1
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Senoo A, Hoshino M, Shiomi T, Nakakido M, Nagatoishi S, Kuroda D, Nakagawa I, Tame JRH, Caaveiro JMM, Tsumoto K. Structural basis for the recognition of human hemoglobin by the heme-acquisition protein Shr from Streptococcus pyogenes. Sci Rep 2024; 14:5374. [PMID: 38438508 PMCID: PMC10912661 DOI: 10.1038/s41598-024-55734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/27/2024] [Indexed: 03/06/2024] Open
Abstract
In Gram-positive bacteria, sophisticated machineries to acquire the heme group of hemoglobin (Hb) have evolved to extract the precious iron atom contained in it. In the human pathogen Streptococcus pyogenes, the Shr protein is a key component of this machinery. Herein we present the crystal structure of hemoglobin-interacting domain 2 (HID2) of Shr bound to Hb. HID2 interacts with both, the protein and heme portions of Hb, explaining the specificity of HID2 for the heme-bound form of Hb, but not its heme-depleted form. Further mutational analysis shows little tolerance of HID2 to interfacial mutations, suggesting that its interaction surface with Hb could be a suitable candidate to develop efficient inhibitors abrogating the binding of Shr to Hb.
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Affiliation(s)
- Akinobu Senoo
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Masato Hoshino
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Toshiki Shiomi
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
| | - Makoto Nakakido
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Jose M M Caaveiro
- Laboratory of Protein Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.
- The Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8629, Japan.
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2
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Mortier E, Maillasson M, Quéméner A. Counteracting Interleukin-15 to Elucidate Its Modes of Action in Physiology and Pathology. J Interferon Cytokine Res 2023; 43:2-22. [PMID: 36651845 DOI: 10.1089/jir.2022.0198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Interleukin (IL)-15 belongs to the common gamma-dependent cytokine family, along with IL-2, IL-4, IL-7, IL-9, and IL-21. IL-15 is crucial for the homeostasis of Natural Killer (NK) and memory CD8 T cells, and to fight against cancer progression. However, dysregulations of IL-15 expression could occur and participate in the emergence of autoimmune inflammatory diseases as well as hematological malignancies. It is therefore important to understand the different modes of action of IL-15 to decrease its harmful action in pathology without affecting its beneficial effects in the immune system. In this review, we present the different approaches used by researchers to inhibit the action of IL-15, from most broad to the most selective. Indeed, it appears that it is important to selectively target the mode of action of the cytokine rather than the cytokine itself as they are involved in numerous biological processes.
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Affiliation(s)
- Erwan Mortier
- Nantes Université, CNRS, Inserm, CRCI2NA, Nantes, France.,LabEX IGO, Immuno-Onco-Greffe, Nantes, France
| | - Mike Maillasson
- Nantes Université, CNRS, Inserm, CRCI2NA, Nantes, France.,LabEX IGO, Immuno-Onco-Greffe, Nantes, France
| | - Agnès Quéméner
- Nantes Université, CNRS, Inserm, CRCI2NA, Nantes, France.,LabEX IGO, Immuno-Onco-Greffe, Nantes, France
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3
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Akiba H, Tamura H, Caaveiro JMM, Tsumoto K. Epitope-dependent thermodynamic signature of single-domain antibodies against hen egg lysozyme. J Biochem 2021; 170:623-629. [PMID: 34519785 DOI: 10.1093/jb/mvab082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/10/2021] [Indexed: 11/14/2022] Open
Abstract
A substantial body of work has been carried out describing the structural features of the complex between single-domain antibodies (VHHs) and antigens, and the preeminence for epitopes located at concave surfaces of the antigen. However, the thermodynamic basis of binding is far less clear. Here, we have analyzed the energetic profiles of five VHHs binding to the catalytic cleft as well as a non-cleft epitope of hen egg lysozyme. Various binding energetic profiles with distinctive enthalpic/entropic contributions and structural distribution of critical residues were found in the five antibodies analyzed. Collectively, we suggest that from an energetic point of view the binding mechanism is influenced by the shape of the epitope. This information may be beneficial for the design of tailored epitopes for VHHs and their practical use.
