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Caveney NA, Rodriguez GE, Pollmann C, Meyer T, Borowska MT, Wilson SC, Wang N, Xiang X, Householder KD, Tao P, Su LL, Saxton RA, Piehler J, Garcia KC. Structure of the interleukin-5 receptor complex exemplifies the organizing principle of common beta cytokine signaling. Mol Cell 2024; 84:1995-2005.e7. [PMID: 38614096 DOI: 10.1016/j.molcel.2024.03.023] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 02/20/2024] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
Cytokines regulate immune responses by binding to cell surface receptors, including the common subunit beta (βc), which mediates signaling for GM-CSF, IL-3, and IL-5. Despite known roles in inflammation, the structural basis of IL-5 receptor activation remains unclear. We present the cryo-EM structure of the human IL-5 ternary receptor complex, revealing architectural principles for IL-5, GM-CSF, and IL-3. In mammalian cell culture, single-molecule imaging confirms hexameric IL-5 complex formation on cell surfaces. Engineered chimeric receptors show that IL-5 signaling, as well as IL-3 and GM-CSF, can occur through receptor heterodimerization, obviating the need for higher-order assemblies of βc dimers. These findings provide insights into IL-5 and βc receptor family signaling mechanisms, aiding in the development of therapies for diseases involving deranged βc signaling.
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Affiliation(s)
- Nathanael A Caveney
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
| | - Grayson E Rodriguez
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christoph Pollmann
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Thomas Meyer
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Marta T Borowska
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven C Wilson
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nan Wang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Xinyu Xiang
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Biophysics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Karsten D Householder
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pingdong Tao
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leon L Su
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Jacob Piehler
- Department of Biology/Chemistry and Center for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - K Christopher Garcia
- Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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2
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Borowska MT, Boughter CT, Bunker JJ, Guthmiller JJ, Wilson PC, Roux B, Bendelac A, Adams EJ. Biochemical and biophysical characterization of natural polyreactivity in antibodies. Cell Rep 2023; 42:113190. [PMID: 37804505 PMCID: PMC10858392 DOI: 10.1016/j.celrep.2023.113190] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/25/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023] Open
Abstract
To become specialized binders, antibodies undergo a process called affinity maturation to maximize their binding affinity. Despite this process, some antibodies retain low-affinity binding to diverse epitopes in a phenomenon called polyreactivity. Here we seek to understand the molecular basis of this polyreactivity in antibodies. Our results highlight that polyreactive antigen-binding fragments (Fabs) bind their targets with low affinities, comparable to T cell receptor recognition of autologous classical major histocompatibility complex. Extensive mutagenic studies find no singular amino acid residue or biochemical property responsible for polyreactive interaction, suggesting that polyreactive antibodies use multiple strategies for engagement. Finally, our crystal structures and all-atom molecular dynamics simulations of polyreactive Fabs show increased rigidity compared to their monoreactive relatives, forming a neutral and accessible platform for diverse antigens to bind. Together, these data support a cooperative strategy of rigid neutrality in establishing the polyreactive status of an antibody molecule.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | | | - Jeffrey J Bunker
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Patrick C Wilson
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ. The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe. Proc Natl Acad Sci U S A 2021; 118:e2023898118. [PMID: 34548394 PMCID: PMC8488583 DOI: 10.1073/pnas.2023898118] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2021] [Indexed: 11/18/2022] Open
Abstract
Microorganisms have coevolved diverse mechanisms to impair host defenses. A major one, superantigens, can result in devastating effects on the immune system. While all known superantigens induce vast immune cell proliferation and come from opportunistic pathogens, recently, proteins with similar broad specificity to antibody variable (V) domain families were identified in a commensal microbiota. These proteins, identified in the human commensal Ruminococcus gnavus, are called immunoglobulin-binding protein (Ibp) A and B and have been shown to activate B cells in vitro expressing either human VH3 or murine VH5/6/7. Here, we provide molecular and functional studies revealing the basis of this Ibp/immunoglobulin (Ig) interaction. The crystal structure and biochemical assays of a truncated IbpA construct in complex with mouse VH5 antigen-binding fragment (Fab) shows a binding of Ig heavy chain framework residues to the Ibp Domain D and the C-terminal heavy chain binding domain (HCBD). We used targeted mutagenesis of contact residues and affinity measurements and performed studies of the Fab-IbpA complex to determine the stoichiometry between Ibp and VH domains, suggesting Ibp may serve to cluster full-length IgA antibodies in vivo. Furthermore, in vitro stimulation experiments indicate that binding of the Ibp HCBD alone is sufficient to activate responsive murine B cell receptors. The presence of these proteins in a commensal microbe suggest that binding a broad repertoire of immunoglobulins, particularly in the gut/microbiome environment, may provide an important function in the maintenance of host/microbiome homeostasis contrasting with the pathogenic role of structurally homologous superantigens expressed by pathogens.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637
