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Guloglu B, Deane CM. Specific attributes of the V L domain influence both the structure and structural variability of CDR-H3 through steric effects. Front Immunol 2023; 14:1223802. [PMID: 37564639 PMCID: PMC10410447 DOI: 10.3389/fimmu.2023.1223802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
Antibodies, through their ability to target virtually any epitope, play a key role in driving the adaptive immune response in jawed vertebrates. The binding domains of standard antibodies are their variable light (VL) and heavy (VH) domains, both of which present analogous complementarity-determining region (CDR) loops. It has long been known that the VH CDRs contribute more heavily to the antigen-binding surface (paratope), with the CDR-H3 loop providing a major modality for the generation of diverse paratopes. Here, we provide evidence for an additional role of the VL domain as a modulator of CDR-H3 structure, using a diverse set of antibody crystal structures and a large set of molecular dynamics simulations. We show that specific attributes of the VL domain such as subtypes, CDR canonical forms and genes can influence the structural diversity of the CDR-H3 loop, and provide a physical model for how this effect occurs through inter-loop contacts and packing of CDRs against each other. Our results indicate that the rigid minor loops fine-tune the structure of CDR-H3, thereby contributing to the generation of surfaces complementary to the vast number of possible epitope topologies, and provide insights into the interdependent nature of CDR conformations, an understanding of which is important for the rational antibody design process.
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Affiliation(s)
- Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
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Abstract
The immune systems protect vertebrates from foreign molecules or antigens, and antibodies are important mediators of this system. The sequences and structural features of antibodies vary depending on species. Many of antibodies from vertebrates, including camelids, have both heavy and light chain variable domains, but camelids also have antibodies that lack the light chains. In antibodies that lack light chains, the C-terminal variable region is called the VHH domain. Antibodies recognize antigens through six complementarity-determining regions (CDRs). The third CDR of the heavy chain (CDR-H3) is at the center of the antigen-binding site and is diverse in terms of sequence and structure. Due to the importance of antibodies in basic science as well as in medical applications, there have been many studies of CDR-H3s of antibodies that possess both light and heavy chains. However, nature of CDR-H3s of single-domain VHH antibodies is less well studied. In this chapter, we describe current knowledge of sequence-structure-function correlations of single-domain VHH antibodies with emphasis on CDR-H3. Based on the 370 crystal structures in the Protein Data Bank, we also attempt structural classification of CDR-H3 in single-domain VHH antibodies and discuss lessons learned from the ever-increasing number of the structures.
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Affiliation(s)
- Daisuke Kuroda
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Kouhei Tsumoto
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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Cheng Y, Wu J, Han Y, Xu J, Da Y, Zhao Q, Guo G, Zhou Y, Chen Y, Liu J, Chen H, Jiang X, Cai X. A CDR-based approach to generate covalent inhibitory antibody for human rhinovirus protease. Bioorg Med Chem 2021; 42:116219. [PMID: 34077853 DOI: 10.1016/j.bmc.2021.116219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/13/2021] [Accepted: 05/14/2021] [Indexed: 11/21/2022]
Abstract
Covalent target modulation with small molecules has been emerging as a promising strategy for drug discovery. However, covalent inhibitory antibody remains unexplored due to the lack of efficient strategies to engineer antibody with desired bioactivity. Herein, we developed an intracellular selection method to generate covalent inhibitory antibody against human rhinovirus 14 (HRV14) 3C protease through unnatural amino acid mutagenesis along the heavy chain complementarity-determining region 3 (CDR-H3). A library of antibody mutants was thus constructed and screened in vivo through co-expression with the target protease. Using this screening strategy, six covalent antibodies with proximity-enabled bioactivity were identified, which were shown to covalently target HRV14-3C protease with high inhibitory potency and exquisite selectivity. Compared to structure-based rational design, this library-based screening method provides a simple and efficient way for the discovery and engineering of covalent antibody for enzyme inhibition.
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Wang H, Yan K, Wang R, Yang Y, Shen Y, Yu C, Chen L. Antibody heavy chain CDR3 length-dependent usage of human IGHJ4 and IGHJ6 germline genes. Antib Ther 2021; 4:101-108. [PMID: 34195544 PMCID: PMC8237691 DOI: 10.1093/abt/tbab010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
Therapeutic antibody discovery using synthetic diversity has been proved productive, especially for target proteins not suitable for traditional animal immunization-based antibody discovery approaches. Recently, many lines of evidences suggest that the quality of synthetic diversity design limits the development success of synthetic antibody hits. The aim of our study is to understand the quality limitation and to properly address the challenges with a better design. Using VH3–23 as a model framework, we observed and quantitatively mapped CDR-H3 loop length-dependent usage of human IGHJ4 and IGHJ6 germline genes in the natural human immune repertoire. Skewed usage of DH2-JH6 and DH3-JH6 rearrangements was quantitatively determined in a CDR-H3 length-dependent manner in natural human antibodies with long CDR-H3 loops. Structural modeling suggests choices of JH help to stabilize antibody CDR-H3 loop and JH only partially contributes to the paratope. Our observations shed light on the design of next-generation synthetic diversity with improved probability of success.
