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Karyu H, Niki T, Sorimachi Y, Hata S, Shimabukuro-Demoto S, Hirabayashi T, Mukai K, Kasahara K, Takubo K, Goda N, Honke K, Taguchi T, Sorimachi H, Toyama-Sorimachi N. Collaboration between a cis-interacting natural killer cell receptor and membrane sphingolipid is critical for the phagocyte function. Front Immunol 2024; 15:1401294. [PMID: 38720899 PMCID: PMC11076679 DOI: 10.3389/fimmu.2024.1401294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Inhibitory natural killer (NK) cell receptors recognize MHC class I (MHC-I) in trans on target cells and suppress cytotoxicity. Some NK cell receptors recognize MHC-I in cis, but the role of this interaction is uncertain. Ly49Q, an atypical Ly49 receptor expressed in non-NK cells, binds MHC-I in cis and mediates chemotaxis of neutrophils and type I interferon production by plasmacytoid dendritic cells. We identified a lipid-binding motif in the juxtamembrane region of Ly49Q and found that Ly49Q organized functional membrane domains comprising sphingolipids via sulfatide binding. Ly49Q recruited actin-remodeling molecules to an immunoreceptor tyrosine-based inhibitory motif, which enabled the sphingolipid-enriched membrane domain to mediate complicated actin remodeling at the lamellipodia and phagosome membranes during phagocytosis. Thus, Ly49Q facilitates integrative regulation of proteins and lipid species to construct a cell type-specific membrane platform. Other Ly49 members possess lipid binding motifs; therefore, membrane platform organization may be a primary role of some NK cell receptors.
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Affiliation(s)
- Hitomi Karyu
- Division of Human Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Takahiro Niki
- Laboratory for Neural Cell Dynamics, RIKEN Center for Brain Science, Saitama, Japan
| | - Yuriko Sorimachi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Shoji Hata
- Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Shiho Shimabukuro-Demoto
- Division of Human Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Tetsuya Hirabayashi
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kojiro Mukai
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Kohji Kasahara
- Laboratory of Biomembrane, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan
| | - Nobuhito Goda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Koichi Honke
- Department of Biochemistry and Kochi System Glycobiology Center, Kochi University Medical School, Kochi, Japan
| | - Tomohiko Taguchi
- Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hiroyuki Sorimachi
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Noriko Toyama-Sorimachi
- Division of Human Immunology, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
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Gingrich AA, Razmara AM, Gingrich PW, Rebhun RB, Murphy WJ, Kent MS, Brown CT, Siegel JB, Canter RJ. Missing a "Missing Self" Mechanism: Modeling and Detection of Ly49 Expression in Canine NK Cells. Immunohorizons 2023; 7:760-770. [PMID: 37971282 PMCID: PMC10696421 DOI: 10.4049/immunohorizons.2300092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
NK cells are a key focus in immuno-oncology, based on their ability to eliminate malignant cells without prior sensitization. Dogs are valuable models for translational immunotherapy studies, especially for NK cells, where critical species differences exist between mice and humans. Given that the mechanism for recognition of "self" by canine NK cells is currently unknown, we sought to evaluate expression of Ly49 in canine NK cells using in silico and high-throughput techniques. We interrogated the identified polymorphism/mutation in canine Ly49 and assessed the potential impact on structure using computational modeling of three-dimensional protein structure and protein-protein docking of canine Ly49 with MHC class I (MHC-I). Bulk and single-cell RNA-sequencing analysis was performed to detect gene expression of Ly49/KLRA1 in resting and activated NK cells. Tertiary protein structure demonstrated significant structural similarity to the known murine system. Molecular docking of canine Ly49 with MHC-I was favorable, converging at a single low-energy conformation. RNA sequencing revealed expression of Ly49/KLRA1 in both resting and activated NK cells and demonstrated almost exclusive expression of the gene in the NK cluster at the single-cell level. Despite prior reports of a mutated, nonfunctional canine Ly49, our data support that the protein product is predicted to bind to MHC-I in a comparable conformation to the murine system and is expressed in canine NK cells with upregulation following activation. Taken together, these data suggest that Ly49 is capable of recognizing MHC-I and therefore regulating NK cell function in dogs.
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Affiliation(s)
- Alicia A. Gingrich
- Department of Surgery, University of California, Davis School of Medicine, Sacramento, CA
| | - Aryana M. Razmara
- Department of Surgery, University of California, Davis School of Medicine, Sacramento, CA
| | - Phillip W. Gingrich
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Sacramento, CA
| | - Robert B. Rebhun
- Department of Surgical and Radiological Sciences, University of California, Davis School of Veterinary Medicine, Davis, CA
| | - William J. Murphy
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA
| | - Michael S. Kent
- Department of Surgical and Radiological Sciences, University of California, Davis School of Veterinary Medicine, Davis, CA
| | - C. Titus Brown
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA
| | - Justin B. Siegel
- Department of Biochemistry and Molecular Medicine, University of California, Davis School of Medicine, Sacramento, CA
| | - Robert J. Canter
- Department of Surgery, University of California, Davis School of Medicine, Sacramento, CA
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Zhang H, Yuan Z, Wang J, Tang Q, Miao Y, Yuan Z, Huang X, Zhu Y, Nong C, Zhang L, Jiang Z, Yu Q. Triptolide leads to hepatic intolerance to exogenous lipopolysaccharide and natural-killer-cell mediated hepatocellular damage by inhibiting MHC class I molecules. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 109:154621. [PMID: 36610139 DOI: 10.1016/j.phymed.2022.154621] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Tripterygium wilfordii Hook. F (TWHF) is used as a traditional Chinese medicine, called thunder god vine, based on its efficacy for treating inflammatory diseases. However, its hepatotoxicity has limited its clinical application. Triptolide (TP) is the major active and toxic component of TWHF. Previous studies reported that a toxic pretreatment dose of TP leads to hepatic intolerance to exogenous lipopolysaccharide (LPS) stimulation, and to acute liver failure, in mice, but the immune mechanisms of TP-sensitised hepatocytes and the TP-induced excessive immune response to LPS stimulation are unknown. PURPOSE To identify both the key immune cell population and mechanism involved in TP-induced hepatic intolerance of exogenous LPS. STUDY DESIGN In vitro and in vivo experiments were conducted to investigate the inhibitory signal of natural killer (NK) cells maintained in hepatocytes, and the ability of TP to impair that signal. METHODS Flow cytometry was performed to determine NK cell activity and hepatocyte histocompatibility complex (MHC) class I molecules expression; the severity of liver injury was determined based on blood chemistry values, and drug- or cell-mediated hepatocellular damage, by measuring lactate dehydrogenase (LDH) release. In vivo H-2Kb transduction was carried out using an adeno-associated viral vector. RESULTS Interferon (IFN)-γ-mediated necroptosis occurred in C57BL/6N mice treated with 500 μg TP/kg and 0.1 mg LPS/kg to induce fulminant hepatitis. Primary hepatocytes pretreated with TP were more prone to necroptosis when exposed to recombinant murine IFN-γ. In mice administered TP and LPS, the intracellular IFN-γ levels of NK cells increased significantly. Subsequent study confirmed that NK cells were activated and resulted in potent hepatocellular toxicity. In vivo and in vitro TP administration significantly inhibited MHC class I molecules in murine hepatocytes. An in vitro analysis demonstrated the susceptibility of TP-pretreated hepatocytes to NK-cell-mediated cytotoxicity, an effect that was significantly attenuated by the induction of hepatocyte MHC-I molecules by IFN-α. In vivo induction or overexpression of hepatocyte MHC-I also protected mouse liver against TP and LPS-induced injury. CONCLUSION The TP-induced inhibition of hepatocyte MHC-I molecules expression leads to hepatic intolerance to exogenous LPS and NK-cell mediated cytotoxicity against self-hepatocytes. These findings shed light on the toxicity of traditional Chinese medicines administered for their immunomodulatory effects.
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Affiliation(s)
- Haoran Zhang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zihang Yuan
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Jie Wang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Qianhui Tang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yingying Miao
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Ziqiao Yuan
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Xinliang Huang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Ying Zhu
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Cheng Nong
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Luyong Zhang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Zhenzhou Jiang
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing, 210009, China.
| | - Qinwei Yu
- New Drug Screening Center, Jiangsu Center for Pharmacodynamics Research and Evaluation, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China.
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Bourayou E, Golub R. Inflammatory-driven NK cell maturation and its impact on pathology. Front Immunol 2022; 13:1061959. [PMID: 36569860 PMCID: PMC9780665 DOI: 10.3389/fimmu.2022.1061959] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022] Open
Abstract
NK cells are innate lymphocytes involved in a large variety of contexts and are crucial in the immunity to intracellular pathogens as well as cancer due to their ability to kill infected or malignant cells. Thus, they harbor a strong potential for clinical and therapeutic use. NK cells do not require antigen exposure to get activated; their functional response is rather based on a balance between inhibitory/activating signals and on the diversity of germline-encoded receptors they express. In order to reach optimal functional status, NK cells go through a step-wise development in the bone marrow before their egress, and dissemination into peripheral organs via the circulation. In this review, we summarize bone marrow NK cell developmental stages and list key factors involved in their differentiation before presenting newly discovered and emerging factors that regulate NK cell central and peripheral maturation. Lastly, we focus on the impact inflammatory contexts themselves can have on NK cell development and functional maturation.
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Weaver GC, Arya R, Schneider CL, Hudson AW, Stern LJ. Structural Models for Roseolovirus U20 And U21: Non-Classical MHC-I Like Proteins From HHV-6A, HHV-6B, and HHV-7. Front Immunol 2022; 13:864898. [PMID: 35444636 PMCID: PMC9013968 DOI: 10.3389/fimmu.2022.864898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/08/2022] [Indexed: 01/08/2023] Open
Abstract
Human roseolovirus U20 and U21 are type I membrane glycoproteins that have been implicated in immune evasion by interfering with recognition of classical and non-classical MHC proteins. U20 and U21 are predicted to be type I glycoproteins with extracytosolic immunoglobulin-like domains, but detailed structural information is lacking. AlphaFold and RoseTTAfold are next generation machine-learning-based prediction engines that recently have revolutionized the field of computational three-dimensional protein structure prediction. Here, we review the structural biology of viral immunoevasins and the current status of computational structure prediction algorithms. We use these computational tools to generate structural models for U20 and U21 proteins, which are predicted to adopt MHC-Ia-like folds with closed MHC platforms and immunoglobulin-like domains. We evaluate these structural models and place them within current understanding of the structural basis for viral immune evasion of T cell and natural killer cell recognition.
