1
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Ambrosetti F, Jandova Z, Bonvin AMJJ. Information-Driven Antibody-Antigen Modelling with HADDOCK. Methods Mol Biol 2023; 2552:267-282. [PMID: 36346597 DOI: 10.1007/978-1-0716-2609-2_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the recent years, therapeutic use of antibodies has seen a huge growth, "due to their inherent proprieties and technological advances in the methods used to study and characterize them. Effective design and engineering of antibodies for therapeutic purposes are heavily dependent on knowledge of the structural principles that regulate antibody-antigen interactions. Several experimental techniques such as X-ray crystallography, cryo-electron microscopy, NMR, or mutagenesis analysis can be applied, but these are usually expensive and time-consuming. Therefore computational approaches like molecular docking may offer a valuable alternative for the characterization of antibody-antigen complexes.Here we describe a protocol for the prediction of the 3D structure of antibody-antigen complexes using the integrative modelling platform HADDOCK. The protocol consists of (1) the identification of the antibody residues belonging to the hypervariable loops which are known to be crucial for the binding and can be used to guide the docking and (2) the detailed steps to perform docking with the HADDOCK 2.4 webserver following different strategies depending on the availability of information about epitope residues.
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Affiliation(s)
- Francesco Ambrosetti
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Zuzana Jandova
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht, The Netherlands.
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2
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Gilodi M, Lisi S, F. Dudás E, Fantini M, Puglisi R, Louka A, Marcatili P, Cattaneo A, Pastore A. Selection and Modelling of a New Single-Domain Intrabody Against TDP-43. Front Mol Biosci 2022; 8:773234. [PMID: 35237655 PMCID: PMC8884700 DOI: 10.3389/fmolb.2021.773234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disorder associated to deteriorating motor and cognitive functions, and short survival. The disease is caused by neuronal death which results in progressive muscle wasting and weakness, ultimately leading to lethal respiratory failure. The misbehaviour of a specific protein, TDP-43, which aggregates and becomes toxic in ALS patient’s neurons, is supposed to be one of the causes. TDP-43 is a DNA/RNA-binding protein involved in several functions related to nucleic acid metabolism. Sequestration of TDP-43 aggregates is a possible therapeutic strategy that could alleviate or block pathology. Here, we describe the selection and characterization of a new intracellular antibody (intrabody) against TDP-43 from a llama nanobody library. The structure of the selected intrabody was predicted in silico and the model was used to suggest mutations that enabled to improve its expression yield, facilitating its experimental validation. We showed how coupling experimental methodologies with in silico design may allow us to obtain an antibody able to recognize the RNA binding regions of TDP-43. Our findings illustrate a strategy for the mitigation of TDP-43 proteinopathy in ALS and provide a potential new tool for diagnostics.
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Affiliation(s)
- Martina Gilodi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Simonetta Lisi
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Erika F. Dudás
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Marco Fantini
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
| | - Rita Puglisi
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Alexandra Louka
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
| | - Paolo Marcatili
- Department of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Antonino Cattaneo
- Bio@SNS Laboratory, Scuola Normale Superiore, Piazza dei Cavalieri, Pisa, Italy
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
| | - Annalisa Pastore
- Dementia Research Institute at King’s College London, The Wohl Institute, London, United Kingdom
- *Correspondence: Annalisa Pastore, ; Antonino Cattaneo,
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3
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Wan H, Zhang J, Ding Y, Wang H, Tian G. Immunoglobulin Classification Based on FC* and GC* Features. Front Genet 2022; 12:827161. [PMID: 35140745 PMCID: PMC8819591 DOI: 10.3389/fgene.2021.827161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
Immunoglobulins have a pivotal role in disease regulation. Therefore, it is vital to accurately identify immunoglobulins to develop new drugs and research related diseases. Compared with utilizing high-dimension features to identify immunoglobulins, this research aimed to examine a method to classify immunoglobulins and non-immunoglobulins using two features, FC* and GC*. Classification of 228 samples (109 immunoglobulin samples and 119 non-immunoglobulin samples) revealed that the overall accuracy was 80.7% in 10-fold cross-validation using the J48 classifier implemented in Weka software. The FC* feature identified in this study was found in the immunoglobulin subtype domain, which demonstrated that this extracted feature could represent functional and structural properties of immunoglobulins for forecasting.