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Affiliation(s)
- Huimin Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, #15 Beisanhuandong Rd, Chaoyang District, Beijing 100029, China
| | - Kai Yan
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Ruixue Wang
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Yi Yang
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Yuelei Shen
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, #15 Beisanhuandong Rd, Chaoyang District, Beijing 100029, China
| | - Lei Chen
- Biotherapeutics, Biocytogen Pharmaceuticals (Beijing) Co. Ltd., #12 Baoshennan St, Daxing District, Beijing 102629, China
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Khass M, Vale AM, Burrows PD, Schroeder HW. The sequences encoded by immunoglobulin diversity (D H ) gene segments play key roles in controlling B-cell development, antigen-binding site diversity, and antibody production. Immunol Rev 2019; 284:106-119. [PMID: 29944758 DOI: 10.1111/imr.12669] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although at first glance the diversity of the immunoglobulin repertoire appears random, there are a number of mechanisms that act to constrain diversity. For example, key mechanisms controlling the diversity of the third complementarity determining region of the immunoglobulin heavy chain (CDR-H3) include natural selection of germline diversity (DH ) gene segment sequence and somatic selection upon passage through successive B-cell developmental checkpoints. To test the role of DH gene segment sequence, we generated a panel of mice limited to the use of a single germline or frameshifted DH gene segment. Specific individual amino acids within core DH gene segment sequence heavily influenced the absolute numbers of developing and mature B-cell subsets, antibody production, epitope recognition, protection against pathogen challenge, and susceptibility to the production of autoreactive antibodies. At the tip of the antigen-binding loop (PDB position 101) in CDR-H3, both natural (germline) and somatic selection favored tyrosine while disfavoring the presence of hydrophobic amino acids. Enrichment for arginine in CDR-H3 appeared to broaden recognition of epitopes of varying hydrophobicity, but led to diminished binding intensity and an increased likelihood of generating potentially pathogenic dsDNA-binding autoreactive antibodies. The phenotype of altering the sequence of the DH was recessive for T-independent antibody production, but dominant for T-cell-dependent responses. Our work suggests that the antibody repertoire is structured, with the sequence of individual DH selected by evolution to preferentially generate an apparently preferred category of antigen-binding sites. The result of this structured approach appears to be a repertoire that has been adapted, or optimized, to produce protective antibodies for a wide range of pathogen epitopes while reducing the likelihood of generating autoreactive specificities.
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Affiliation(s)
- Mohamed Khass
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.,Division of Genetic Engineering and Biotechnology, National Research Center, Cairo, Egypt
| | - Andre M Vale
- Program in Immunobiology, Laboratory of Lymphocyte Biology, Carlos Chagas Filho Biophysics Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Peter D Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Harry W Schroeder
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
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Khass M, Blackburn T, Elgavish A, Burrows PD, Schroeder HW. In the Absence of Central pre-B Cell Receptor Selection, Peripheral Selection Attempts to Optimize the Antibody Repertoire by Enriching for CDR-H3 Y101. Front Immunol 2018; 9:120. [PMID: 29472919 PMCID: PMC5810287 DOI: 10.3389/fimmu.2018.00120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/15/2018] [Indexed: 01/13/2023] Open
Abstract
Sequential developmental checkpoints are used to “optimize” the B cell antigen receptor repertoire by minimizing production of autoreactive or useless immunoglobulins and enriching for potentially protective antibodies. The first and apparently most impactful checkpoint requires μHC to form a functional pre-B cell receptor (preBCR) by associating with surrogate light chain, which is composed of VpreB and λ5. Absence of any of the preBCR components causes a block in B cell development that is characterized by severe immature B cell lymphopenia. Previously, we showed that preBCR controls the amino acid content of the third complementary determining region of the H chain (CDR-H3) by using a VpreB amino acid motif (RDR) to select for tyrosine at CDR-H3 position 101 (Y101). In antibodies bound to antigen, Y101 is commonly in direct contact with the antigen, thus preBCR selection impacts the antigen binding characteristics of the repertoire. In this work, we sought to determine the forces that shape the peripheral B cell repertoire when it is denied preBCR selection. Using bromodeoxyuridine incorporation and evaluation of apoptosis, we found that in the absence of preBCR there is increased turnover of B cells due to increased apoptosis. CDR-H3 sequencing revealed that this is accompanied by adjustments to DH identity, DH reading frame, JH, and CDR-H3 amino acid content. These adjustments in the periphery led to wild-type levels of CDR-H3 Y101 content among transitional (T1), mature recirculating, and marginal zone B cells. However, peripheral selection proved incomplete, with failure to restore Y101 levels in follicular B cells and increased production of dsDNA-binding IgM antibodies.