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Affiliation(s)
- Grant C. Weaver
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, United States
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
| | - Richa Arya
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
| | | | - Amy W. Hudson
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Lawrence J. Stern
- Immunology and Microbiology Graduate Program, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, United States
- Department of Pathology, UMass Chan Medical School, Worcester, MA, United States
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, United States
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6
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Dohnálek J, Skálová T. C-type lectin-(like) fold - Protein-protein interaction patterns and utilization. Biotechnol Adv 2022; 58:107944. [PMID: 35301089 DOI: 10.1016/j.biotechadv.2022.107944] [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: 10/02/2021] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/02/2022]
Abstract
The C-type lectin-like fold (CTL fold) is a building block of many proteins, including saccharide-binding lectins, natural killer cell receptors, macrophage mannose receptor, selectins, collectins, snake venoms and others. Some are important players in innate immunity and are involved in the first-line response to virally infected cells or cancer cells, some play a role in antimicrobial defense, and some are potential targets for fight against problems connected with allergies, obesity, and autoimmunity. The structure of a CTL domain typically contains two α-helices, two small β-sheets and a long surface loop, with two or three disulfide bridges stabilizing the structure. This small domain is often involved in interactions with a target molecule, however, utilizing varied parts of the domain surface, with or without structural modifications. More than 500 three-dimensional structures of CTL fold-containing proteins are available in the Protein Data Bank, including a significant number of complexes with their key interacting partners (protein:protein complexes). The amount of available structural data enables a detailed analysis of the rules of interaction patterns utilized in activation, inhibition, attachment and other pathways or functionalities. Interpretation of known CTL receptor structures and all other CTL-containing proteins and complexes with described three-dimensional structures, complemented with sequence/structure/interaction correlation analysis offers a comprehensive view of the rules of interaction patterns of the CTL fold. The results are of value for prediction of interaction behavior of so far not understood CTL-containing proteins and development of new protein binders based on this fold, with applications in biomedicine or biotechnologies. It follows from the available structural data that almost the whole surface of the CTL fold is utilized in protein:protein interactions, with the heaviest frequency of utilization in the canonical interaction region. The individual categories of interactions differ in the interface buildup strategy. The strongest CTL binders rely on interfaces with large interaction area, presence of hydrophobic core, or high surface complementarity. The typical interaction surfaces of the fold are not conserved in amino acid sequence and can be utilized in design of new binders for biotechnological applications.
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Affiliation(s)
- Jan Dohnálek
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic.
| | - Tereza Skálová
- Institute of Biotechnology of the Czech Academy of Sciences, Biocev, Průmyslová 595, 25250 Vestec, Czech Republic
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7
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Parikh BA, Bern MD, Piersma SJ, Yang L, Beckman DL, Poursine-Laurent J, Plougastel-Douglas B, Yokoyama WM. Control of Viral Infection by Natural Killer Cell Inhibitory Receptors. Cell Rep 2021; 32:107969. [PMID: 32726632 PMCID: PMC7458139 DOI: 10.1016/j.celrep.2020.107969] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/27/2020] [Accepted: 07/08/2020] [Indexed: 12/11/2022] Open
Abstract
Major histocompatibility complex class I (MHC-I)-restricted immune responses are largely attributed to cytotoxic T lymphocytes (CTLs). However, natural killer (NK) cells, as predicted by the missing-self hypothesis, have opposing requirements for MHC-I, suggesting that they may also demonstrate MHC-I-restricted effects. In mice, the Ly49 inhibitory receptors prevent NK cell killing of missing-self targets in effector responses, and they have a proposed second function in licensing or educating NK cells via self-MHC-I in vivo. Here we show MHC-I-restricted control of murine cytomegalovirus (MCMV) infection in vivo that is NK cell dependent. Using mice lacking specific Ly49 receptors, we show that control of MCMV requires inhibitory Ly49 receptors and an inhibitory signaling motif and the capacity for MCMV to downregulate MHC-I. Taken together, these data provide definitive evidence that the inhibitory receptors are required for missing-self rejection and are relevant to MHC-I-restricted NK cell control of a viral infection in vivo. Parikh et al. show that major histocompatibility complex class I (MHC-I)-restricted control of viral infection is due to natural killer (NK) cells rather than cytotoxic T cells. Inhibitory NK cell receptors are essential for protection, requiring NK cell licensing (education) by self-MHC-I and missing-self recognition due to virus-induced MHC-I downregulation.
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Affiliation(s)
- Bijal A Parikh
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Michael D Bern
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Liping Yang
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Diana L Beckman
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jennifer Poursine-Laurent
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Béatrice Plougastel-Douglas
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Wayne M Yokoyama
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
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8
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Ma J, Ayres CM, Hellman LM, Devlin JR, Baker BM. Dynamic allostery controls the peptide sensitivity of the Ly49C natural killer receptor. J Biol Chem 2021; 296:100686. [PMID: 33891944 PMCID: PMC8138769 DOI: 10.1016/j.jbc.2021.100686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 04/14/2021] [Accepted: 04/19/2021] [Indexed: 11/30/2022] Open
Abstract
Using a variety of activating and inhibitory receptors, natural killer (NK) cells protect against disease by eliminating cells that have downregulated class I major histocompatibility complex (MHC) proteins, such as in response to cell transformation or viral infection. The inhibitory murine NK receptor Ly49C specifically recognizes the class I MHC protein H-2Kb. Unusual among NK receptors, Ly49C exhibits a peptide-dependent sensitivity to H-2Kb recognition, which has not been explained despite detailed structural studies. To gain further insight into Ly49C peptide sensitivity, we examined Ly49C recognition biochemically and through the lens of dynamic allostery. We found that the peptide sensitivity of Ly49C arises through small differences in H-2Kb-binding affinity. Although molecular dynamics simulations supported a role for peptide-dependent protein dynamics in producing these differences in binding affinity, calorimetric measurements indicated an enthalpically as opposed to entropically driven process. A quantitative linkage analysis showed that this emerges from peptide-dependent dynamic tuning of electrostatic interactions across the Ly49C–H-2Kb interface. We propose a model whereby different peptides alter the flexibility of H-2Kb, which in turn changes the strength of electrostatic interactions across the protein–protein interface. Our results provide a quantitative assessment of how peptides alter Ly49C-binding affinity, suggest the underlying mechanism, and demonstrate peptide-driven allostery at work in class I MHC proteins. Lastly, our model provides a solution for how dynamic allostery could impact binding of some, but not all, class I MHC partners depending on the structural and chemical composition of the interfaces.
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Affiliation(s)
- Jiaqi Ma
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Cory M Ayres
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Lance M Hellman
- Department of Physical and Life Sciences, Nevada State College, Henderson, Nevada, USA
| | - Jason R Devlin
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA
| | - Brian M Baker
- Department of Chemistry & Biochemistry and the Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana, USA.
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9
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Singh NK, Alonso JA, Harris DT, Anderson SD, Ma J, Hellman LM, Rosenberg AM, Kolawole EM, Evavold BD, Kranz DM, Baker BM. An Engineered T Cell Receptor Variant Realizes the Limits of Functional Binding Modes. Biochemistry 2020; 59:4163-4175. [PMID: 33074657 DOI: 10.1021/acs.biochem.0c00689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
T cell receptors (TCRs) orchestrate cellular immunity by recognizing peptides presented by a range of major histocompatibility complex (MHC) proteins. Naturally occurring TCRs bind the composite peptide/MHC surface, recognizing peptides that are structurally and chemically compatible with the TCR binding site. Here we describe a molecularly evolved TCR variant that binds the human class I MHC protein HLA-A2 independent of the bound peptide, achieved by a drastic perturbation of the TCR binding geometry that places the molecule far from the peptide binding groove. This unique geometry is unsupportive of normal T cell signaling. A substantial divergence between affinity measurements in solution and in two dimensions between proximal cell membranes leads us to attribute the lack of signaling to steric hindrance that limits binding in the confines of a cell-cell interface. Our results provide an example of how receptor binding geometry can impact T cell function and provide further support for the view that germline-encoded residues in TCR binding loops evolved to drive productive TCR recognition and signaling.
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Affiliation(s)
- Nishant K Singh
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jesus A Alonso
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Daniel T Harris
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Scott D Anderson
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Jiaqi Ma
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Aaron M Rosenberg
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elizabeth M Kolawole
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - Brian D Evavold
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, Utah 84112, United States
| | - David M Kranz
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana, Illinois 61801, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, Indiana 46556, United States
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10
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Iborra-Egea O, Rueda F, García-García C, Borràs E, Sabidó E, Bayes-Genis A. Molecular signature of cardiogenic shock. Eur Heart J 2019; 41:3839-3848. [DOI: 10.1093/eurheartj/ehz783] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/16/2019] [Accepted: 10/25/2019] [Indexed: 12/24/2022] Open
Abstract
AbstractThe incidence of cardiogenic shock (CS) has increased remarkably over the past decade and remains a challenging condition with mortality rates of ∼50%. Cardiogenic shock encompasses cardiac contractile dysfunction; however, it is also a multiorgan dysfunction syndrome, often complicated by a systemic inflammatory response with severe cellular and metabolic dysregulations. Here, we review the evidence on the biochemical manifestations of CS, elaborating on current gold standard biomarkers and novel candidates from molecular signatures of CS. Glucose and lactate, both identified over a century ago, remain the only clinically used biomarkers in current predictive risk scores. Novel genomic, transcriptomic, and proteomic data are discussed, and a recently reported molecular score derived from unbiased proteomic discovery, the CS4P, which includes liver fatty acid-binding protein, beta-2-microglobulin, fructose-bisphosphate aldolase B, and SerpinG1 is comprehensively described. Recent advances in -omics technologies provide new insight into a more holistic molecular signature of CS. Thus, we need to open new diagnostic and therapeutic avenues if we aim to improve outcomes.