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Affiliation(s)
- Hao Wan
- Institute of Advanced Cross-field Science, College of Life Science, Qingdao University, Qingdao, China
| | - Jina Zhang
- Geneis (Beijing) Co., Ltd., Beijing, China
| | - Yijie Ding
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, China
| | - Hetian Wang
- Beidahuang Industry Group General Hospital, Harbin, China
- *Correspondence: Hetian Wang, ; Geng Tian,
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, China
- *Correspondence: Hetian Wang, ; Geng Tian,
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4
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Lepore R, Olimpieri PP, Messih MA, Tramontano A. PIGSPro: prediction of immunoGlobulin structures v2. Nucleic Acids Res 2019; 45:W17-W23. [PMID: 28472367 PMCID: PMC5570210 DOI: 10.1093/nar/gkx334] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/19/2017] [Indexed: 01/14/2023] Open
Abstract
PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins. The software has been completely rewritten in python following a similar pipeline as in the original method, but including, at various steps, relevant modifications found to improve its prediction accuracy, as demonstrated here. The steps of the pipeline include the selection of the appropriate framework for predicting the conserved regions of the molecule by homology; the target template alignment for this portion of the molecule; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical structures are not available and the packing of the light and heavy chain if derived from different templates. Each of these steps has been improved including updated methods developed along the years. Last but not least, the user interface has been completely redesigned and an automatic monthly update of the underlying database has been implemented. The method is available as a web server at http://biocomputing.it/pigspro.
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Affiliation(s)
- Rosalba Lepore
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
| | - Pier P Olimpieri
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy
| | - Mario A Messih
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy
| | - Anna Tramontano
- Department of Physics, Sapienza University, Piazzale Aldo Moro 500-184 Rome, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy
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5
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Nie Y, Li S, Zhu J, Hu R, Liu M, He T, Yang Y. Chemical shift assignments of a camelid nanobody against aflatoxin B 1. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:75-78. [PMID: 30328057 DOI: 10.1007/s12104-018-9855-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 06/08/2023]
Abstract
Nanobodies (Nbs) are the variable domain of the heavy-chain antibodies produced from Camelidae, which possess comparable binding affinities and specificity to conventional antibodies. Nbs have become valuable and versatile tools for numerous biotechnology applications due to their small size (12-15 kDa), high solubility, exceptional stability, and facile genetic manipulation. The interactions between Nbs and protein antigens have been well-studied, but less work has been done to characterize their ability to bind small molecule haptens. Here we present the backbone and side-chain assignments of the 1H, 13C and 15N resonances of Nb26 (123 amino acids), a nanobody that recognizes the hapten aflatoxin B1 (AFB1). These assignments are preliminary work towards the determination of the structure of free Nb26 using NMR spectroscopy, which will provide useful information about the complex structure of "Nb26-AFB1" and the recognition mechanism about how Nb26 binds to AFB1.
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Affiliation(s)
- Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shuangli Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan Center for Magnetic Resonance, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan, 430071, China.