| | - Christoph Drees
- Department of Pathology, University of Chicago, Chicago, IL 60637
| | - Alexander E Yarawsky
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | | | - Sean M Ryan
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Jeffrey J Bunker
- Department of Pathology, University of Chicago, Chicago, IL 60637
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Andrew B Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229
| | - Albert Bendelac
- Department of Pathology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
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4
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Guthmiller JJ, Lan LYL, Fernández-Quintero ML, Han J, Utset HA, Bitar DJ, Hamel NJ, Stovicek O, Li L, Tepora M, Henry C, Neu KE, Dugan HL, Borowska MT, Chen YQ, Liu STH, Stamper CT, Zheng NY, Huang M, Palm AKE, García-Sastre A, Nachbagauer R, Palese P, Coughlan L, Krammer F, Ward AB, Liedl KR, Wilson PC. Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses. Immunity 2020; 53:1230-1244.e5. [PMID: 33096040 PMCID: PMC7772752 DOI: 10.1016/j.immuni.2020.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
Polyreactivity is the ability of a single antibody to bind to multiple molecularly distinct antigens and is a common feature of antibodies induced upon pathogen exposure. However, little is known about the role of polyreactivity during anti-influenza virus antibody responses. By analyzing more than 500 monoclonal antibodies (mAbs) derived from B cells induced by numerous influenza virus vaccines and infections, we found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive. Polyreactive mAbs were preferentially induced by novel viral exposures due to their broad viral binding breadth. Polyreactivity augmented mAb viral binding strength by increasing antibody flexibility, allowing for adaption to imperfectly conserved epitopes. Lastly, we found affinity-matured polyreactive B cells were typically derived from germline polyreactive B cells that were preferentially selected to participate in B cell responses over time. Together, our data reveal that polyreactivity is a beneficial feature of antibodies targeting conserved epitopes.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Linda Yu-Ling Lan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Natalie J Hamel
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Micah Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Sean T H Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Microbiology and Immunology and Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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5
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Boughter CT, Borowska MT, Guthmiller JJ, Bendelac A, Wilson PC, Roux B, Adams EJ. Biochemical patterns of antibody polyreactivity revealed through a bioinformatics-based analysis of CDR loops. eLife 2020; 9:61393. [PMID: 33169668 PMCID: PMC7755423 DOI: 10.7554/elife.61393] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 07/23/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Antibodies are critical components of adaptive immunity, binding with high affinity to pathogenic epitopes. Antibodies undergo rigorous selection to achieve this high affinity, yet some maintain an additional basal level of low affinity, broad reactivity to diverse epitopes, a phenomenon termed ‘polyreactivity’. While polyreactivity has been observed in antibodies isolated from various immunological niches, the biophysical properties that allow for promiscuity in a protein selected for high-affinity binding to a single target remain unclear. Using a database of over 1000 polyreactive and non-polyreactive antibody sequences, we created a bioinformatic pipeline to isolate key determinants of polyreactivity. These determinants, which include an increase in inter-loop crosstalk and a propensity for a neutral binding surface, are sufficient to generate a classifier able to identify polyreactive antibodies with over 75% accuracy. The framework from which this classifier was built is generalizable, and represents a powerful, automated pipeline for future immune repertoire analysis. To defend itself against bacteria and viruses, the body depends on a group of proteins known as antibodies. Each subset of antibodies undergoes a rigorous training regimen to ensure it recognizes a single epitope well – that is, one specific region on the surface of foreign, harmful organisms. Most antibodies stick extremely tightly to their one unique epitope, but some can also weakly bind to molecules that are vastly different from their main trained targets. This feature – known as polyreactivity – can in some cases help the immune system fight against multiple strains of viruses. On the other hand, when antibodies are designed in the laboratory to treat diseases, this characteristic can sometimes lead to the failure of pre-clinical trials. Yet it is currently unclear why some antibodies are polyreactive when others are not. To investigate this question, Boughter et al. compared over 1,000 polyreactive and non-polyreactive antibody sequences from a large database, revealing differences in the physical properties of the region of the antibodies that attaches to epitopes. Using these defining features, Boughter et al. went on to design a new piece of freely available, automated software that could predict which antibodies would be polyreactive more than 75% of the time. Such software could ultimately help to guide the design of antibody-based treatments, while bypassing the need for costly laboratory tests.