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Affiliation(s)
- Oriol Iborra-Egea
- Department of Cardiology, Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n 08916, Barcelona, Spain
- Department of Medicine, CIBERCV, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ferran Rueda
- Department of Cardiology, Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n 08916, Barcelona, Spain
- Department of Medicine, CIBERCV, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Cosme García-García
- Department of Cardiology, Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n 08916, Barcelona, Spain
- Department of Medicine, CIBERCV, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eva Borràs
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Eduard Sabidó
- Proteomics Unit, Centre de Regulació Genòmica (CRG), Barcelona Institute of Science and Technology (BIST), Dr Aiguader 88, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Antoni Bayes-Genis
- Department of Cardiology, Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n 08916, Barcelona, Spain
- Department of Medicine, CIBERCV, Universitat Autònoma de Barcelona, Barcelona, Spain
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11
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Ayres CM, Abualrous ET, Bailey A, Abraham C, Hellman LM, Corcelli SA, Noé F, Elliott T, Baker BM. Dynamically Driven Allostery in MHC Proteins: Peptide-Dependent Tuning of Class I MHC Global Flexibility. Front Immunol 2019; 10:966. [PMID: 31130956 PMCID: PMC6509175 DOI: 10.3389/fimmu.2019.00966] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/15/2019] [Indexed: 11/21/2022] Open
Abstract
T cell receptor (TCR) recognition of antigenic peptides bound and presented by class I major histocompatibility complex (MHC) proteins underlies the cytotoxic immune response to diseased cells. Crystallographic structures of TCR-peptide/MHC complexes have demonstrated how TCRs simultaneously interact with both the peptide and the MHC protein. However, it is increasingly recognized that, beyond serving as a static platform for peptide presentation, the physical properties of class I MHC proteins are tuned by different peptides in ways that are not always structurally visible. These include MHC protein motions, or dynamics, which are believed to influence interactions with a variety of MHC-binding proteins, including not only TCRs, but other activating and inhibitory receptors as well as components of the peptide loading machinery. Here, we investigated the mechanisms by which peptides tune the dynamics of the common class I MHC protein HLA-A2. By examining more than 50 lengthy molecular dynamics simulations of HLA-A2 presenting different peptides, we identified regions susceptible to dynamic tuning, including regions in the peptide binding domain as well as the distal α3 domain. Further analyses of the simulations illuminated mechanisms by which the influences of different peptides are communicated throughout the protein, and involve regions of the peptide binding groove, the β2-microglobulin subunit, and the α3 domain. Overall, our results demonstrate that the class I MHC protein is a highly tunable peptide sensor whose physical properties vary considerably with bound peptide. Our data provides insight into the underlying principles and suggest a role for dynamically driven allostery in the immunological function of MHC proteins.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Esam T Abualrous
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Alistair Bailey
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Christian Abraham
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Lance M Hellman
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Frank Noé
- Computational Molecular Biology Group, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Tim Elliott
- Institute for Life Sciences and Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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12
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Balaji GR, Aguilar OA, Tanaka M, Shingu-Vazquez MA, Fu Z, Gully BS, Lanier LL, Carlyle JR, Rossjohn J, Berry R. Recognition of host Clr-b by the inhibitory NKR-P1B receptor provides a basis for missing-self recognition. Nat Commun 2018; 9:4623. [PMID: 30397201 PMCID: PMC6218473 DOI: 10.1038/s41467-018-06989-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 10/09/2018] [Indexed: 01/16/2023] Open
Abstract
The interaction between natural killer (NK) cell inhibitory receptors and their cognate ligands constitutes a key mechanism by which healthy tissues are protected from NK cell-mediated lysis. However, self-ligand recognition remains poorly understood within the prototypical NKR-P1 receptor family. Here we report the structure of the inhibitory NKR-P1B receptor bound to its cognate host ligand, Clr-b. NKR-P1B and Clr-b interact via a head-to-head docking mode through an interface that includes a large array of polar interactions. NKR-P1B:Clr-b recognition is extremely sensitive to mutations at the heterodimeric interface, with most mutations severely impacting both Clr-b binding and NKR-P1B receptor function to implicate a low affinity interaction. Within the structure, two NKR-P1B:Clr-b complexes are cross-linked by a non-classic NKR-P1B homodimer, and the disruption of homodimer formation abrogates Clr-b recognition. These data provide an insight into a fundamental missing-self recognition system and suggest an avidity-based mechanism underpins NKR-P1B receptor function.
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MESH Headings
- Animals
- Carrier Proteins
- Crystallography, X-Ray
- HEK293 Cells
- Humans
- Lectins, C-Type/chemistry
- Lectins, C-Type/genetics
- Mice
- Mice, Inbred C57BL
- Models, Molecular
- Mutagenesis, Site-Directed
- Mutation
- NK Cell Lectin-Like Receptor Subfamily B/chemistry
- NK Cell Lectin-Like Receptor Subfamily B/genetics
- Protein Conformation
- Protein Conformation, alpha-Helical
- Protein Domains
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Natural Killer Cell/chemistry
- Receptors, Natural Killer Cell/genetics
- X-Ray Diffraction
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Affiliation(s)
- Gautham R Balaji
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
| | - Oscar A Aguilar
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, 94143, USA
| | - Miho Tanaka
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada
| | - Miguel A Shingu-Vazquez
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
| | - Zhihui Fu
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
| | - Benjamin S Gully
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia
| | - Lewis L Lanier
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, University of California, San Francisco, CA, 94143, USA
| | - James R Carlyle
- Department of Immunology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
- Sunnybrook Research Institute, Toronto, ON, M4N 3M5, Canada.
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia.
- Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, CF14 4XN, UK.
| | - Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
- ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, 3800, Australia.
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13
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Kajikawa M, Ose T, Fukunaga Y, Okabe Y, Matsumoto N, Yonezawa K, Shimizu N, Kollnberger S, Kasahara M, Maenaka K. Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility. Nat Commun 2018; 9:4330. [PMID: 30337538 PMCID: PMC6193965 DOI: 10.1038/s41467-018-06797-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 09/27/2018] [Indexed: 12/23/2022] Open
Abstract
The MILL family, composed of MILL1 and MILL2, is a group of nonclassical MHC class I molecules that occur in some orders of mammals. It has been reported that mouse MILL2 is involved in wound healing; however, the molecular mechanisms remain unknown. Here, we determine the crystal structure of MILL2 at 2.15 Å resolution, revealing an organization similar to classical MHC class I. However, the α1-α2 domains are not tightly fixed on the α3-β2m domains, indicating unusual interdomain flexibility. The groove between the two helices in the α1-α2 domains is too narrow to permit ligand binding. Notably, an unusual basic patch on the α3 domain is involved in the binding to heparan sulfate which is essential for MILL2 interactions with fibroblasts. These findings suggest that MILL2 has a unique structural architecture and physiological role, with binding to heparan sulfate proteoglycans on fibroblasts possibly regulating cellular recruitment in biological events. The MILL (MHC-I-like located near the leukocyte receptor complex) family is a group of related nonclassical MHC-I molecules. Here the authors present the crystal structure of MILL2, which reveals an unusual interdomain flexibility, and show that MILL2 binds heparan sulfate on the surface of fibroblasts through a basic patch.
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Affiliation(s)
- Mizuho Kajikawa
- Laboratory of Microbiology, Showa Pharmaceutical University, Machida, Tokyo, 190-8543, Japan.,Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Toyoyuki Ose
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Yuko Fukunaga
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yuki Okabe
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kento Yonezawa
- Photon Factory, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan
| | - Nobutaka Shimizu
- Photon Factory, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, 305-0801, Japan
| | - Simon Kollnberger
- Cardiff Institute of Infection & Immunity, University of Cardiff, Henry Wellcome Building, Heath Park, Cardiff, CF14 4XN, UK
| | - Masanori Kasahara
- Department of Pathology, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, 060-8638, Japan
| | - Katsumi Maenaka
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. .,Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan.
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14
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Paul S, Lal G. The Molecular Mechanism of Natural Killer Cells Function and Its Importance in Cancer Immunotherapy. Front Immunol 2017; 8:1124. [PMID: 28955340 PMCID: PMC5601256 DOI: 10.3389/fimmu.2017.01124] [Citation(s) in RCA: 431] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/28/2017] [Indexed: 12/31/2022] Open
Abstract
Natural killer (NK) cells are innate immune cells that show strong cytolytic function against physiologically stressed cells such as tumor cells and virus-infected cells. NK cells show a broad array of tissue distribution and phenotypic variability. NK cells express several activating and inhibitory receptors that recognize the altered expression of proteins on target cells and control the cytolytic function. NK cells have been used in several clinical trials to control tumor growth. However, the results are encouraging only in hematological malignancies but not very promising in solid tumors. Increasing evidence suggests that tumor microenvironment regulate the phenotype and function of NK cells. In this review, we discussed the NK cell phenotypes and its effector function and impact of the tumor microenvironment on effector and cytolytic function of NK cells. We also summarized various NK cell-based immunotherapeutic strategies used in the past and the possibilities to improve the function of NK cell for the better clinical outcome.
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Affiliation(s)
- Sourav Paul
- National Centre for Cell Science, Pune, India
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15
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Ayres CM, Corcelli SA, Baker BM. Peptide and Peptide-Dependent Motions in MHC Proteins: Immunological Implications and Biophysical Underpinnings. Front Immunol 2017; 8:935. [PMID: 28824655 PMCID: PMC5545744 DOI: 10.3389/fimmu.2017.00935] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/21/2017] [Indexed: 01/28/2023] Open
Abstract
Structural biology of peptides presented by class I and class II MHC proteins has transformed immunology, impacting our understanding of fundamental immune mechanisms and allowing researchers to rationalize immunogenicity and design novel vaccines. However, proteins are not static structures as often inferred from crystallographic structures. Their components move and breathe individually and collectively over a range of timescales. Peptides bound within MHC peptide-binding grooves are no exception and their motions have been shown to impact recognition by T cell and other receptors in ways that influence function. Furthermore, peptides tune the motions of MHC proteins themselves, which impacts recognition of peptide/MHC complexes by other proteins. Here, we review the motional properties of peptides in MHC binding grooves and discuss how peptide properties can influence MHC motions. We briefly review theoretical concepts about protein motion and highlight key data that illustrate immunological consequences. We focus primarily on class I systems due to greater availability of data, but segue into class II systems as the concepts and consequences overlap. We suggest that characterization of the dynamic “energy landscapes” of peptide/MHC complexes and the resulting functional consequences is one of the next frontiers in structural immunology.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, United States.,Harper Cancer Research Institute, University of Notre Dame, South Bend, IN, United States
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16
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Deuss FA, Gully BS, Rossjohn J, Berry R. Recognition of nectin-2 by the natural killer cell receptor T cell immunoglobulin and ITIM domain (TIGIT). J Biol Chem 2017; 292:11413-11422. [PMID: 28515320 DOI: 10.1074/jbc.m117.786483] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/12/2017] [Indexed: 02/06/2023] Open
Abstract
T cell immunoglobulin and ITIM domain (TIGIT) is an inhibitory receptor expressed on the surface of natural killer (NK) cells. TIGIT recognizes nectin and nectin-like adhesion molecules and thus plays a critical role in the innate immune response to malignant transformation. Although the TIGIT nectin-like protein-5 (necl-5) interaction is well understood, how TIGIT engages nectin-2, a receptor that is broadly over-expressed in breast and ovarian cancer, remains unknown. Here, we show that TIGIT bound to the immunoglobulin domain of nectin-2 that is most distal from the membrane with an affinity of 6 μm, which was moderately lower than the affinity observed for the TIGIT/necl-5 interaction (3.2 μm). The TIGIT/nectin-2 binding disrupted pre-assembled nectin-2 oligomers, suggesting that receptor-ligand and ligand-ligand associations are mutually exclusive events. Indeed, the crystal structure of TIGIT bound to the first immunoglobulin domain of nectin-2 indicated that the receptor and ligand dock using the same molecular surface and a conserved "lock and key" binding motifs previously observed to mediate nectin/nectin homotypic interactions as well as TIGIT/necl-5 recognition. Using a mutagenesis approach, we dissected the energetic basis for the TIGIT/nectin-2 interaction and revealed that an "aromatic key" of nectin-2 is critical for this interaction, whereas variations in the lock were tolerated. Moreover, we found that the C-C' loop of the ligand dictates the TIGIT binding hierarchy. Altogether, these findings broaden our understanding of nectin/nectin receptor interactions and have implications for better understanding the molecular basis for autoimmune disease and cancer.