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6
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Lai JY, Klatt S, Lim TS. Potential application of Leishmania tarentolae as an alternative platform for antibody expression. Crit Rev Biotechnol 2019; 39:380-394. [DOI: 10.1080/07388551.2019.1566206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Stephan Klatt
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang, Malaysia
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7
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He T, Zhu J, Nie Y, Hu R, Wang T, Li P, Zhang Q, Yang Y. Nanobody Technology for Mycotoxin Detection in the Field of Food Safety: Current Status and Prospects. Toxins (Basel) 2018; 10:E180. [PMID: 29710823 PMCID: PMC5983236 DOI: 10.3390/toxins10050180] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 01/18/2023] Open
Abstract
Mycotoxins, which are toxic, carcinogenic, and/or teratogenic, have posed a threat to food safety and public health. Sensitive and effective determination technologies for mycotoxin surveillance are required. Immunoassays have been regarded as useful supplements to chromatographic techniques. However, conventional antibodies involved in immunoassays are difficult to be expressed recombinantly and are susceptible to harsh environments. Nanobodies (or VHH antibodies) are antigen-binding sites of the heavy-chain antibodies produced from Camelidae. They are found to be expressed easily in prokaryotic or eukaryotic expression systems, more robust in extreme conditions, and facile to be used as surrogates for artificial antigens. These properties make them the promising and environmentally friendly immunoreagents in the next generation of immunoassays. This review briefly describes the latest developments in the area of nanobodies used in mycotoxin detection. Moreover, by integrating the introduction of the principle of nanobodies production and the critical assessment of their performance, this paper also proposes the prospect of nanobodies in the field of food safety in the foreseeable future.
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Affiliation(s)
- Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Yao Nie
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Ting Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Peiwu Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Qi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.
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8
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NMR Detection of Semi-Specific Antibody Interactions in Serum Environments. Molecules 2017; 22:molecules22101619. [PMID: 28953258 PMCID: PMC6151507 DOI: 10.3390/molecules22101619] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/22/2017] [Indexed: 11/29/2022] Open
Abstract
Although antibody functions are executed in heterogeneous blood streams characterized by molecular crowding and promiscuous intermolecular interaction, detailed structural characterizations of antibody interactions have thus far been performed under homogeneous in vitro conditions. NMR spectroscopy potentially has the ability to study protein structures in heterogeneous environments, assuming that the target protein can be labeled with NMR-active isotopes. Based on our successful development of isotope labeling of antibody glycoproteins, here we apply NMR spectroscopy to characterize antibody interactions in heterogeneous extracellular environments using mouse IgG-Fc as a test molecule. In human serum, many of the HSQC peaks originating from the Fc backbone exhibited attenuation in intensity of various magnitudes. Similar spectral changes were induced by the Fab fragment of polyclonal IgG isolated from the serum, but not by serum albumin, indicating that a subset of antibodies reactive with mouse IgG-Fc exists in human serum without preimmunization. The metaepitopes recognized by serum polyclonal IgG cover the entire molecular surface of Fc, including the binding sites to Fc receptors and C1q. In-serum NMR observation will offer useful tools for the detailed characterization of biopharamaceuticals, including therapeutic antibodies in physiologically relevant heterogeneous environments, also giving deeper insight into molecular recognition by polyclonal antibodies in the immune system.
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9
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Abstract
The antiviral activity of antibodies reflects the bifunctional properties of these molecules. While the Fab domains mediate highly specific antigenic recognition to block virus entry, the Fc domain interacts with diverse types of Fcγ receptors (FcγRs) expressed on the surface of effector leukocytes to induce the activation of distinct immunomodulatory pathways. Fc-FcγR interactions are tightly regulated to control IgG-mediated inflammation and immunity and are largely determined by the structural heterogeneity of the IgG Fc domain, stemming from differences in the primary amino acid sequence of the various subclasses, as well as the structure and composition of the Fc-associated N-linked glycan. Engagement of specific FcγR types on effector leukocytes has diverse consequences that affect several aspects of innate and adaptive immunity. In this review, we provide an overview of the complexity of FcγR-mediated pathways, discussing their role in the in vivo protective activity of anti-HIV-1 antibodies. We focus on recent studies on broadly neutralizing anti-HIV-1 antibodies that revealed that Fc-FcγR interactions are required to achieve full therapeutic activity through clearance of IgG-opsonized virions and elimination of HIV-infected cells. Manipulation of Fc-FcγR interactions to specifically activate distinct FcγR-mediated pathways has the potential to affect downstream effector responses, influencing thereby the in vivo protective activity of anti-HIV-1 antibodies; a strategy that has already been successfully applied to other IgG-based therapeutics, substantially improving their clinical efficacy.
