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Hu S, Han P, Wang M, Cao X, Liu H, Zhang S, Zhang S, Liu J, Han Y, Xiao J, Chen Q, Miao K, Qi J, Tan S, Gao GF, Wang H. Structural basis for the immune recognition and selectivity of the immune receptor PVRIG for ligand Nectin-2. Structure 2024:S0969-2126(24)00094-7. [PMID: 38626767 DOI: 10.1016/j.str.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/27/2024] [Accepted: 03/20/2024] [Indexed: 06/27/2024]
Abstract
Nectin and nectin-like (Necl) co-receptor axis, comprised of receptors DNAM-1, TIGIT, CD96, PVRIG, and nectin/Necl ligands, is gaining prominence in immuno-oncology. Within this axis, the inhibitory receptor PVRIG recognizes Nectin-2 with high affinity, but the underlying molecular basis remains unknown. By determining the crystal structure of PVRIG in complex with Nectin-2, we identified a unique CC' loop in PVRIG, which complements the double-lock-and-key binding mode and contributes to its high affinity for Nectin-2. The association of the corresponding charged residues in the F-strands explains the ligand selectivity of PVRIG toward Nectin-2 but not for Necl-5. Moreover, comprehensive comparisons of the binding capacities between co-receptors and ligands provide innovative insights into the intra-axis immunoregulatory mechanism. Taken together, these findings broaden our understanding of immune recognition and regulation mediated by nectin/Necl co-receptors and provide a rationale for the development of immunotherapeutic strategies targeting the nectin/Necl axis.
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Affiliation(s)
- Songtao Hu
- Institutes of Physical Science and Information Technology, Anhui University, Anhui 230601, China; Cancer Center, Faculty of Health Sciences, University of Macau, Taipa Macau SAR, China; Beijing Life Science Academy, Beijing 102200, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Meiyu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Anhui 230601, China
| | - Xiaoqing Cao
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101125, China
| | - Hao Liu
- Cancer Center, Faculty of Health Sciences, University of Macau, Taipa Macau SAR, China
| | - Shuailong Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Anhui 230601, China
| | - Shuijun Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Liu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China
| | - Yi Han
- Department of Thoracic Surgery, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing 101125, China
| | - Jinhe Xiao
- Department of Prevention and Treatment of Breast Disease, Haidian District Maternal and Child Health Care Hospital, Beijing 100080, China
| | - Qiang Chen
- Cancer Center, Faculty of Health Sciences, University of Macau, Taipa Macau SAR, China
| | - Kai Miao
- Cancer Center, Faculty of Health Sciences, University of Macau, Taipa Macau SAR, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - George Fu Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Han Wang
- Beijing Life Science Academy, Beijing 102200, China; Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100080, China.
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Vázquez-Martínez JA, Gómez-Lim MA, Morales-Ríos E, Gonzalez-y-Merchand JA, Ortiz-Navarrete V. Short Disordered Epitope of CRTAM Ig-Like V Domain as a Potential Target for Blocking Antibodies. Int J Mol Sci 2020; 21:ijms21228798. [PMID: 33233764 PMCID: PMC7699905 DOI: 10.3390/ijms21228798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 11/25/2022] Open
Abstract
Class-I Restricted T Cell-Associated Molecule (CRTAM) is a protein that is expressed after T cell activation. The interaction of CRTAM with its ligand, nectin-like 2 (Necl2), is required for the efficient production of IL-17, IL-22, and IFNγ by murine CD4 T cells, and it plays a role in optimal CD8 T and NK cell cytotoxicity. CRTAM promotes the pro-inflammatory cytokine profile; therefore, it may take part in the immunopathology of autoimmune diseases such as diabetes type 1 or colitis. Thus, antibodies that block the interaction between CRTAM and Necl2 would be useful for controlling the production of these inflammatory cytokines. In this work, using bioinformatics predictions, we identified three short disordered epitopes (sDE1-3) that are located in the Ig-like domains of murine CRTAM and are conserved in mammalian species. We performed a structural analysis by molecular dynamics simulations of sDE1 (QHPALKSSKY, Ig-like V), sDE2 (QRNGEKSVVK, Ig-like C1), and sDE3 (CSTERSKKPPPQI, Ig-like C1). sDE1, which is located within a loop of the contact interface of the heterotypic interaction with Nectl2, undergoes an order–disorder transition. On the contrary, even though sDE2 and sDE3 are flexible and also located within loops, they do not undergo order–disorder transitions. We evaluated the immunogenicity of sDE1 and sDE3 through the expression of these epitopes in chimeric L1 virus-like particles. We confirmed that sDE1 induces polyclonal antibodies that recognize the native folding of CRTAM expressed in activated murine CD4 T cells. In contrast, sDE3 induces polyclonal antibodies that recognize the recombinant protein hCRTAM-Fc, but not the native CRTAM. Thus, in this study, an exposed disordered epitope in the Ig-like V domain of CRTAM was identified as a potential site for therapeutic antibodies.