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Affiliation(s)
- Felix A Deuss
- From the Infection and Immunity Program, Biomedicine Discovery Institute and.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, and
| | - Benjamin S Gully
- From the Infection and Immunity Program, Biomedicine Discovery Institute and.,the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, and
| | - Jamie Rossjohn
- From the Infection and Immunity Program, Biomedicine Discovery Institute and .,the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, and.,the Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, United Kingdom
| | - Richard Berry
- From the Infection and Immunity Program, Biomedicine Discovery Institute and .,the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,the Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, and
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17
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Abstract
Triggering of cell-mediated immunity is largely dependent on the recognition of foreign or abnormal molecules by a myriad of cell surface-bound receptors. Many activating immune receptors do not possess any intrinsic signaling capacity but instead form noncovalent complexes with one or more dimeric signaling modules that communicate with a common set of kinases to initiate intracellular information-transfer pathways. This modular architecture, where the ligand binding and signaling functions are detached from one another, is a common theme that is widely employed throughout the innate and adaptive arms of immune systems. The evolutionary advantages of this highly adaptable platform for molecular recognition are visible in the variety of ligand-receptor interactions that can be linked to common signaling pathways, the diversification of receptor modules in response to pathogen challenges, and the amplification of cellular responses through incorporation of multiple signaling motifs. Here we provide an overview of the major classes of modular activating immune receptors and outline the current state of knowledge regarding how these receptors assemble, recognize their ligands, and ultimately trigger intracellular signal transduction pathways that activate immune cell effector functions.
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Affiliation(s)
- Richard Berry
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University , Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University , Clayton, Victoria 3800, Australia
| | - Matthew E Call
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3052, Australia
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18
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Kinetic and thermodynamic studies of the interaction between activating and inhibitory Ly49 natural killer receptors and MHC class I molecules. Biochem J 2017; 474:179-194. [PMID: 27831490 DOI: 10.1042/bcj20160876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/01/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022]
Abstract
Natural killer (NK) cells are lymphocytes of the innate immune system that eliminate virally infected or malignantly transformed cells. NK cell function is regulated by diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 receptors control NK cell cytotoxicity by sensing major histocompatibility complex class I molecules (MHC-I) on target cells. Although crystal structures have been reported for Ly49/MHC-I complexes, the underlying binding mechanism has not been elucidated. Accordingly, we carried out thermodynamic and kinetic experiments on the interaction of four NK Ly49 receptors (Ly49G, Ly49H, Ly49I and Ly49P) with two MHC-I ligands (H-2Dd and H-2Dk). These Ly49s embrace the structural and functional diversity of the highly polymorphic Ly49 family. Combining surface plasmon resonance, fluorescence anisotropy and far-UV circular dichroism (CD), we determined that the best model to describe both inhibitory and activating Ly49/MHC-I interactions is one in which the two MHC-I binding sites of the Ly49 homodimer present similar binding constants for the two sites (∼106 M-1) with a slightly positive co-operativity in some cases, and without far-UV CD observable conformational changes. Furthermore, Ly49/MHC-I interactions are diffusion-controlled and enthalpy-driven. These features stand in marked contrast with the activation-controlled and entropy-driven interaction of Ly49s with the viral immunoevasin m157, which is characterized by strong positive co-operativity and conformational selection. These differences are explained by the distinct structures of Ly49/MHC-I and Ly49/m157 complexes. Moreover, they reflect the opposing roles of NK cells to rapidly scan for virally infected cells and of viruses to escape detection using immunoevasins such as m157.
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19
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Sullivan LC, Berry R, Sosnin N, Widjaja JML, Deuss FA, Balaji GR, LaGruta NL, Mirams M, Trapani JA, Rossjohn J, Brooks AG, Andrews DM. Recognition of the Major Histocompatibility Complex (MHC) Class Ib Molecule H2-Q10 by the Natural Killer Cell Receptor Ly49C. J Biol Chem 2016; 291:18740-52. [PMID: 27385590 DOI: 10.1074/jbc.m116.737130] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Indexed: 01/15/2023] Open
Abstract
Murine natural killer (NK) cells are regulated by the interaction of Ly49 receptors with major histocompatibility complex class I molecules (MHC-I). Although the ligands for inhibitory Ly49 were considered to be restricted to classical MHC (MHC-Ia), we have shown that the non-classical MHC molecule (MHC-Ib) H2-M3 was a ligand for the inhibitory Ly49A. Here we establish that another MHC-Ib, H2-Q10, is a bona fide ligand for the inhibitory Ly49C receptor. H2-Q10 bound to Ly49C with a marginally lower affinity (∼5 μm) than that observed between Ly49C and MHC-Ia (H-2K(b)/H-2D(d), both ∼1 μm), and this recognition could be prevented by cis interactions with H-2K in situ To understand the molecular details underpinning Ly49·MHC-Ib recognition, we determined the crystal structures of H2-Q10 and Ly49C bound H2-Q10. Unliganded H2-Q10 adopted a classical MHC-I fold and possessed a peptide-binding groove that exhibited features similar to those found in MHC-Ia, explaining the diverse peptide binding repertoire of H2-Q10. Ly49C bound to H2-Q10 underneath the peptide binding platform to a region that encompassed residues from the α1, α2, and α3 domains, as well as the associated β2-microglobulin subunit. This docking mode was conserved with that previously observed for Ly49C·H-2K(b) Indeed, structure-guided mutation of Ly49C indicated that Ly49C·H2-Q10 and Ly49C·H-2K(b) possess similar energetic footprints focused around residues located within the Ly49C β4-stand and L5 loop, which contact the underside of the peptide-binding platform floor. Our data provide a structural basis for Ly49·MHC-Ib recognition and demonstrate that MHC-Ib represent an extended family of ligands for Ly49 molecules.
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Affiliation(s)
- Lucy C Sullivan
- From the Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Richard Berry
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Natasha Sosnin
- the Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia, The Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Parkville, Australia
| | - Jacqueline M L Widjaja
- From the Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Felix A Deuss
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Gautham R Balaji
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Nicole L LaGruta
- From the Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia, the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Michiko Mirams
- From the Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph A Trapani
- the Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3000, Australia, The Sir Peter MacCallum Department of Oncology, University of Melbourne, Victoria 3010, Parkville, Australia
| | - Jamie Rossjohn
- the Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia, the ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia, the Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff CF14 4XN, Wales, United Kingdom, and
| | - Andrew G Brooks
- From the Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria 3010, Australia,
| | - Daniel M Andrews
- the Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
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20
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Mahmoud AB, Tu MM, Wight A, Zein HS, Rahim MMA, Lee SH, Sekhon HS, Brown EG, Makrigiannis AP. Influenza Virus Targets Class I MHC-Educated NK Cells for Immunoevasion. PLoS Pathog 2016; 12:e1005446. [PMID: 26928844 PMCID: PMC4771720 DOI: 10.1371/journal.ppat.1005446] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/19/2016] [Indexed: 12/13/2022] Open
Abstract
The immune response to influenza virus infection comprises both innate and adaptive defenses. NK cells play an early role in the destruction of tumors and virally-infected cells. NK cells express a variety of inhibitory receptors, including those of the Ly49 family, which are functional homologs of human killer-cell immunoglobulin-like receptors (KIR). Like human KIR, Ly49 receptors inhibit NK cell-mediated lysis by binding to major histocompatibility complex class I (MHC-I) molecules that are expressed on normal cells. During NK cell maturation, the interaction of NK cell inhibitory Ly49 receptors with their MHC-I ligands results in two types of NK cells: licensed (“functional”), or unlicensed (“hypofunctional”). Despite being completely dysfunctional with regard to rejecting MHC-I-deficient cells, unlicensed NK cells represent up to half of the mature NK cell pool in rodents and humans, suggesting an alternative role for these cells in host defense. Here, we demonstrate that after influenza infection, MHC-I expression on lung epithelial cells is upregulated, and mice bearing unlicensed NK cells (Ly49-deficient NKCKD and MHC-I-deficient B2m-/- mice) survive the infection better than WT mice. Importantly, transgenic expression of an inhibitory self-MHC-I-specific Ly49 receptor in NKCKD mice restores WT influenza susceptibility, confirming a direct role for Ly49. Conversely, F(ab’)2-mediated blockade of self-MHC-I-specific Ly49 inhibitory receptors protects WT mice from influenza virus infection. Mechanistically, perforin-deficient NKCKD mice succumb to influenza infection rapidly, indicating that direct cytotoxicity is necessary for unlicensed NK cell-mediated protection. Our findings demonstrate that Ly49:MHC-I interactions play a critical role in influenza virus pathogenesis. We suggest a similar role may be conserved in human KIR, and their blockade may be protective in humans. Influenza virus has developed a number of immune-evasion mechanisms to prolong its survival within the host. Development of functional NK cells is dependent on multiple factors such as the interaction between MHC-I and Ly49 receptors. NK cells that develop in the absence of these interactions are referred to as ‘unlicensed’ and represent up to half of the total number of NK cells. We show that significant MHC-I upregulation on lung epithelial cells following influenza virus infection most likely allows influenza virus to evade detection by licensed NK cells. Importantly, we demonstrate that unlicensed NK cells play a major role in protecting mice from influenza infection. Both Ly49- and MHC-I-deficient mice, which possess unlicensed NK cells, exhibit better survival than WT mice when infected with a lethal dose of influenza virus. Survival of Ly49-deficient mice is associated with reduced viral titers and lung pathology, compared to the infected WT mice. Moreover, disrupting the interaction between MHC-I and inhibitory Ly49 receptors protects WT mice from a lethal influenza virus infection. These results suggest that the so-called unlicensed NK cells, previously characterized as being hyporesponsive, actually possess potent antiviral activity, and are crucial for protection from influenza virus and possibly other viral infections.