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Affiliation(s)
- Stylianos Bournazos
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY, USA
| | - Jeffrey V Ravetch
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY, USA
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10
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Abstract
A key determinant for the survival of organisms is their capacity to recognize and respond efficiently to foreign antigens. This is largely accomplished by the orchestrated activity of the innate and adaptive branches of the immune system. Antibodies are specifically generated in response to foreign antigens, facilitating thereby the specific recognition of antigens of almost infinite diversity. Receptors specific for the Fc domain of antibodies, Fc receptors, are expressed on the surface of the various myeloid leukocyte populations and mediate the binding and recognition of antibodies by innate leukocytes. By directly linking the innate and the adaptive components of immunity, Fc receptors play a central role in host defense and the maintenance of tissue homeostasis through the induction of diverse proinflammatory, anti-inflammatory, and immunomodulatory processes that are initiated upon engagement by the Fc domain. In this chapter, we discuss the mechanisms that regulate Fc domain binding to the various types of Fc receptors and provide an overview of the astonishing diversity of effector functions that are mediated through Fc-FcR interactions on myeloid cells. Lastly, we discuss the impact of FcR-mediated interactions in the context of IgG-mediated inflammation, autoimmunity, susceptibility to infection, and responsiveness to antibody-based therapeutics.
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11
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Khass M, Blackburn T, Burrows PD, Walter MR, Capriotti E, Schroeder HW. VpreB serves as an invariant surrogate antigen for selecting immunoglobulin antigen-binding sites. Sci Immunol 2016; 1:aaf6628. [PMID: 28217764 PMCID: PMC5315267 DOI: 10.1126/sciimmunol.aaf6628] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Developmental checkpoints eliminate B cells synthesizing defective immunoglobulin heavy (HC) and light (LC) chains. The first checkpoint tests for formation of a VpreB/λ5/µHC-containing preB-cell receptor (preBCR) and predicts whether µHCs will bind conventional LCs to form membrane IgM. VpreB and λ5 also create a sensing site that interacts with µHC antigen-binding region CDR-H3, but whether it plays a role in immunoglobulin repertoire selection and function is unknown. On a position-by-position basis, we analyzed the amino acid content of CDR-H3s from H chains cloned from living and apoptotic preB cells and from IgG:Antigen structures. Using a panel of DH gene-targeted mice, we show that progressively reducing CDR-H3 tyrosine content increasingly impairs preBCR checkpoint passage. Counting from cysteine at Framework 3 position 96, we found that VpreB particularly selects for tyrosine at CDR-H3 position 101, and that Y101 also binds antigen in IgG:Antigen structures. VpreB thus acts as an early invariant antigen. It selects for particular CDR-H3 amino acids and shapes the specificity of the IgG humoral response. This helps explain why some neutralizing antibodies against pathogens are readily produced while others are rare.