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Affiliation(s)
- Hiroki Akiba
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroko Tamura
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113- 8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka City, 812-8582, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki City, Osaka, 567-0085, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113- 8656, Japan.,Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8629, Japan
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4
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Akiba H, Tamura H, Caaveiro JMM, Tsumoto K. Computer-guided library generation applied to the optimization of single-domain antibodies. Protein Eng Des Sel 2019; 32:423-431. [PMID: 32167147 DOI: 10.1093/protein/gzaa006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/30/2020] [Accepted: 03/02/2020] [Indexed: 12/16/2022] Open
Abstract
Computer-guided library generation is a plausible strategy to optimize antibodies. Herein, we report the improvement of the affinity of a single-domain camelid antibody for its antigen using such approach. We first conducted experimental and computational alanine scanning to describe the precise energetic profile of the antibody-antigen interaction surface. Based on this characterization, we hypothesized that in-silico mutagenesis could be employed to guide the development of a small library for phage display with the goal of improving the affinity of an antibody for its antigen. Optimized antibody mutants were identified after three rounds of selection, in which an alanine residue at the core of the antibody-antigen interface was substituted by residues with large side-chains, generating diverse kinetic responses, and resulting in greater affinity (>10-fold) for the antigen.
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Affiliation(s)
- Hiroki Akiba
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroko Tamura
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,Medical Proteomics Laboratory, Institute of Medical Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8629, Japan
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5
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Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody. Sci Rep 2019; 9:15481. [PMID: 31664051 PMCID: PMC6820745 DOI: 10.1038/s41598-019-50722-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/10/2019] [Indexed: 01/06/2023] Open
Abstract
Single-domain antibodies (VHHs or nanobodies), developed from heavy chain-only antibodies of camelids, are gaining attention as next-generation therapeutic agents. Despite their small size, the high affinity and specificity displayed by VHHs for antigen molecules rival those of IgGs. How such small antibodies achieve that level of performance? Structural studies have revealed that VHHs tend to recognize concave surfaces of their antigens with high shape-complementarity. However, the energetic contribution of individual residues located at the binding interface has not been addressed in detail, obscuring the actual mechanism by which VHHs target the concave surfaces of proteins. Herein, we show that a VHH specific for hen egg lysozyme, D3-L11, not only displayed the characteristic binding of VHHs to a concave region of the surface of the antigen, but also exhibited a distribution of energetic hot-spots like those of IgGs and conventional protein-protein complexes. The highly preorganized and energetically compact interface of D3-L11 recognizes the concave epitope with high shape complementarity by the classical lock-and-key mechanism. Our results shed light on the fundamental basis by which a particular VHH accommodate to the concave surface of an antigens with high affinity in a specific manner, enriching the mechanistic landscape of VHHs.
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6
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Sousa RP, Laurent AD, Quéméner A, Mortier E, Questel JYL. Mechanistic and Structural Insights on the IL-15 System through Molecular Dynamics Simulations. Molecules 2019; 24:molecules24183261. [PMID: 31500206 PMCID: PMC6767322 DOI: 10.3390/molecules24183261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 11/16/2022] Open
Abstract
Interleukin 15 (IL-15), a four-helix bundle cytokine, is involved in a plethora of different cellular functions and, particularly, plays a key role in the development and activation of immune responses. IL-15 forms receptor complexes by binding with IL-2Rβ- and common γ (γc)-signaling subunits, which are shared with other members of the cytokines family (IL-2 for IL-2Rβ- and all other γc- cytokines for γc). The specificity of IL-15 is brought by the non-signaling α-subunit, IL-15Rα. Here we present the results of molecular dynamics simulations carried out on four relevant forms of IL-15: its monomer, IL-15 interacting individually with IL-15Rα (IL-15/IL-15Rα), with IL-2Rβ/γc subunits (IL-15/IL-2Rβ/γc) or with its three receptors simultaneously (IL-15/IL-15Rα/IL-2Rβ/γc). Through the analyses of the various trajectories, new insights on the structural features of the interfaces are highlighted, according to the considered form. The comparison of the results with the experimental data, available from X-ray crystallography, allows, in particular, the rationalization of the importance of IL-15 key residues (e.g., Asp8, Lys10, Glu64). Furthermore, the pivotal role of water molecules in the stabilization of the various protein-protein interfaces and their H-bonds networks are underlined for each of the considered complexes.