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MESH Headings
- Animals
- Antigens, Ly/genetics
- Antigens, Ly/metabolism
- Cell Line, Tumor
- Cells, Cultured
- Coculture Techniques
- Crosses, Genetic
- Immune Evasion
- Immunity, Innate
- Influenza A virus/immunology
- Influenza A virus/physiology
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Killer Cells, Natural/pathology
- Killer Cells, Natural/virology
- Lung/immunology
- Lung/metabolism
- Lung/pathology
- Lung/virology
- Mice, Knockout
- Mice, Transgenic
- NK Cell Lectin-Like Receptor Subfamily A/agonists
- NK Cell Lectin-Like Receptor Subfamily A/antagonists & inhibitors
- NK Cell Lectin-Like Receptor Subfamily A/genetics
- NK Cell Lectin-Like Receptor Subfamily A/metabolism
- Orthomyxoviridae Infections/immunology
- Orthomyxoviridae Infections/metabolism
- Orthomyxoviridae Infections/pathology
- Orthomyxoviridae Infections/virology
- Pore Forming Cytotoxic Proteins/genetics
- Pore Forming Cytotoxic Proteins/metabolism
- Receptors, KIR/agonists
- Receptors, KIR/antagonists & inhibitors
- Receptors, KIR/genetics
- Receptors, KIR/metabolism
- Respiratory Mucosa/immunology
- Respiratory Mucosa/metabolism
- Respiratory Mucosa/pathology
- Respiratory Mucosa/virology
- Specific Pathogen-Free Organisms
- Survival Analysis
- beta 2-Microglobulin/genetics
- beta 2-Microglobulin/metabolism
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Affiliation(s)
- Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Madinah Munawwarah, Kingdom of Saudi Arabia
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Megan M. Tu
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrew Wight
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Haggag S. Zein
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- Cairo University Research Park, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mir Munir A. Rahim
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Seung-Hwan Lee
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Harman S. Sekhon
- Department of Pathology and Laboratory Medicine, The Ottawa Hospital, University of Ottawa, Ottawa, Ontario, Canada
| | - Earl G. Brown
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Andrew P. Makrigiannis
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail:
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HERNYCHOVÁ L, MRÁZEK H, IVANOVA L, KUKAČKA Z, CHMELÍK J, NOVÁK P. Recombinant Expression, In Vitro Refolding and Characterizing Disulfide Bonds of a Mouse Inhibitory C-Type Lectin-Like Receptor Nkrp1b. Physiol Res 2015; 64:S85-93. [DOI: 10.33549/physiolres.933136] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
As a part of the innate immunity, NK (Natural Killer) cells provide an early immune response to different stimuli, e.g. viral infections and tumor growths. However, their functions are more complex; they play an important role in reproduction, alloimmunity, autoimmunity and allergic diseases. NK cell activities require an intricate system of regulation that is ensured by many different receptors on a cell surface which integrate signals from interacting cells and soluble factors. One way to understand NK cell biology is through the structure of NK receptors, which can reveal ligand binding conditions. We present a modified protocol for recombinant expression in Escherichia coli and in vitro refolding of the ligand-binding domain of the inhibitory Nkrp1b (SJL/J) protein. Nkrp1b identity and folding was confirmed using mass spectrometry (accurate mass of the intact protein and evaluation of disulfide bonds) and one-dimensional nuclear magnetic resonance spectroscopy. The intention is to provide the basis for conducting structural studies of the inhibitory Nkrp1b protein, since only the activating Nkrp1a receptor structure is known.
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Affiliation(s)
- L. HERNYCHOVÁ
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | | | | | | | | | - P. NOVÁK
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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22
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Marquez EA, Kane KP. Identities of P2 and P3 Residues of H-2Kb-Bound Peptides Determine Mouse Ly49C Recognition. PLoS One 2015; 10:e0131308. [PMID: 26147851 PMCID: PMC4493100 DOI: 10.1371/journal.pone.0131308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/31/2015] [Indexed: 11/18/2022] Open
Abstract
Ly49 receptors can be peptide selective in their recognition of MHC-I-peptide complexes, affording them a level of discrimination beyond detecting the presence or absence of specific MHC-I allele products. Despite this ability, little is understood regarding the properties that enable some peptides, when bound to MHC-I molecules, to support Ly49 recognition, but not others. Using RMA-S target cells expressing MHC-I molecules loaded with individual peptides and effector cells expressing the ectodomain of the inhibitory Ly49C receptor, we found that two adjacent amino acid residues, P2 and P3, both buried in the peptide binding groove of H-2Kb, determine mouse Ly49C specificity. If both are aliphatic residues, this is supportive. Whereas, small amino acids at P2 and aromatic amino acids at the P3 auxiliary anchor residue are detrimental to Ly49C recognition. These results resemble those with a rat Ly49 where the identity of a peptide anchor residue determines recognition, suggesting that dependence on specific peptide residues buried in the MHC-I peptide-binding groove may be fundamental to Ly49 peptide selectivity and recognition.
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Affiliation(s)
- Elsa A. Marquez
- Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin P. Kane
- Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
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23
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Forbes CA, Coudert JD. Mechanisms regulating NK cell activation during viral infection. Future Virol 2015. [DOI: 10.2217/fvl.14.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT NK cells constitute a population of lymphocytes involved in innate immune functions. They play a critical role in antiviral immune surveillance. Viruses have evolved with their host species for millions of years, each exerting a selective pressure upon the other. As a corollary, the pathways used by the immune system that are critical to control viral infection can be revealed by defining the role of viral gene products that are nonessential for virus replication. We relate here the battery of resources available to NK cells to recognize and eliminate viruses and reciprocally the immune evasion mechanisms developed by viruses to prevent NK cell activation.
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Affiliation(s)
- Catherine A Forbes
- Centre for Experimental Immunology, Lions Eye Institute, 2 Verdun St, Nedlands, WA 6009, Australia
| | - Jerome D Coudert
- Centre for Experimental Immunology, Lions Eye Institute, 2 Verdun St, Nedlands, WA 6009, Australia
- Centre for Ophthalmology & Vision Science, M517, University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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24
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Kirkham CL, Carlyle JR. Complexity and Diversity of the NKR-P1:Clr (Klrb1:Clec2) Recognition Systems. Front Immunol 2014; 5:214. [PMID: 24917862 PMCID: PMC4041007 DOI: 10.3389/fimmu.2014.00214] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022] Open
Abstract
The NKR-P1 receptors were identified as prototypical natural killer (NK) cell surface antigens and later shown to be conserved from rodents to humans on NK cells and subsets of T cells. C-type lectin-like in nature, they were originally shown to be capable of activating NK cell function and to recognize ligands on tumor cells. However, certain family members have subsequently been shown to be capable of inhibiting NK cell activity, and to recognize proteins encoded by a family of genetically linked C-type lectin-related ligands. Some of these ligands are expressed by normal, healthy cells, and modulated during transformation, infection, and cellular stress, while other ligands are upregulated during the immune response and during pathological circumstances. Here, we discuss historical and recent developments in NKR-P1 biology that demonstrate this NK receptor–ligand system to be far more complex and diverse than originally anticipated.
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Affiliation(s)
- Christina L Kirkham
- Department of Immunology, University of Toronto, Sunnybrook Research Institute , Toronto, ON , Canada
| | - James R Carlyle
- Department of Immunology, University of Toronto, Sunnybrook Research Institute , Toronto, ON , Canada
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25
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The activating Ly49W and inhibitory Ly49G NK cell receptors display similar affinities for identical MHC class I ligands. Immunogenetics 2014; 66:467-77. [DOI: 10.1007/s00251-014-0777-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 04/23/2014] [Indexed: 01/26/2023]
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26
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Li Y, Mariuzza RA. Structural basis for recognition of cellular and viral ligands by NK cell receptors. Front Immunol 2014; 5:123. [PMID: 24723923 PMCID: PMC3972465 DOI: 10.3389/fimmu.2014.00123] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/10/2014] [Indexed: 11/13/2022] Open
Abstract
Natural killer (NK) cells are key components of innate immune responses to tumors and viral infections. NK cell function is regulated by NK cell receptors that recognize both cellular and viral ligands, including major histocompatibility complex (MHC), MHC-like, and non-MHC molecules. These receptors include Ly49s, killer immunoglobulin-like receptors, leukocyte immunoglobulin-like receptors, and NKG2A/CD94, which bind MHC class I (MHC-I) molecules, and NKG2D, which binds MHC-I paralogs such as the stress-induced proteins MICA and ULBP. In addition, certain viruses have evolved MHC-like immunoevasins, such as UL18 and m157 from cytomegalovirus, that act as decoy ligands for NK receptors. A growing number of NK receptor–ligand interaction pairs involving non-MHC molecules have also been identified, including NKp30–B7-H6, killer cell lectin-like receptor G1–cadherin, and NKp80–AICL. Here, we describe crystal structures determined to date of NK cell receptors bound to MHC, MHC-related, and non-MHC ligands. Collectively, these structures reveal the diverse solutions that NK receptors have developed to recognize these molecules, thereby enabling the regulation of NK cytolytic activity by both host and viral ligands.
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Affiliation(s)
- Yili Li
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD , USA ; Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD , USA
| | - Roy A Mariuzza
- W. M. Keck Laboratory for Structural Biology, Institute for Bioscience and Biotechnology Research, University of Maryland , Rockville, MD , USA ; Department of Cell Biology and Molecular Genetics, University of Maryland , College Park, MD , USA
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27
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Berry R, Rossjohn J, Brooks AG. The Ly49 natural killer cell receptors: a versatile tool for viral self‐discrimination. Immunol Cell Biol 2014; 92:214-20. [DOI: 10.1038/icb.2013.100] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 11/10/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Richard Berry
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash UniversityClaytonVictoriaAustralia
| | - Jamie Rossjohn
- Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash UniversityClaytonVictoriaAustralia
- Institute of Infection and Immunity, School of Medicine, Cardiff UniversityCardiffUK
| | - Andrew G Brooks
- Department of Microbiology and Immunology, University of MelbourneParkvilleVictoriaAustralia
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28
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Mickiewicz KM, Gays F, Lewis RJ, Brooks CG. Mutagenesis of Ly49B reveals key structural elements required for promiscuous binding to MHC class I molecules and new insights into the molecular evolution of Ly49s. THE JOURNAL OF IMMUNOLOGY 2014; 192:1558-69. [PMID: 24403531 DOI: 10.4049/jimmunol.1301643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ly49B is a potentially important immunoregulator expressed on mouse myeloid cells, and it is thus an unusual member of the wider Ly49 family whose members are ordinarily found on NK cells. Ly49B displays substantial sequence divergence from other Ly49s and in particular shares virtually no amino acid sequence identity with the residues that have been reported to bind to MHC class I (cI) ligands in other Ly49s. Despite this, we show in this study that the BALB/c, but not the C57, isoform of Ly49B displays promiscuous cI binding. Binding was not significantly affected by inactivation of any of the four predicted N-linked glycosylation sites of Ly49B, nor was it affected by removal of the unique 20-aa C-terminal extension found in Ly49B. However, transfer of these C-terminal 20 aa to Ly49A inhibited cI binding, as did the addition of a hemagglutinin tag to the C terminus of Ly49B, demonstrating unexpectedly that the C-terminal region of Ly49s can play a significant role in ligand binding. Systematic exchange of BALB/c and C57 residues revealed that Trp(166), Asn(167), and Cys(251) are of major importance for cI binding in Ly49B. These residues are highly conserved in the Ly49 family. Remarkably, however, Ly49B(BALB) variants that have C57 residues at positions 166 or 167, and are unable to bind cI multimers, regain substantial cI binding when amino acid changes are made at distal positions, providing an explanation of how highly divergent Ly49s that retain the ability to bind cI molecules might have evolved.