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Affiliation(s)
- Julio Angel Vázquez-Martínez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de Mexico, Mexico; (J.A.V.-M.); (J.A.G.-y.-M.)
- Departamento de Biomedicina Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico
- Departamento de Ingeniería Genética, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821 Irapuato, Guanajuato, Mexico;
| | - Miguel Angel Gómez-Lim
- Departamento de Ingeniería Genética, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 36821 Irapuato, Guanajuato, Mexico;
| | - Edgar Morales-Ríos
- Departamento de Bioquímica, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico;
| | - Jorge Alberto Gonzalez-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de Mexico, Mexico; (J.A.V.-M.); (J.A.G.-y.-M.)
| | - Vianney Ortiz-Navarrete
- Departamento de Biomedicina Molecular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), 07360 Ciudad de Mexico, Mexico
- Correspondence:
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Barragan-Galvez JC, Gonzalez-Orozco M, Hernandez-Flores A, Maravillas-Montero JL, Chavez-Guerrero Y, Ortiz-Navarrete V. Prokaryotic Expression of the Immunoglobulin's Domains of CRTAM to Characterize a Monoclonal Antibody. Protein J 2020; 39:224-231. [PMID: 32300914 DOI: 10.1007/s10930-020-09896-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Class-I restricted T cell-associated molecule (CRTAM) is a member of the immunoglobulin superfamily, and it is closely related to nectin-like protein. CRTAM is expressed in activated CD8 T cells, NKT cells, NK cells and in a subpopulation CD4 T cells. In this study, we produce as recombinant proteins, the Ig-domains of CRTAM (IgV-IgC), the IgV, and the IgC. These proteins were successfully purified in the soluble fraction only if the stalk region was included. The recombinant CRTAM recognizes its ligand nectin-like 2 in a cell-free system. We also demonstrate that the IgC domain of CRTAM is recognized by the anti-hCRTAM monoclonal antibody C8 with a 0.62 nM affinity. In conclusion, the stalk region of CRTAM provides solubility for the expression of its Ig-domains as recombinant proteins.
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Affiliation(s)
- Juan Carlos Barragan-Galvez
- Biomedical Sciences Program, National Autonomous University of Mexico, Circuito Interior s/n, Cd. Universitaria, Mexico City, Mexico
| | - Maria Gonzalez-Orozco
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV), Av. IPN 2508. Col. San Pedro Zacatenco, Gustavo A Madero, 07360, Mexico City, Mexico.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Jose Luis Maravillas-Montero
- Research Support Network, Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Yedhani Chavez-Guerrero
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV), Av. IPN 2508. Col. San Pedro Zacatenco, Gustavo A Madero, 07360, Mexico City, Mexico
| | - Vianney Ortiz-Navarrete
- Department of Molecular Biomedicine, Center for Research and Advanced Studies (CINVESTAV), Av. IPN 2508. Col. San Pedro Zacatenco, Gustavo A Madero, 07360, Mexico City, Mexico.