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Affiliation(s)
- Rui P Sousa
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
| | - Adèle D Laurent
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
| | - Agnès Quéméner
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
| | - Erwan Mortier
- CRCINA, CNRS, Inserm, Université d'Angers, Université de Nantes, F-44200 Nantes, France.
- Immunotherapy, Graft, Oncology (IGO) LabEx, Nantes, France.
- IMPACT Platform, SFR Santé, CNRS, Inserm, Université de Nantes, Nantes, F-44000, France.
| | - Jean-Yves Le Questel
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, F-44000 Nantes, France.
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7
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Beilin C, Choudhuri K, Bouma G, Malinova D, Llodra J, Stokes DL, Shimaoka M, Springer TA, Dustin ML, Thrasher AJ, Burns SO. Dendritic cell-expressed common gamma-chain recruits IL-15 for trans-presentation at the murine immunological synapse. Wellcome Open Res 2018; 3:84. [PMID: 30483599 PMCID: PMC6234741 DOI: 10.12688/wellcomeopenres.14493.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Mutations of the common cytokine receptor gamma chain (γc) cause Severe Combined Immunodeficiency characterized by absent T and NK cell development. Although stem cell therapy restores these lineages, residual immune defects are observed that may result from selective persistence of γc-deficiency in myeloid lineages. However, little is known about the contribution of myeloid-expressed γc to protective immune responses. Here we examine the importance of γc for myeloid dendritic cell (DC) function. Methods: We utilize a combination of in vitro DC/T-cell co-culture assays and a novel lipid bilayer system mimicking the T cell surface to delineate the role of DC-expressed γc during DC/T-cell interaction. Results: We observed that γc in DC was recruited to the contact interface following MHCII ligation, and promoted IL-15Rα colocalization with engaged MHCII. Unexpectedly, trans-presentation of IL-15 was required for optimal CD4+T cell activation by DC and depended on DC γc expression. Neither recruitment of IL-15Rα nor IL-15 trans-signaling at the DC immune synapse (IS), required γc signaling in DC, suggesting that γc facilitates IL-15 transpresentation through induced intermolecular cis associations or cytoskeletal reorganization following MHCII ligation. Conclusions: These findings show that DC-expressed γc is required for effective antigen-induced CD4+ T cell activation. We reveal a novel mechanism for recruitment of DC IL-15/IL-15Rα complexes to the IS, leading to CD4+ T cell costimulation through localized IL-15 transpresentation that is coordinated with antigen-recognition.
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Affiliation(s)
- Chiara Beilin
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Kaushik Choudhuri
- Program in Molecular Pathogenesis, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Gerben Bouma
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Dessislava Malinova
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Jaime Llodra
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - David L. Stokes
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Motumu Shimaoka
- Immune Disease Institute, Children's Hospital Boston, Boston, MA, 02115, USA
| | - Timothy A. Springer
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Michael L. Dustin
- Program in Molecular Pathogenesis, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, OX3 7FY, UK
| | - Adrian J. Thrasher
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Siobhan O. Burns
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- University College London Institute of Immunity and Transplantation, Department of Immunology, Royal Free London NHS Foundation Trust, London, NW3 2PF, UK
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8
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Tashiro S, Caaveiro JMM, Nakakido M, Tanabe A, Nagatoishi S, Tamura Y, Matsuda N, Liu D, Hoang QQ, Tsumoto K. Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1. ACS Chem Biol 2018; 13:2783-2793. [PMID: 30063823 DOI: 10.1021/acschembio.8b00701] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DJ-1 is a Parkinson's disease associated protein endowed with enzymatic, redox sensing, regulatory, chaperoning, and neuroprotective activities. Although DJ-1 has been vigorously studied for the past decade and a half, its exact role in the progression of the disease remains uncertain. In addition, little is known about the spatiotemporal regulation of DJ-1, or the biochemical basis explaining its numerous biological functions. Progress has been hampered by the lack of inhibitors with precisely known mechanisms of action. Herein, we have employed biophysical methodologies and X-ray crystallography to identify and to optimize a family of compounds inactivating the critical Cys106 residue of human DJ-1. We demonstrate these compounds are potent inhibitors of various activities of DJ-1 in vitro and in cell-based assays. This study reports a new family of DJ-1 inhibitors with a defined mechanism of action, and contributes toward the understanding of the biological function of DJ-1.