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Affiliation(s)
- Katarzyna M Mickiewicz
- Institute of Cell and Molecular Biosciences, University of Newcastle, Newcastle NE2 4HH, United Kingdom
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29
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Romasanta PN, Curto LM, Urtasun N, Sarratea MB, Chiappini S, Miranda MV, Delfino JM, Mariuzza RA, Fernández MM, Malchiodi EL. A positive cooperativity binding model between Ly49 natural killer cell receptors and the viral immunoevasin m157: kinetic and thermodynamic studies. J Biol Chem 2013; 289:5083-96. [PMID: 24379405 DOI: 10.1074/jbc.m113.532929] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Natural killer (NK) cells discriminate between healthy and virally infected or transformed cells using diverse surface receptors that are both activating and inhibitory. Among them, the homodimeric Ly49 NK receptors, which can adopt two distinct conformations (backfolded and extended), are of particular importance for detecting cells infected with mouse cytomegalovirus (CMV) via recognition of the viral immunoevasin m157. The interaction of m157 with activating (Ly49H) and inhibitory (Ly49I) receptors governs the spread of mouse CMV. We carried out kinetic and thermodynamic experiments to elucidate the Ly49/m157 binding mechanism. Combining surface plasmon resonance, fluorescence anisotropy, and circular dichroism (CD), we determined that the best model to describe both the Ly49H/m157 and Ly49I/m157 interactions is a conformational selection mechanism where only the extended conformation of Ly49 (Ly49*) is able to bind the first m157 ligand followed by binding of the Ly49*/m157 complex to the second m157. The interaction is characterized by strong positive cooperativity such that the second m157 binds the Ly49 homodimer with a 1000-fold higher sequential constant than the first m157 (∼10(8) versus ∼10(5) M(-1)). Using far-UV CD, we obtained evidence for a conformational change in Ly49 upon binding m157 that could explain the positive cooperativity. The rate-limiting step of the overall mechanism is a conformational transition in Ly49 from its backfolded to extended form. The global thermodynamic parameters from the initial state (backfolded Ly49 and m157) to the final state (Ly49*/(m157)2) are characterized by an unfavorable enthalpy that is compensated by a favorable entropy, making the interaction spontaneous.
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Affiliation(s)
- Pablo N Romasanta
- From the Cátedra de Inmunología and Instituto de Estudios de la Inmunidad Humoral (IDEHU), Consejo Nacional de Investigaciones Científicas y técnicas - Universidad de Buenos Aires (CONICET-UBA) and
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30
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Bartel Y, Bauer B, Steinle A. Modulation of NK cell function by genetically coupled C-type lectin-like receptor/ligand pairs encoded in the human natural killer gene complex. Front Immunol 2013; 4:362. [PMID: 24223577 PMCID: PMC3819593 DOI: 10.3389/fimmu.2013.00362] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 10/24/2013] [Indexed: 12/28/2022] Open
Abstract
Functional responses of natural killer (NK) cells including eradication of “harmful” cells and modulation of immune responses are regulated by a broad variety of activating and inhibitory NK receptors. Whereas the leukocyte receptor complex (LRC) encodes for NK receptors of the immunoglobulin superfamily, genes of C-type lectin-like NK receptors are clustered in the mammalian natural killer gene complex (NKC). Besides the thoroughly studied C-type lectin-like receptors NKG2D, CD94/NKG2x, and members of the murine Ly49 subfamily, the NKC also encodes for NK receptors of the less characterized NKRP1 subfamily. The prototypic mouse NKRP1 receptor is Nkrp1c (also known as NK1.1), while human members of the NKRP1 subfamily are NKRP1A, NKp80, and NKp65. The latter are not straight homologs of mouse NKRP1 receptors, but share distinct subfamily-specific traits classifying them as members of the NKRP1 subfamily. Ligands of the human NKPR1 receptors are likewise C-type lectin-like glycoproteins belonging to the CLEC2 subfamily (i.e., LLT1, AICL, and KACL), and are encoded in the NKC in tight genetic linkage to their respective receptors. Similarly, certain members of the mouse NKRP1 subfamily interact with genetically coupled CLEC2 glycoproteins, while the reasons for this intriguing tight genetic linkage remain unknown. Recent studies provided new and unique insights into the expression, interaction, and signaling of NKRP1 receptors and their ligands, thereby substantially advancing our understanding of their function and biology. Here, we review our current knowledge on NKRP1 receptors and their genetically linked CLEC2 ligands with an emphasis on the human receptor/ligand pairs NKRP1A-LLT1, NKp80-AICL, and NKp65-KACL.
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Affiliation(s)
- Yvonne Bartel
- Institute for Molecular Medicine, Goethe-University Frankfurt am Main , Frankfurt am Main , Germany
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31
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Hawse WF, Gloor BE, Ayres CM, Kho K, Nuter E, Baker BM. Peptide modulation of class I major histocompatibility complex protein molecular flexibility and the implications for immune recognition. J Biol Chem 2013; 288:24372-81. [PMID: 23836912 DOI: 10.1074/jbc.m113.490664] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
T cells use the αβ T cell receptor (TCR) to recognize antigenic peptides presented by class I major histocompatibility complex proteins (pMHCs) on the surfaces of antigen-presenting cells. Flexibility in both TCRs and peptides plays an important role in antigen recognition and discrimination. Less clear is the role of flexibility in the MHC protein; although recent observations have indicated that mobility in the MHC can impact TCR recognition in a peptide-dependent fashion, the extent of this behavior is unknown. Here, using hydrogen/deuterium exchange, fluorescence anisotropy, and structural analyses, we show that the flexibility of the peptide binding groove of the class I MHC protein HLA-A*0201 varies significantly with different peptides. The variations extend throughout the binding groove, impacting regions contacted by TCRs as well as other activating and inhibitory receptors of the immune system. Our results are consistent with statistical mechanical models of protein structure and dynamics, in which the binding of different peptides alters the populations and exchange kinetics of substates in the MHC conformational ensemble. Altered MHC flexibility will influence receptor engagement, impacting conformational adaptations, entropic penalties associated with receptor recognition, and the populations of binding-competent states. Our results highlight a previously unrecognized aspect of the "altered self" mechanism of immune recognition and have implications for specificity, cross-reactivity, and antigenicity in cellular immunity.
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Affiliation(s)
- William F Hawse
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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32
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Structure of NKp65 bound to its keratinocyte ligand reveals basis for genetically linked recognition in natural killer gene complex. Proc Natl Acad Sci U S A 2013; 110:11505-10. [PMID: 23803857 DOI: 10.1073/pnas.1303300110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The natural killer (NK) gene complex (NKC) encodes numerous C-type lectin-like receptors that govern the activity of NK cells. Although some of these receptors (Ly49s, NKG2D, CD94/NKG2A) recognize MHC or MHC-like molecules, others (Nkrp1, NKRP1A, NKp80, NKp65) instead bind C-type lectin-like ligands to which they are genetically linked in the NKC. To understand the basis for this recognition, we determined the structure of human NKp65, an activating receptor implicated in the immunosurveillance of skin, bound to its NKC-encoded ligand keratinocyte-associated C-type lectin (KACL). Whereas KACL forms a homodimer resembling other C-type lectin-like dimers, NKp65 is monomeric. The binding mode in the NKp65-KACL complex, in which a monomeric receptor engages a dimeric ligand, is completely distinct from those used by Ly49s, NKG2D, or CD94/NKG2A. The structure explains the exceptionally high affinity of the NKp65-KACL interaction compared with other cell-cell interaction pairs (KD = 6.7 × 10(-10) M), which may compensate for the monomeric nature of NKp65 to achieve cell activation. This previously unreported structure of an NKC-encoded receptor-ligand complex, coupled with mutational analysis of the interface, establishes a docking template that is directly applicable to other genetically linked pairs in the NKC, including Nkrp1-Clr, NKRP1A-LLT1, and NKp80-AICL.
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Alvarez M, Sungur CM, Ames E, Anderson SK, Pomeroy C, Murphy WJ. Contrasting effects of anti-Ly49A due to MHC class I cis binding on NK cell-mediated allogeneic bone marrow cell resistance. THE JOURNAL OF IMMUNOLOGY 2013; 191:688-98. [PMID: 23752612 DOI: 10.4049/jimmunol.1300202] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
NK subsets have activating and inhibitory receptors that bind MHC-I. Ly49A is a mouse inhibitory receptor that binds with high affinity to H2(d) in both a cis- and trans-manner. Ly49A cis-associations limit trans-interactions with H2(d)-expressing targets as well as mAb binding. We demonstrate that cis-interactions affect mAb effector functions. In vivo administration of anti-Ly49A depleted NK cells in H2(b) but not H2(d) mice. Despite lack of depletion, in vivo treatment with anti-Ly49A reduced NK killing capabilities and inhibited activation, partially due to its agonistic effect. These data explain the previously described in vivo effects on bone marrow allograft rejection observed with anti-Ly49A treatment in H2(d)-haplotype mice. However, prior treatment of mice with poly(I:C) or mouse CMV infection resulted in increased Ly49A expression and Ly49A(+) NK cell depletion in H2(d) mice. These data indicate that, although Ly49 mAbs can exert similar in vivo effects in mice with different MHC haplotypes, these effects are mediated via different mechanisms of action correlating with Ly49A expression levels and can be altered within the same strain contingent on stimuli. This illustrates the marked diversity of mAb effector functions due to the regulation of the level of expression of target Ags and responses by stimulatory incidents such as infection.