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Yang F, Lin S, Ye F, Yang J, Qi J, Chen Z, Lin X, Wang J, Yue D, Cheng Y, Chen Z, Chen H, You Y, Zhang Z, Yang Y, Yang M, Sun H, Li Y, Cao Y, Yang S, Wei Y, Gao GF, Lu G. Structural Analysis of Rabies Virus Glycoprotein Reveals pH-Dependent Conformational Changes and Interactions with a Neutralizing Antibody. Cell Host Microbe 2020; 27:441-453.e7. [DOI: 10.1016/j.chom.2019.12.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/06/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
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Structure of the heterophilic interaction between the nectin-like 4 and nectin-like 1 molecules. Proc Natl Acad Sci U S A 2019; 116:2068-2077. [PMID: 30674679 DOI: 10.1073/pnas.1810969116] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nectin-like (Necl) molecules are Ca2+-independent Ig-like transmembrane cell adhesion molecules that participate in junctions between different cell types. The specific cell-cell adhesions mediated by Necl proteins are important in neural development and have been implicated in neurodegenerative diseases. Here, we present the crystal structure of the mouse Necl-4 full ectodomain and the structure of the heterophilic Necl ectodomain complex formed by the mNecl-4 and mNecl-1 ectodomains. We demonstrate that, while the ectodomain of mNecl-4 is monomeric, it forms a stable heterodimer with Ig1 of mNecl-1, with an affinity significantly higher than that observed for self-dimerization of the mNecl-1 ectodomain. We validated our structural characterizations by performing a surface plasmon resonance assay and an Fc fusion protein binding assay in mouse primary dorsal root ganglia neurites and Schwann cells and identified a selection of residues important for heterophilic interactions. Finally, we proposed a model of Necl binding specificity that involves an induced-fit conformational change at the dimerization interface.
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Binding mode of the side-by-side two-IgV molecule CD226/DNAM-1 to its ligand CD155/Necl-5. Proc Natl Acad Sci U S A 2018; 116:988-996. [PMID: 30591568 DOI: 10.1073/pnas.1815716116] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natural killer (NK) cells are important component of innate immunity and also contribute to activating and reshaping the adaptive immune responses. The functions of NK cells are modulated by multiple inhibitory and stimulatory receptors. Among these receptors, the activating receptor CD226 (DNAM-1) mediates NK cell activation via binding to its nectin-like (Necl) family ligand, CD155 (Necl-5). Here, we present a unique side-by-side arrangement pattern of two tandem immunoglobulin V-set (IgV) domains deriving from the ectodomains of both human CD226 (hCD226-ecto) and mouse CD226 (mCD226-ecto), which is substantially different from the conventional head-to-tail arrangement of other multiple Ig-like domain molecules. The hybrid complex structure of mCD226-ecto binding to the first domain of human CD155 (hCD155-D1) reveals a conserved binding interface with the first domain of CD226 (D1), whereas the second domain of CD226 (D2) both provides structural supports for the unique architecture of CD226 and forms direct interactions with CD155. In the absence of the D2 domain, CD226-D1 exhibited substantially reduced binding efficacy to CD155. Collectively, these findings would broaden our knowledge of the interaction between NK cell receptors and the nectin/Necl family ligands, as well as provide molecular basis for the development of CD226-targeted antitumor immunotherapeutics.