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Affiliation(s)
- Mohamed Khass
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
- Division of Genetic Engineering, National Research Center of Egypt, Cairo, Egypt
| | - Tessa Blackburn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Peter D Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Mark R. Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
| | - Emidio Capriotti
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
- Institute for Mathematical Modeling of Biological Systems, Department of Biology, University of Düsseldorf, Düsseldorf, Germany
| | - Harry W Schroeder
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL
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12
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Bessire AJ, Ballard TE, Charati M, Cohen J, Green M, Lam MH, Loganzo F, Nolting B, Pierce B, Puthenveetil S, Roberts L, Schildknegt K, Subramanyam C. Determination of Antibody–Drug Conjugate Released Payload Species Using Directed in Vitro Assays and Mass Spectrometric Interrogation. Bioconjug Chem 2016; 27:1645-54. [DOI: 10.1021/acs.bioconjchem.6b00192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Bessire
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - T. Eric Ballard
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Manoj Charati
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Justin Cohen
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Michael Green
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - My-Hanh Lam
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Frank Loganzo
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Birte Nolting
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Betsy Pierce
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Sujiet Puthenveetil
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Lee Roberts
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Klaas Schildknegt
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
| | - Chakrapani Subramanyam
- Pharmacokinetics, Dynamics and Metabolism, ∥Worldwide Medicinal Chemistry, and ¶Pharmaceutical Sciences Chemical R&D, Pfizer Worldwide R&D, Groton, Connecticut 06340, United States
- Oncology Research Unit, and ⊥Bioprocess R&D, Pfizer Worldwide R&D, Pearl River, New York 10965, United States
- Worldwide Medicinal Chemistry, and §Global Biotherapeutics Technologies, Pfizer Worldwide R&D, Cambridge, Massachusetts 02139, United States
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13
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Abstract
IgG antibodies are actively produced in response to antigenic challenge or passively administered as an effective form of immunotherapy to confer immunity against foreign antigens. Their protective activity is mediated through their bifunctional nature: a variable Fab domain mediates antigen-binding specificity, whereas the constant Fc domain engages Fcγ receptors (FcγRs) expressed on the surface of leukocytes to mediate effector functions. While traditionally considered the invariant domain of an IgG molecule, the Fc domain displays remarkable structural heterogeneity determined primarily by differences in the amino acid sequence of the various IgG subclasses and by the composition of the complex, Fc-associated biantennary N-linked glycan. These structural determinants regulate the conformational flexibility of the IgG Fc domain and affect its capacity to interact with distinct types of FcγRs (type I or type II FcγRs). FcγR engagement activates diverse downstream immunomodulatory pathways with pleiotropic functional consequences including cytotoxicity and phagocytosis of IgG-coated targets, differentiation and activation of antigen presenting cells, modulation of T-cell activation, plasma cell survival, and regulation of antibody responses. These functions highlight the importance of FcγR-mediated pathways in the modulation of adaptive immune responses and suggest a central role for IgG-FcγR interactions during active and passive immunization.
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Affiliation(s)
- Stylianos Bournazos
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, 1230 York Ave, New York, NY 10065
| | - Jeffrey V. Ravetch
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, 1230 York Ave, New York, NY 10065
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14
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Eylenstein R, Weinfurtner D, Härtle S, Strohner R, Böttcher J, Augustin M, Ostendorp R, Steidl S. Molecular basis of in vitro affinity maturation and functional evolution of a neutralizing anti-human GM-CSF antibody. MAbs 2015; 8:176-86. [PMID: 26406987 DOI: 10.1080/19420862.2015.1099774] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
X-ray structure analysis of 4 antibody Fab fragments, each in complex with human granulocyte macrophage colony stimulating factor (GM-CSF), was performed to investigate the changes at the protein-protein binding interface during the course of in vitro affinity maturation by phage display selection. The parental antibody MOR03929 was compared to its derivatives MOR04252 (CDR-H2 optimized), MOR04302 (CDR-L3 optimized) and MOR04357 (CDR-H2 and CDR-L3 optimized). All antibodies bind to a conformational epitope that can be divided into 3 sub-epitopes. Specifically, MOR04357 binds to a region close to the GM-CSF N-terminus (residues 11-24), a short second sub-epitope (residues 83-89) and a third at the C-terminus (residues 112-123). Modifications introduced during affinity maturation in CDR-H2 and CDR-L3 led to the establishment of additional hydrogen bonds and van der Waals contacts, respectively, providing a rationale for the observed improvement in binding affinity and neutralization potency. Once GM-CSF is complexed to the antibodies, modeling predicts a sterical clash with GM-CSF binding to GM-CSF receptor α and β chain. This predicted mutually exclusive binding was confirmed by a GM-CSF receptor α chain ligand binding inhibition assay. Finally, high throughput sequencing of clones obtained after affinity maturation phage display pannings revealed highly selected consensus sequences for CDR-H2 as well for CDR-L3, which are in accordance with the sequence of the highest affinity antibody MOR04357. The resolved crystal structures highlight the criticality of these strongly selected residues for high affinity interaction with GM-CSF.