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Affiliation(s)
- Maite Alvarez
- Department of Dermatology, University of California, Davis, Sacramento, CA 95817, USA
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34
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Targeting of a natural killer cell receptor family by a viral immunoevasin. Nat Immunol 2013; 14:699-705. [DOI: 10.1038/ni.2605] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 04/03/2013] [Indexed: 02/01/2023]
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Schenkel AR, Kingry LC, Slayden RA. The ly49 gene family. A brief guide to the nomenclature, genetics, and role in intracellular infection. Front Immunol 2013; 4:90. [PMID: 23596445 PMCID: PMC3627126 DOI: 10.3389/fimmu.2013.00090] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/04/2013] [Indexed: 12/19/2022] Open
Abstract
Understanding the Ly49 gene family can be challenging in terms of nomenclature and genetic organization. The Ly49 gene family has two major gene nomenclature systems, Ly49 and Killer Cell Lectin-like Receptor subfamily A (klra). Mice from different strains have varying numbers of these genes with strain specific allelic variants, duplications, deletions, and pseudogene sequences. Some members activate NK lymphocytes, invariant NKT (iNKT) lymphocytes and γδ T lymphocytes while others inhibit killing activity. One family member, Ly49Q, is expressed only on myeloid cells and is not found on NK, iNKT, or γδ T cells. There is growing evidence that these receptors may regulate not just the immune response to viruses, but other intracellular pathogens as well. Thus, this review’s primary goal is to provide a guide for researchers first encountering the Ly49 gene family and a foundation for future studies on the role that these gene products play in the immune response, particularly the response to intracellular viral and bacterial pathogens.
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Affiliation(s)
- Alan Rowe Schenkel
- Department of Microbiology, Immunology and Pathology, Colorado State University Fort Collins, CO, USA
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36
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Baker BM, Scott DR, Blevins SJ, Hawse WF. Structural and dynamic control of T-cell receptor specificity, cross-reactivity, and binding mechanism. Immunol Rev 2013; 250:10-31. [PMID: 23046120 DOI: 10.1111/j.1600-065x.2012.01165.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Over the past two decades, structural biology has shown how T-cell receptors engage peptide/major histocompatibility complex (MHC) complexes and provided insight into the mechanisms underlying antigen specificity and cross-reactivity. Here we review and contextualize our contributions, which have emphasized the influence of structural changes and molecular flexibility. A repeated observation is the presence of conformational melding, in which the T-cell receptor (TCR), peptide, and in some cases, MHC protein cooperatively adjust in order for recognition to proceed. The structural changes reflect the intrinsic dynamics of the unligated proteins. Characterization of the dynamics of unligated TCR shows how binding loop motion can influence TCR cross-reactivity as well as specificity towards peptide and MHC. Examination of peptide dynamics indicates not only peptide-specific variation but also a peptide dependence to MHC flexibility. This latter point emphasizes that the TCR engages a composite peptide/MHC surface and that physically the receptor makes little distinction between the peptide and MHC. Much additional evidence for this can be found within the database of available structures, including our observations of a peptide dependence to the TCR binding mode and structural compensations for altered interatomic interactions, in which lost TCR-peptide interactions are replaced with TCR-MHC interactions. The lack of a hard-coded physical distinction between peptide and MHC has implications not only for specificity and cross-reactivity but also the mechanisms underlying MHC restriction as well as attempts to modulate and control TCR recognition.
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Affiliation(s)
- Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, IN, USA.
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Long EO, Kim HS, Liu D, Peterson ME, Rajagopalan S. Controlling natural killer cell responses: integration of signals for activation and inhibition. Annu Rev Immunol 2013; 31:227-58. [PMID: 23516982 PMCID: PMC3868343 DOI: 10.1146/annurev-immunol-020711-075005] [Citation(s) in RCA: 867] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Understanding how signals are integrated to control natural killer (NK) cell responsiveness in the absence of antigen-specific receptors has been a challenge, but recent work has revealed some underlying principles that govern NK cell responses. NK cells use an array of innate receptors to sense their environment and respond to alterations caused by infections, cellular stress, and transformation. No single activation receptor dominates; instead, synergistic signals from combinations of receptors are integrated to activate natural cytotoxicity and cytokine production. Inhibitory receptors for major histocompatibility complex class I (MHC-I) have a critical role in controlling NK cell responses and, paradoxically, in maintaining NK cells in a state of responsiveness to subsequent activation events, a process referred to as licensing. MHC-I-specific inhibitory receptors both block activation signals and trigger signals to phosphorylate and inactivate the small adaptor Crk. These different facets of inhibitory signaling are incorporated into a revocable license model for the reversible tuning of NK cell responsiveness.
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Affiliation(s)
- Eric O. Long
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Hun Sik Kim
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
- Department of Medicine, Graduate School, University of Ulsan, Seoul 138-736, Korea;
| | - Dongfang Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
- Center for Human Immunobiology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030;
| | - Mary E. Peterson
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
| | - Sumati Rajagopalan
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852
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38
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Dynamics of free versus complexed β2-microglobulin and the evolution of interfaces in MHC class I molecules. Immunogenetics 2012; 65:157-72. [PMID: 23229474 DOI: 10.1007/s00251-012-0667-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
In major histocompatibility complex (MHC) class I molecules, monomorphic β(2)-microglobulin (β(2)m) is non-covalently bound to a heavy chain (HC) exhibiting a variable degree of polymorphism. β(2)M can stabilize a wide variety of complexes ranging from classical peptide binding to nonclassical lipid presenting MHC class I molecules as well as to MHC class I-like molecules that do not bind small ligands. Here we aim to assess the dynamics of individual regions in free as well as complexed β(2)m and to understand the evolution of the interfaces between β(2)m and different HC. Using human β(2)m and the HLA-B*27:09 complex as a model system, a comparison of free and HC-bound β(2)m by nuclear magnetic resonance spectroscopy was initially carried out. Although some regions retain their flexibility also after complex formation, these studies reveal that most parts of β(2)m gain rigidity upon binding to the HC. Sequence analyses demonstrate that some of the residues exhibiting flexibility participate in evolutionarily conserved β(2)m-HC contacts which are detectable in diverse vertebrate species or characterize a particular group of MHC class I complexes such as peptide- or lipid-binding molecules. Therefore, the spectroscopic experiments and the interface analyses demonstrate that β(2)m fulfills its role of interacting with diverse MHC class I HC as well as effector cell receptors not only by engaging in conserved intermolecular contacts but also by falling back upon key interface residues that exhibit a high degree of flexibility.
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39
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Sattler S, Reiche D, Sturtzel C, Karas I, Richter S, Kalb ML, Gregor W, Hofer E. The human C-type lectin-like receptor CLEC-1 is upregulated by TGF-β and primarily localized in the endoplasmic membrane compartment. Scand J Immunol 2012; 75:282-92. [PMID: 22117783 DOI: 10.1111/j.1365-3083.2011.02665.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The orphan receptor CLEC-1 is part of a subfamily of C-type lectin-like receptors, which is encoded in the human natural killer gene complex and comprises several pattern recognition receptors important for innate immune functions. As information on human CLEC-1 is still very limited, we aimed to further characterize this receptor. Similar to another subfamily member, LOX-1, expression of CLEC-1 mRNA was detected in myeloid cells as well as in endothelial cells. CLEC-1 protein displayed N-linked glycosylation and formed dimers. However, in contrast to other members of the subfamily, expression levels were upregulated by transforming growth factor (TGF)-β, but not significantly affected by proinflammatory stimuli. It is intriguing that human CLEC-1 could only be detected intracellularly with a staining pattern resembling endoplasmic reticulum proteins. Neither TGF-β nor inflammatory stimuli could promote significant translocation to the cell surface. These findings are in accordance with a primarily intracellular localization and function of human CLEC-1.
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Affiliation(s)
- S Sattler
- Department of Vascular Biology and Thrombosis Research Immunology Dermatology, Division of Immunology, Allergy and Infectious Diseases, Medical University of Vienna, Vienna, Austria.
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40
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Abstract
Yeast display is an efficient technology for selection of antibodies and other proteins with high affinity and thermal stability. Here, we describe a method for affinity maturation of engineered antibody domains (eAds) using yeast display. EAd yeast libraries of relatively large size (∼10⁹) were generated and subjected to alternating rounds of magnetic-activated cell sorting (MACS), fluorescent-activated cell sorting (FACS), and random mutagenesis. The highest affinity clones from the final round of maturation were identified and analyzed. We discuss extensively each key step, and provide detailed protocols and helpful notes.
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Affiliation(s)
- Qi Zhao
- Protein Interactions Group, Center for Cancer Research Nanobiology Program, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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41
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Ma BJ, Kane KP. Recognition of class I MHC by a rat Ly49 NK cell receptor is dependent on the identity of the P2 anchor amino acid of bound peptide. THE JOURNAL OF IMMUNOLOGY 2011; 187:3267-76. [PMID: 21841133 DOI: 10.4049/jimmunol.1002809] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Members of the rodent Ly49 receptor family control NK cell responsiveness and demonstrate allele specificity for MHC class I (MHC-I) ligands. For example, the rat Ly49i2 inhibitory NK cell receptor binds RT1-A1(c) but not other rat MHC class Ia or Ib molecules. RT1-A1(c) preferentially binds peptides with proline at the second, or P2, position, which defines it as an HLA-B7 supertype MHC-I molecule. Previously, our laboratory showed that mutations within the MHC-I supertype-defining B-pocket of RT1-A1(c) could lead to alterations in P2 anchor residues of the peptide repertoire bound by RT1-A1(c) and loss of recognition by Ly49i2. Although suggestive of peptide involvement, it was unclear whether the peptide P2 anchor residue or alteration of the RT1-A1(c) primary sequence influenced Ly49i2 recognition. Therefore, we directly investigated the role of the P2 anchor residue of RT1-A1(c)-bound peptides in Ly49i2 recognition. First, fluorescent multimers generated by refolding soluble recombinant RT1-A1(c) with individual synthetic peptides differing only at the P2 anchor residue were examined for binding to Ly49i2 NK cell transfectants. Second, cytotoxicity by Ly49i2-expressing NK cells toward RMA-S target cells expressing RT1-A1(c) bound with peptides that only differ at the P2 anchor residue was evaluated. Our results demonstrate that Ly49i2 recognizes RT1-A1(c) bound with peptides that have Pro or Val at P2, whereas little or no recognition is observed when RT1-A1(c) is complexed with peptide bearing Gln at P2. Thus, the identity of the P2 peptide anchor residue is an integral component of MHC-I recognition by Ly49i2.