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Ito T, Kasai Y, Kumagai Y, Suzuki D, Ochiai-Noguchi M, Irikura D, Miyake S, Murakami Y. Quantitative Analysis of Interaction Between CADM1 and Its Binding Cell-Surface Proteins Using Surface Plasmon Resonance Imaging. Front Cell Dev Biol 2018; 6:86. [PMID: 30131958 PMCID: PMC6090299 DOI: 10.3389/fcell.2018.00086] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/20/2018] [Indexed: 12/11/2022] Open
Abstract
The cell adhesion molecule (CADM) family of the immunoglobulin superfamily (IgSF) comprises four members, CADM1-CADM4, and participates in the formation of epithelial and synaptic adhesion through cell-cell homophilic and heterophilic interactions. To identify the partners that interact with each member of the CADM family proteins, we set up a platform for multiple detection of the extracellular protein-protein interactions using surface plasmon resonance imaging (SPRi) and analyzed the interactions between the CADM family proteins and 10 IgSF of their structurally related cell adhesion molecules. SPRi analysis identified a new interaction between CADM1 and CADM4, where this heterophilic interaction was shown to be involved in morphological spreading of adult T-cell leukemia (ATL) cells expressing CADM1 when incubated on CADM4-coated glass. Moreover, class-I MHC-restricted T-cell-associated molecule (CRTAM) was identified to show the highest affinity to CADM1 among its binding partners by comparing the dissociation constants calculated from the SPR sensorgrams. These results suggest that the SPRi platform would provide a novel screening tool to characterize extracellular protein-protein interactions among cell-surface and secreted proteins, including IgSF molecules.
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Affiliation(s)
- Takeshi Ito
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
| | - Yutaka Kasai
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
| | - Yuki Kumagai
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
| | - Daisuke Suzuki
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
| | - Misaki Ochiai-Noguchi
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
| | - Daisuke Irikura
- Bio/Life Science Team, Advanced R&D Center HORIBA Ltd., Kyoto, Japan
| | - Shiro Miyake
- Bio/Life Science Team, Advanced R&D Center HORIBA Ltd., Kyoto, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, The Institute of Medical Science The University of Tokyo, Tokyo, Japan
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Kuttner YY, Engel S. Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots. Proteins 2017; 86:229-236. [DOI: 10.1002/prot.25430] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 11/08/2017] [Accepted: 11/22/2017] [Indexed: 12/13/2022]
Affiliation(s)
- Yosef Y. Kuttner
- Department of Clinical Biochemistry and Pharmacology; Faculty of Health Sciences, Ben-Gurion University of the Negev; Beer-Sheva Israel
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology; Faculty of Health Sciences, Ben-Gurion University of the Negev; Beer-Sheva Israel
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PILRα and PILRβ have a siglec fold and provide the basis of binding to sialic acid. Proc Natl Acad Sci U S A 2014; 111:8221-6. [PMID: 24843130 DOI: 10.1073/pnas.1320716111] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Paired immunoglobulin-like type 2 receptor α (PILRα) and β (PILRβ) belong to the PILR family and are related to innate immune regulation in various species. Despite their high sequence identity, PILRα and PILRβ are shown to have variant sialic acid (SA) binding avidities. To explore the molecular basis of this interaction, we solved the crystal structures of PILRα and PILRβ at resolutions of 1.6 Å and 2.2 Å, respectively. Both molecules adopt a typical siglec fold but use a hydrophobic bond to substitute the siglec-specific disulfide linkage for protein stabilization. We further used HSV-1 glycoprotein B (gB) as a representative molecule to study the PILR-SA interaction. Deploying site-directed mutagenesis, we demonstrated that three residues (Y2, R95, and W108) presented on the surface of PILRα form the SA binding site equivalent to those in siglecs but are arranged in a unique linear mode. PILRβ differs from PILRα in one of these three residues (L108), explaining its inability to engage gB. Mutation of L108 to tryptophan in PILRβ restored the gB-binding capacity. We further solved the structure of this PILRβ mutant complexed with SA, which reveals the atomic details mediating PILR/SA recognition. In comparison with the free PILR structures, amino acid Y2 oriented variantly in the complex structure, thereby disrupting the linear arrangement of PILR residues Y2, R95, and W108. In conclusion, our study provides significant implications for the PILR-SA interaction and paves the way for understanding PILR-related ligand binding.
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