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Affiliation(s)
- Roy Eylenstein
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany.,d These authors contributed equally to this work
| | - Daniel Weinfurtner
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany.,d These authors contributed equally to this work
| | - Stefan Härtle
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Ralf Strohner
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Jark Böttcher
- b Proteros Biostructures GmbH ; Bunsenstr. 7a; 82152 Martinsried ; Germany.,c Current affiliation: Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11,1121 Vienna , Austria
| | - Martin Augustin
- b Proteros Biostructures GmbH ; Bunsenstr. 7a; 82152 Martinsried ; Germany
| | - Ralf Ostendorp
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
| | - Stefan Steidl
- a MorphoSys AG ; Lena-Christ-Str. 48; 82152 Martinsried ; Germany
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15
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Pincetic A, Bournazos S, DiLillo DJ, Maamary J, Wang TT, Dahan R, Fiebiger BM, Ravetch JV. Type I and type II Fc receptors regulate innate and adaptive immunity. Nat Immunol 2014; 15:707-16. [PMID: 25045879 DOI: 10.1038/ni.2939] [Citation(s) in RCA: 361] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/09/2014] [Indexed: 12/15/2022]
Abstract
Antibodies produced in response to a foreign antigen are characterized by polyclonality, not only in the diverse epitopes to which their variable domains bind but also in the various effector molecules to which their constant regions (Fc domains) engage. Thus, the antibody's Fc domain mediates diverse effector activities by engaging two distinct classes of Fc receptors (type I and type II) on the basis of the two dominant conformational states that the Fc domain may adopt. These conformational states are regulated by the differences among antibody subclasses in their amino acid sequence and by the complex, biantennary Fc-associated N-linked glycan. Here we discuss the diverse downstream proinflammatory, anti-inflammatory and immunomodulatory consequences of the engagement of type I and type II Fc receptors in the context of infectious, autoimmune, and neoplastic disorders.
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Affiliation(s)
- Andrew Pincetic
- 1] The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA. [2]
| | - Stylianos Bournazos
- 1] The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA. [2]
| | - David J DiLillo
- 1] The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA. [2]
| | - Jad Maamary
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
| | - Taia T Wang
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
| | - Rony Dahan
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
| | | | - Jeffrey V Ravetch
- The Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, New York, USA
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16
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Gonçalves AM, Pedro AQ, Santos FM, Martins LM, Maia CJ, Queiroz JA, Passarinha LA. Trends in protein-based biosensor assemblies for drug screening and pharmaceutical kinetic studies. Molecules 2014; 19:12461-85. [PMID: 25153865 PMCID: PMC6270898 DOI: 10.3390/molecules190812461] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 08/02/2014] [Accepted: 08/05/2014] [Indexed: 12/20/2022] Open
Abstract
The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.