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Affiliation(s)
- Mohamed Khass
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.,Genetic Engineering and Biotechnology Division, National Research Center, Cairo, Egypt
| | - Tessa Blackburn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ada Elgavish
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Peter D Burrows
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Harry W Schroeder
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States.,Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, United States
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Mroczek ES, Ippolito GC, Rogosch T, Hoi KH, Hwangpo TA, Brand MG, Zhuang Y, Liu CR, Schneider DA, Zemlin M, Brown EE, Georgiou G, Schroeder HW. Differences in the composition of the human antibody repertoire by B cell subsets in the blood. Front Immunol 2014; 5:96. [PMID: 24678310 PMCID: PMC3958703 DOI: 10.3389/fimmu.2014.00096] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 02/23/2014] [Indexed: 12/23/2022] Open
Abstract
The vast initial diversity of the antibody repertoire is generated centrally by means of a complex series of V(D)J gene rearrangement events, variation in the site of gene segment joining, and TdT catalyzed N-region addition. Although the diversity is great, close inspection has revealed distinct and unique characteristics in the antibody repertoires expressed by different B cell developmental subsets. In order to illustrate our approach to repertoire analysis, we present an in-depth comparison of V(D)J gene usage, hydrophobicity, length, DH reading frame, and amino acid usage between heavy chain repertoires expressed by immature, transitional, mature, memory IgD+, memory IgD−, and plasmacytes isolated from the blood of a single individual. Our results support the view that in both human and mouse, the H chain repertoires expressed by individual, developmental B cell subsets appear to differ in sequence content. Sequencing of unsorted B cells from the blood is thus likely to yield an incomplete or compressed view of what is actually happening in the immune response of the individual. Our findings support the view that studies designed to correlate repertoire expression with diseases of immune function will likely require deep sequencing of B cells sorted by subset.
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Affiliation(s)
- Eva Szymanska Mroczek
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Gregory C Ippolito
- Department of Molecular Biosciences, University of Texas at Austin , Austin, TX , USA
| | - Tobias Rogosch
- Laboratory for Neonatology and Pediatric Immunology, Department of Pediatrics, Philipps-University , Marburg , Germany
| | - Kam Hon Hoi
- Department of Chemical Engineering, University of Texas at Austin , Austin, TX , USA ; Department of Biomedical Engineering, University of Texas at Austin , Austin, TX , USA
| | - Tracy A Hwangpo
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Marsha G Brand
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Yingxin Zhuang
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Cun Ren Liu
- Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham , Birmingham, AL , USA
| | - Michael Zemlin
- Laboratory for Neonatology and Pediatric Immunology, Department of Pediatrics, Philipps-University , Marburg , Germany
| | - Elizabeth E Brown
- Department of Epidemiology, University of Alabama at Birmingham , Birmingham, AL , USA
| | - George Georgiou
- Department of Molecular Biosciences, University of Texas at Austin , Austin, TX , USA ; Department of Chemical Engineering, University of Texas at Austin , Austin, TX , USA ; Department of Biomedical Engineering, University of Texas at Austin , Austin, TX , USA
| | - Harry W Schroeder
- Department of Microbiology, University of Alabama at Birmingham , Birmingham, AL , USA ; Department of Medicine, University of Alabama at Birmingham , Birmingham, AL , USA
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Wu YCB, Kipling D, Dunn-Walters DK. The relationship between CD27 negative and positive B cell populations in human peripheral blood. Front Immunol 2011; 2:81. [PMID: 22566870 PMCID: PMC3341955 DOI: 10.3389/fimmu.2011.00081] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/05/2011] [Indexed: 12/25/2022] Open
Abstract
CD27 expression has been used to distinguish between memory and naive B cells in humans. However, low levels of mutated and isotype-switched CD27−IgD− cells are seen in healthy adults, and these are increased in some autoimmune diseases and in the elderly. Thus CD27 is not a universal marker of memory B cells in humans. Various hypotheses have been put forward as to the function of the CD27− memory population. Since we have previously found high-throughput IGHV repertoire analysis useful to distinguish “innate-like” memory B cells (CD27+IgD+), we have employed similar analyses to elucidate the relationship between CD27− and CD27+ memory B cells. IgM+IgD− memory cells in both the CD27+ and CD27− compartments share the unique characteristics of the “innate-like” IgM+IgD+CD27+ cells. The switched CD27+ and CD27− memory cells share a similar IGHV repertoire, having more in common with each other than with “innate-like” memory cells, although it is interesting that IgG2 and IgA2 subclasses of antibody in both switched memory populations have a more “innate-like” repertoire. Clonality analysis shows evidence of a close clonal relationship between the two populations in that both CD27− and CD27+ switched memory cells can be found in the same genealogical tree. The expression of CD27 does not appear to occur in a linear developmental fashion, since we see CD27− cells as precursors of CD27+ cells and vice versa. Despite the similarities, the CDR-H3 repertoire of the CD27− cells is significantly different from both the CD27+IgD+ and CD27+IgD− populations, indicating that perhaps the lack of CD27 might be related to binding properties of the Ig CDR-H3 region.
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Affiliation(s)
- Yu-Chang Bryan Wu
- Department of Immunobiology, Kings' College London School of Medicine, Guy's Campus London, UK
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