuh G. High affinity antigen recognition of the dual specific variants of herceptin is entropy-driven in spite of structural plasticity. PLoS One 2011; 6:e17887. [PMID: 21526167 PMCID: PMC3081289 DOI: 10.1371/journal.pone.0017887] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 02/16/2011] [Indexed: 12/25/2022] Open
Abstract
The antigen-binding site of Herceptin, an anti-human Epidermal Growth Factor Receptor 2 (HER2) antibody, was engineered to add a second specificity toward Vascular Endothelial Growth Factor (VEGF) to create a high affinity two-in-one antibody bH1. Crystal structures of bH1 in complex with either antigen showed that, in comparison to Herceptin, this antibody exhibited greater conformational variability, also called "structural plasticity". Here, we analyzed the biophysical and thermodynamic properties of the dual specific variants of Herceptin to understand how a single antibody binds two unrelated protein antigens. We showed that while bH1 and the affinity-improved bH1-44, in particular, maintained many properties of Herceptin including binding affinity, kinetics and the use of residues for antigen recognition, they differed in the binding thermodynamics. The interactions of bH1 and its variants with both antigens were characterized by large favorable entropy changes whereas the Herceptin/HER2 interaction involved a large favorable enthalpy change. By dissecting the total entropy change and the energy barrier for dual interaction, we determined that the significant structural plasticity of the bH1 antibodies demanded by the dual specificity did not translate into the expected increase of entropic penalty relative to Herceptin. Clearly, dual antigen recognition of the Herceptin variants involves divergent antibody conformations of nearly equivalent energetic states. Hence, increasing the structural plasticity of an antigen-binding site without increasing the entropic cost may play a role for antibodies to evolve multi-specificity. Our report represents the first comprehensive biophysical analysis of a high affinity dual specific antibody binding two unrelated protein antigens, furthering our understanding of the thermodynamics that drive the vast antigen recognition capacity of the antibody repertoire.
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Affiliation(s)
- Jenny Bostrom
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
| | - Lauric Haber
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
| | - Patrick Koenig
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
| | - Robert F. Kelley
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
| | - Germaine Fuh
- Department of Antibody Engineering, Genentech Inc., South San Francisco, California, United States of America
- Department of Protein Engineering, Genentech, Inc., South San Francisco, California, United States of America
- * E-mail:
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25
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Acchione M, Lipschultz CA, DeSantis ME, Shanmuganathan A, Li M, Wlodawer A, Tarasov S, Smith-Gill SJ. Light chain somatic mutations change thermodynamics of binding and water coordination in the HyHEL-10 family of antibodies. Mol Immunol 2009; 47:457-64. [PMID: 19781789 DOI: 10.1016/j.molimm.2009.08.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 08/28/2009] [Indexed: 01/14/2023]
Abstract
Thermodynamic and structural studies addressed the increased affinity due to L-chain somatic mutations in the HyHEL-10 family of affinity matured IgG antibodies, using ITC, SPR with van't Hoff analysis, and X-ray crystallography. When compared to the parental antibody H26L26, the H26L10 and H26L8 chimeras binding to lysozyme showed an increase in favorable DeltaG(o) of -1.2+/-0.1 kcal mol(-1) and -1.3+/-0.1 kcal mol(-1), respectively. Increase in affinity of the H26L10 chimera was due to a net increase in favorable enthalpy change with little difference in change in entropy compared to H26L26. The H26L8 chimera exhibited the greatest increase in favorable enthalpy but also showed an increase in unfavorable entropy change, with the result being that the affinities of both chimeras were essentially equivalent. Site-directed L-chain mutants identified the shared somatic mutation S30G as the dominant contributor to increasing affinity to lysozyme. This mutation was not influenced by H-chain somatic mutations. Residue 30L is at the periphery of the binding interface and S30G effects an increase in hydrophobicity and decrease in H-bonding ability and size, but does not make any new energetically important antigen contacts. A new 1.2-A structure of the H10L10-HEL complex showed changes in the pattern of both inter- and intra-molecular water bridging with no other significant structural alterations near the binding interface compared to the H26L26-HEL complex. These results highlight the necessity for investigating both the structure and the thermodynamics associated with introduced mutations, in order to better assess and understand their impact on binding. Furthermore, it provides an important example of how backbone flexibility and water-bridging may favorably influence the thermodynamics of an antibody-antigen interaction.
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Affiliation(s)
- Mauro Acchione
- Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
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