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Affiliation(s)
- Ana M Gonçalves
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Augusto Q Pedro
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Fátima M Santos
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Luís M Martins
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Cláudio J Maia
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - João A Queiroz
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| | - Luís A Passarinha
- CICS-UBI Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
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Olivieri DN, von Haeften B, Sánchez-Espinel C, Faro J, Gambón-Deza F. Genomic V exons from whole genome shotgun data in reptiles. Immunogenetics 2014; 66:479-92. [DOI: 10.1007/s00251-014-0784-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
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18
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Ponomarenko N, Chatziefthimiou SD, Kurkova I, Mokrushina Y, Mokrushina Y, Stepanova A, Smirnov I, Avakyan M, Bobik T, Mamedov A, Mitkevich V, Belogurov A, Fedorova OS, Dubina M, Golovin A, Lamzin V, Friboulet A, Makarov AA, Wilmanns M, Gabibov A. Role of κ→λ light-chain constant-domain switch in the structure and functionality of A17 reactibody. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:708-19. [PMID: 24598740 PMCID: PMC3949517 DOI: 10.1107/s1399004713032446] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
The engineering of catalytic function in antibodies requires precise information on their structure. Here, results are presented that show how the antibody domain structure affects its functionality. The previously designed organophosphate-metabolizing reactibody A17 has been re-engineered by replacing its constant κ light chain by the λ chain (A17λ), and the X-ray structure of A17λ has been determined at 1.95 Å resolution. It was found that compared with A17κ the active centre of A17λ is displaced, stabilized and made more rigid owing to interdomain interactions involving the CDR loops from the VL and VH domains. These VL/VH domains also have lower mobility, as deduced from the atomic displacement parameters of the crystal structure. The antibody elbow angle is decreased to 126° compared with 138° in A17κ. These structural differences account for the subtle changes in catalytic efficiency and thermodynamic parameters determined with two organophosphate ligands, as well as in the affinity for peptide substrates selected from a combinatorial cyclic peptide library, between the A17κ and A17λ variants. The data presented will be of interest and relevance to researchers dealing with the design of antibodies with tailor-made functions.
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Affiliation(s)
- Natalia Ponomarenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Spyros D. Chatziefthimiou
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Inna Kurkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Yuliana Mokrushina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Anastasiya Stepanova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Ivan Smirnov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Marat Avakyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Tatyana Bobik
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Azad Mamedov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Alexey Belogurov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
| | - Olga S. Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russian Federation
| | - Michael Dubina
- St Petersburg Academic University, St Petersburg 194021, Russian Federation
| | - Andrey Golovin
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Victor Lamzin
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alain Friboulet
- Université de Technologie de Compiègne, Unité Mixte de Recherche 6022, Centre National de la Recherche Scientifique, 60205 Compiègne, France
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany
| | - Alexander Gabibov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow 117871, Russian Federation
- Institute of Gene Biology, Moscow 117334, Russian Federation
- Lomonosov Moscow State University, Moscow 119991, Russian Federation
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19
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Nagy G, Oostenbrink C. Dihedral-based segment identification and classification of biopolymers I: proteins. J Chem Inf Model 2014; 54:266-77. [PMID: 24364820 PMCID: PMC3904766 DOI: 10.1021/ci400541d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Indexed: 12/29/2022]
Abstract
A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.
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Affiliation(s)
- Gabor Nagy
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
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20