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Affiliation(s)
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States
| | - Albert Bendelac
- Committee on Immunology, University of Chicago, Chicago, United States.,Department of Pathology, University of Chicago, Chicago, United States
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, United States.,Committee on Immunology, University of Chicago, Chicago, United States
| | - Benoit Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Erin J Adams
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Committee on Immunology, University of Chicago, Chicago, United States
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Boughter CT, Borowska MT, Roux B, Adams EJ. Insights into Polyreactivity via High-throughput Biophysical Characterization of Antibody Sequences. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.2073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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7
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Gu S, Borowska MT, Boughter CT, Adams EJ. Butyrophilin3A proteins and Vγ9Vδ2 T cell activation. Semin Cell Dev Biol 2018; 84:65-74. [PMID: 29471037 PMCID: PMC6129423 DOI: 10.1016/j.semcdb.2018.02.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 12/22/2017] [Accepted: 02/08/2018] [Indexed: 02/07/2023]
Abstract
Despite playing critical roles in the immune response and having significant potential in immunotherapy, γδ T cells have garnered little of the limelight. One major reason for this paradox is that their antigen recognition mechanisms are largely unknown, limiting our understanding of their biology and our potential to modulate their activity. One of the best-studied γδ subsets is the human Vγ9Vδ2T cell population, which predominates in peripheral blood and can combat both microbial infections and cancers. Although it has been known for decades that Vγ9Vδ2T cells respond to the presence of small pyrophosphate-based metabolites, collectively named phosphoantigens (pAgs), derived from microbial sources or malignant cells, the molecular basis for this response has been unclear. A major breakthrough in this area came with the identification of the Butyrophilin 3A (BTN3A) proteins, members of the Butyrophilin/Butyrophilin-like protein family, as mediators between pAgs and Vγ9Vδ2T cells. In this article, we review the most recent studies regarding pAg activation of human Vγ9Vδ2T cells, mainly focusing on the role of BTN3A as the pAg sensing molecule, as well as its potential impact on downstream events of the activation process.
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Affiliation(s)
- Siyi Gu
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637, USA
| | | | - Erin J Adams
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA; Biophysical Sciences, University of Chicago, Chicago, IL 60637, USA; Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA.
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8
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Gu S, Sachleben JR, Boughter CT, Nawrocka WI, Borowska MT, Tarrasch JT, Skiniotis G, Roux B, Adams EJ. Phosphoantigen-induced conformational change of butyrophilin 3A1 (BTN3A1) and its implication on Vγ9Vδ2 T cell activation. Proc Natl Acad Sci U S A 2017; 114:E7311-E7320. [PMID: 28807997 PMCID: PMC5584448 DOI: 10.1073/pnas.1707547114] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human Vγ9Vδ2 T cells respond to microbial infections as well as certain types of tumors. The key initiators of Vγ9Vδ2 activation are small, pyrophosphate-containing molecules called phosphoantigens (pAgs) that are present in infected cells or accumulate intracellularly in certain tumor cells. Recent studies demonstrate that initiation of the Vγ9Vδ2 T cell response begins with sensing of pAg via the intracellular domain of the butyrophilin 3A1 (BTN3A1) molecule. However, it is unknown how downstream events can ultimately lead to T cell activation. Here, using NMR spectrometry and molecular dynamics (MD) simulations, we characterize a global conformational change in the B30.2 intracellular domain of BTN3A1 induced by pAg binding. We also reveal by crystallography two distinct dimer interfaces in the BTN3A1 full-length intracellular domain, which are stable in MD simulations. These interfaces lie in close proximity to the pAg-binding pocket and contain clusters of residues that experience major changes of chemical environment upon pAg binding. This suggests that pAg binding disrupts a preexisting conformation of the BTN3A1 intracellular domain. Using a combination of biochemical, structural, and cellular approaches we demonstrate that the extracellular domains of BTN3A1 adopt a V-shaped conformation at rest, and that locking them in this resting conformation without perturbing their membrane reorganization properties diminishes pAg-induced T cell activation. Based on these results, we propose a model in which a conformational change in BTN3A1 is a key event of pAg sensing that ultimately leads to T cell activation.