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Affiliation(s)
- Brian J Ma
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2S2, Canada
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42
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How the virus outsmarts the host: function and structure of cytomegalovirus MHC-I-like molecules in the evasion of natural killer cell surveillance. J Biomed Biotechnol 2011; 2011:724607. [PMID: 21765638 PMCID: PMC3134397 DOI: 10.1155/2011/724607] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 03/28/2011] [Indexed: 12/18/2022] Open
Abstract
Natural killer (NK) cells provide an initial host immune response to infection by many viral pathogens. Consequently, the viruses have evolved mechanisms to attenuate the host response, leading to improved viral fitness. One mechanism employed by members of the β-herpesvirus family, which includes the cytomegaloviruses, is to modulate the expression of cell surface ligands recognized by NK cell activation molecules. A novel set of cytomegalovirus (CMV) genes, exemplified by the mouse m145 family, encode molecules that have structural and functional features similar to those of host major histocompatibility-encoded (MHC) class I molecules, some of which are known to contribute to immune evasion. In this review, we explore the function, structure, and evolution of MHC-I-like molecules of the CMVs and speculate on the dynamic development of novel immunoevasive functions based on the MHC-I protein fold.
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43
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Kamishikiryo J, Fukuhara H, Okabe Y, Kuroki K, Maenaka K. Molecular basis for LLT1 protein recognition by human CD161 protein (NKRP1A/KLRB1). J Biol Chem 2011; 286:23823-30. [PMID: 21572041 DOI: 10.1074/jbc.m110.214254] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Human Th17 cells express high levels of CD161, a member of the killer cell lectin-like receptor (KLR) family (also referred to as NK receptor-P1A (NKRP1A) or KLRB1), as a representative marker. CD161 is also expressed on natural killer (NK) cells and NKT cells. Lectin-like transcript 1 (LLT1), another KLR family member, was recently identified as a ligand for CD161. This interaction may play pivotal roles in the immunomodulatory functions of Th17 cells as well as those of NK and NKT cells. However, the molecular basis for the interaction is poorly understood. Here we show that the extracellular domain of CD161 bound directly to LLT1 with a K(d) of 48 μM and with the fast kinetics typical of cell-cell recognition receptors. Mutagenesis revealed that the similar membrane-distal β-sheet and loop regions of both CD161 and LLT1 were utilized for the binding, and notably, these regions correspond to the ligand-binding sites for major histocompatibility complex (MHC)-recognizing KLRs. Furthermore, we found a pair of detrimental mutations for both molecules that restored the binding. These results reveal a new template model for the recognition mode between the KLR family members and provide insights into the molecular mechanism underlying Th17/NK/NKT-mediated immune responses.
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Affiliation(s)
- Jun Kamishikiryo
- Laboratory of Biomolecular Science, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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Choi T, Ferris ST, Matsumoto N, Poursine-Laurent J, Yokoyama WM. Ly49-dependent NK cell licensing and effector inhibition involve the same interaction site on MHC ligands. THE JOURNAL OF IMMUNOLOGY 2011; 186:3911-7. [PMID: 21335486 DOI: 10.4049/jimmunol.1004168] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
NK cells become functionally competent to be triggered by their activation receptors through the interaction of NK cell inhibitory receptors with their cognate self-MHC ligands, an MHC-dependent educational process termed "licensing." For example, Ly49A(+) NK cells become licensed by the interaction of the Ly49A inhibitory receptor with its MHC class I ligand, H2D(d), whereas Ly49C(+) NK cells are licensed by H2K(b). Structural studies indicate that the Ly49A inhibitory receptor may interact with two sites, termed site 1 and site 2, on its H2D(d) ligand. Site 2 encompasses the α1/α2/α3 domains of the H2D(d) H chain and β(2)-microglobulin (β2m) and is the functional binding site for Ly49A in effector inhibition. Ly49C functionally interacts with a similar site in H2K(b). However, it is currently unknown whether this same site is involved in Ly49A- or Ly49C-dependent licensing. In this study, we produced transgenic C57BL/6 mice expressing wild-type or site 2 mutant H2D(d) molecules and studied whether Ly49A(+) NK cells are licensed. We also investigated Ly49A- and Ly49C-dependent NK licensing in murine β2m-deficient mice that are transgenic for human β2m, which has species-specific amino acid substitutions in β2m. Our data from these transgenic mice indicate that site 2 on self-MHC is critical for Ly49A- and Ly49C-dependent NK cell licensing. Thus, NK cell licensing through Ly49 involves specific interactions with its MHC ligand that are similar to those involved in effector inhibition.
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Affiliation(s)
- Taewoong Choi
- Rheumatology Division, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
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45
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Cifaldi L, Lo Monaco E, Forloni M, Giorda E, Lorenzi S, Petrini S, Tremante E, Pende D, Locatelli F, Giacomini P, Fruci D. Natural Killer Cells Efficiently Reject Lymphoma Silenced for the Endoplasmic Reticulum Aminopeptidase Associated with Antigen Processing. Cancer Res 2011; 71:1597-606. [DOI: 10.1158/0008-5472.can-10-3326] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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Pegram HJ, Andrews DM, Smyth MJ, Darcy PK, Kershaw MH. Activating and inhibitory receptors of natural killer cells. Immunol Cell Biol 2010; 89:216-24. [PMID: 20567250 DOI: 10.1038/icb.2010.78] [Citation(s) in RCA: 353] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Natural killer (NK) cells are potent immune effector cells that can respond to infection and cancer, as well as allowing maternal adaptation to pregnancy. In response to malignant transformation or pathogenic invasion, NK cells can secrete cytokine and may be directly cytolytic, as well as exerting effects indirectly through other cells of the immune system. To recognize and respond to inflamed or infected tissues, NK cells express a variety of activating and inhibitory receptors including NKG2D, Ly49 or KIR, CD94-NKG2 heterodimers and natural cytotoxicity receptors, as well as co-stimulatory receptors. These receptors recognize cellular stress ligands as well as major histocompatibility complex class I and related molecules, which can lead to NK cell responses. Importantly, NK cells must remain tolerant of healthy tissue, and some of these receptors can also prevent activation of NK cells. In this review, we describe the expression of prominent NK cell receptors, as well as expression of their ligands and their role in immune responses. In addition, we describe the main signaling pathways used by NK cell receptors. Although we now appreciate that NK cell biology is more complicated than first thought, there are still facets of their biology that remain unclear. These will be highlighted and discussed in this review.
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Affiliation(s)
- Hollie J Pegram
- Cancer Immunology Research Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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47
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Chen H, Kshirsagar S, Jensen I, Lau K, Simonson C, Schluter SF. Characterization of arrangement and expression of the beta-2 microglobulin locus in the sandbar and nurse shark. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2010; 34:189-195. [PMID: 19782101 DOI: 10.1016/j.dci.2009.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Accepted: 09/18/2009] [Indexed: 05/28/2023]
Abstract
Beta 2 microglobulin (beta2m) is an essential subunit of major histocompatibility complex (MHC) type I molecules. In this report, beta2m cDNAs were identified and sequenced from sandbar shark spleen cDNA library. Sandbar shark beta2m gene encodes one amino acid less than most teleost beta2m genes, and 3 amino acids less than mammal beta2m genes. Although sandbar shark beta2m protein contains one beta sheet less than that of human in the predicted protein structure, the overall structure of beta2m proteins is conserved during evolution. Germline gene for the beta2m in sandbar and nurse shark is present as a single locus. It contains three exons and two introns. CpG sites are evenly distributed in the shark beta2m loci. Several DNA repeat elements were also identified in the shark beta2m loci. Sequence analysis suggests that the beta2m locus is not linked to the MHC I loci in the shark genome.
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Affiliation(s)
- Hao Chen
- Department of Immunobiology, College of Medicine, University of Arizona, Tucson, AZ 85719, USA
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48
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Watson AA, Christou CM, James JR, Fenton-May AE, Moncayo GE, Mistry AR, Davis SJ, Gilbert RJC, Chakera A, O'Callaghan CA. The platelet receptor CLEC-2 is active as a dimer. Biochemistry 2009; 48:10988-96. [PMID: 19824697 DOI: 10.1021/bi901427d] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The platelet receptor CLEC-2 binds to the snake venom toxin rhodocytin and the tumor cell surface protein podoplanin. Binding of either of these ligands promotes phosphorylation of a single tyrosine residue in the YXXL motif in the intracellular domain of CLEC-2. Phosphorylation of this tyrosine initiates binding of spleen tyrosine kinase (Syk) and triggers further downstream signaling events and ultimately potent platelet activation and aggregation. However, it is unclear how a single YXXL motif can interact efficiently with Syk, which usually recognizes two tandem YXXL repeats presented as an immunoreceptor tyrosine-based activation motif (ITAM). Using bioluminescence resonance energy transfer, coimmunopreciptitation, recombinant protein expression and analytical gel filtration chromatography, surface plasmon resonance, Western blotting, multiangle light scattering (MALS), and analytical ultracentrifugation, we show that CLEC-2 exists as a non-disulfide-linked homodimer which could allow each Syk molecule to interact with two YXXL motifs, one from each CLEC-2 monomer.
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Affiliation(s)
- Aleksandra A Watson
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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49
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Dobromylskyj MJ, Connelley T, Hammond JA, Ellis SA. Cattle Ly49 is polymorphic. Immunogenetics 2009; 61:789-95. [DOI: 10.1007/s00251-009-0406-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Accepted: 10/23/2009] [Indexed: 11/29/2022]
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50
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Distinct conformations of Ly49 natural killer cell receptors mediate MHC class I recognition in trans and cis. Immunity 2009; 31:598-608. [PMID: 19818651 DOI: 10.1016/j.immuni.2009.07.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 07/01/2009] [Accepted: 07/29/2009] [Indexed: 11/21/2022]
Abstract
Certain cell-surface receptors engage ligands expressed on juxtaposed cells and ligands on the same cell. The structural basis for trans versus cis binding is not known. Here, we showed that Ly49 natural killer (NK) cell receptors bound two MHC class I (MHC-I) molecules in trans when the two ligand-binding domains were backfolded onto the long stalk region. In contrast, dissociation of the ligand-binding domains from the stalk and their reorientation relative to the NK cell membrane allowed monovalent binding of MHC-I in cis. The distinct conformations (backfolded and extended) define the structural basis for cis-trans binding by Ly49 receptors and explain the divergent functional consequences of cis versus trans interactions. Further analyses identified specific stalk segments that were not required for MHC-I binding in trans but were essential for inhibitory receptor function. These data identify multiple distinct roles of stalk regions for receptor function.
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