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Olimpieri PP, Chailyan A, Tramontano A, Marcatili P. Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. ACTA ACUST UNITED AC 2013; 29:2285-91. [PMID: 23803466 PMCID: PMC3753563 DOI: 10.1093/bioinformatics/btt369] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Motivation: Antibodies or immunoglobulins are proteins of paramount importance in the immune system. They are extremely relevant as diagnostic, biotechnological and therapeutic tools. Their modular structure makes it easy to re-engineer them for specific purposes. Short of undergoing a trial and error process, these experiments, as well as others, need to rely on an understanding of the specific determinants of the antibody binding mode. Results: In this article, we present a method to identify, on the basis of the antibody sequence alone, which residues of an antibody directly interact with its cognate antigen. The method, based on the random forest automatic learning techniques, reaches a recall and specificity as high as 80% and is implemented as a free and easy-to-use server, named prediction of Antibody Contacts. We believe that it can be of great help in re-design experiments as well as a guide for molecular docking experiments. The results that we obtained also allowed us to dissect which features of the antibody sequence contribute most to the involvement of specific residues in binding to the antigen. Availability:http://www.biocomputing.it/proABC. Contact:anna.tramontano@uniroma1.it or paolo.marcatili@gmail.com Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pier Paolo Olimpieri
- Department of Physics, Sapienza University and Istituto Pasteur - Fondazione Cenci Bolognetti, 00185 Rome, Italy
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21
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An automated algorithm for extracting functional immunologic V-genes from genomes in jawed vertebrates. Immunogenetics 2013; 65:691-702. [DOI: 10.1007/s00251-013-0715-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
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22
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Nelson AD, Hoffmann MM, Parks CA, Dasari S, Schrum AG, Gil D. IgG Fab fragments forming bivalent complexes by a conformational mechanism that is reversible by osmolytes. J Biol Chem 2012; 287:42936-50. [PMID: 23109335 DOI: 10.1074/jbc.m112.410217] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Generated by proteolytic cleavage of immunoglobulin, Fab fragments possess great promise as blocking reagents, able to bind receptors or other targets without inducing cross-linking. However, aggregation of Fab preparations is a common occurrence, which generates intrinsic stimulatory capacity and thwarts signal blockade strategies. Using a panel of biochemical approaches, including size exclusion chromatography, SDS-PAGE, mass spectrometry, and cell stimulation followed by flow cytometry, we have measured the oligomerization and acquisition of stimulatory capacity that occurs in four monoclonal IgG Fabs specific for TCR/CD3. Unexpectedly, we observed that all Fabs spontaneously formed complexes that were precisely bivalent, and these bivalent complexes possessed most of the stimulatory activity of each Fab preparation. Fabs composing bivalent complexes were more susceptible to proteolysis than monovalent Fabs, indicating a difference in conformation between the Fabs involved in these two different states of valency. Because osmolytes represent a class of compounds that stabilize protein folding and conformation, we sought to determine the extent to which the amino acid osmolyte l-proline might impact bivalent Fab complexation. We found that l-proline (i) inhibited the adoption of the conformation associated with bivalent complexation, (ii) preserved Fab monovalency, (iii) reversed the conformation of preformed bivalent Fabs to that of monovalent Fabs, and (iv) separated a significant percentage of preformed bivalent complexes into monovalent species. Thus, Fab fragments can adopt a conformation that is compatible with folding or packing of a bivalent complex in a process that can be inhibited by osmolytes.
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Affiliation(s)
- Alfreda D Nelson
- Department of Immunology, Center for Individualized Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA
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23
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Jefferis R. Isotype and glycoform selection for antibody therapeutics. Arch Biochem Biophys 2012; 526:159-66. [PMID: 22465822 DOI: 10.1016/j.abb.2012.03.021] [Citation(s) in RCA: 195] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 03/12/2012] [Accepted: 03/17/2012] [Indexed: 12/15/2022]
Abstract
We live in a hostile environment but are protected by the innate and adaptive immune system. A major component of the latter is mediated by antibody molecules that bind to pathogens, with exquisite specificity, and the immune complex formed activates cellular mechanisms leading to the removal and destruction of the complex. Five classes of antibody are identified; however, the IgG class predominates in serum and a majority of monoclonal antibody (mAb) therapeutics are based on the IgG format. Selection within the antibody repertoire allows the generation of (mAb) having specificity for any selected target, including human antigens. This review focuses on the structure and function of the Fc region of IgG molecules that mediates biologic functions, within immune complexes, by interactions with cellular Fc receptors (FcγR) and/or the C1q component of complement. A property of IgG that is suited to its use as a therapeutic is the long catabolic half life of ~21 days, mediated through the structurally distinct neonatal Fc receptor (FcRn). Our understanding of structure/function relationships is such that we can contemplate engineering the IgG-Fc to enhance or eliminate biologic activities to generate therapeutics considered optimal for a given disease indication. There are four subclasses of human IgG that exhibit high sequence homology but a unique profile of biologic activities. The FcγR and the C1q binding functions are dependent on glycosylation of the IgG-Fc. Normal human serum IgG is comprised of multiple glycoforms and biologic activities, other than catabolism, varies between glycoforms.
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