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Affiliation(s)
- Siyi Gu
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637
| | - Joseph R Sachleben
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637
- Biomolecular NMR Facility, University of Chicago, Chicago, IL 60637
| | | | - Wioletta I Nawrocka
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637
| | - Jeffrey T Tarrasch
- Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Georgios Skiniotis
- Life Sciences Institute, University of Michigan Medical School, Ann Arbor, MI 48109
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Benoît Roux
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL 60637
| | - Erin J Adams
- Department of Biochemistry and Molecular Biophysics, University of Chicago, Chicago, IL 60637;
- Committee on Immunology, University of Chicago, Chicago, IL 60637
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637
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Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA. Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs. Structure 2015; 24:300-9. [PMID: 26749445 DOI: 10.1016/j.str.2015.11.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/18/2023]
Abstract
A major challenge in membrane biophysics is to define the mechanistic linkages between a protein's conformational transitions and its function. We describe a novel approach to stabilize transient functional states of membrane proteins in native-like lipid environments allowing for their structural and biochemical characterization. This is accomplished by combining the power of antibody Fab-based phage display selection with the benefits of embedding membrane protein targets in lipid-filled nanodiscs. In addition to providing a stabilizing lipid environment, nanodiscs afford significant technical advantages over detergent-based formats. This enables the production of a rich pool of high-performance Fab binders that can be used as crystallization chaperones, as fiducial markers for single-particle cryoelectron microscopy, and as probes of different conformational states. Moreover, nanodisc-generated Fabs can be used to identify detergents that best mimic native membrane environments for use in biophysical studies.
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Affiliation(s)
- Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Olivier Dalmas
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Sangwoo S Kim
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Eduardo Perozo
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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10
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Borowska MT, Dominik PK, Anghel SA, Kossiakoff AA, Keenan RJ. A YidC-like Protein in the Archaeal Plasma Membrane. Structure 2015; 23:1715-1724. [PMID: 26256539 DOI: 10.1016/j.str.2015.06.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 05/29/2015] [Accepted: 06/21/2015] [Indexed: 01/08/2023]
Abstract
Cells possess specialized machinery to direct the insertion of membrane proteins into the lipid bilayer. In bacteria, the essential protein YidC inserts certain proteins into the plasma membrane, and eukaryotic orthologs are present in the mitochondrial inner membrane and the chloroplast thylakoid membrane. The existence of homologous insertases in archaea has been proposed based on phylogenetic analysis. However, limited sequence identity, distinct architecture, and the absence of experimental data have made this assignment ambiguous. Here we describe the 3.5-Å crystal structure of an archaeal DUF106 protein from Methanocaldococcus jannaschii (Mj0480), revealing a lipid-exposed hydrophilic surface presented by a conserved YidC-like fold. Functional analysis reveals selective binding of Mj0480 to ribosomes displaying a stalled YidC substrate, and a direct interaction between the buried hydrophilic surface of Mj0480 and the nascent chain. These data provide direct experimental evidence that the archaeal DUF106 proteins are YidC/Oxa1/Alb3-like insertases of the archaeal plasma membrane.
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Affiliation(s)
- Marta T Borowska
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Pawel K Dominik
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - S Andrei Anghel
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Anthony A Kossiakoff
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA
| | - Robert J Keenan
- Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57(th) Street, Chicago, IL 60637, USA.
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