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Affiliation(s)
- Shinya Tashiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Jose M. M. Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Laboratory of Global Healthcare, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Makoto Nakakido
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Aki Tanabe
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Tamura
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata 990-8560, Japan
| | - Noriyuki Matsuda
- Ubiquitin Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo 156-8506, Japan
| | - Dali Liu
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | | | - Kouhei Tsumoto
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo 108-8639, Japan
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9
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Beilin C, Choudhuri K, Bouma G, Malinova D, Llodra J, Stokes DL, Shimaoka M, Springer TA, Dustin ML, Thrasher AJ, Burns SO. Dendritic cell-expressed common gamma-chain recruits IL-15 for trans-presentation at the murine immunological synapse. Wellcome Open Res 2018; 3:84. [PMID: 30483599 PMCID: PMC6234741 DOI: 10.12688/wellcomeopenres.14493.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2018] [Indexed: 10/05/2023] Open
Abstract
Background: Mutations of the common cytokine receptor gamma chain (γc) cause Severe Combined Immunodeficiency characterized by absent T and NK cell development. Although stem cell therapy restores these lineages, residual immune defects are observed that may result from selective persistence of γc-deficiency in myeloid lineages. However, little is known about the contribution of myeloid-expressed γc to protective immune responses. Here we examine the importance of γc for myeloid dendritic cell (DC) function. Methods: We utilize a combination of in vitro DC/T-cell co-culture assays and a novel lipid bilayer system mimicking the T cell surface to delineate the role of DC-expressed γc during DC/T-cell interaction. Results: We observed that γc in DC was recruited to the contact interface following MHCII ligation, and promoted IL-15Rα colocalization with engaged MHCII. Unexpectedly, trans-presentation of IL-15 was required for optimal CD4+T cell activation by DC and depended on DC γc expression. Neither recruitment of IL-15Rα nor IL-15 trans-signaling at the DC immune synapse (IS), required γc signaling in DC, suggesting that γc facilitates IL-15 transpresentation through induced intermolecular cis associations or cytoskeletal reorganization following MHCII ligation. Conclusions: These findings show that DC-expressed γc is required for effective antigen-induced CD4+ T cell activation. We reveal a novel mechanism for recruitment of DC IL-15/IL-15Rα complexes to the IS, leading to CD4+ T cell costimulation through localized IL-15 transpresentation that is coordinated with antigen-recognition.
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Affiliation(s)
- Chiara Beilin
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Kaushik Choudhuri
- Program in Molecular Pathogenesis, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Gerben Bouma
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Dessislava Malinova
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
| | - Jaime Llodra
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - David L. Stokes
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Motumu Shimaoka
- Immune Disease Institute, Children's Hospital Boston, Boston, MA, 02115, USA
| | - Timothy A. Springer
- Program in Structural Biology, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
| | - Michael L. Dustin
- Program in Molecular Pathogenesis, Skirball Institute of Biomolecular Medicine, New York University, New York, NY, 10016, USA
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Headington, OX3 7FY, UK
| | - Adrian J. Thrasher
- Molecular Immunology Unit, Institute of Child Health, University College London, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Siobhan O. Burns
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
- University College London Institute of Immunity and Transplantation, Department of Immunology, Royal Free London NHS Foundation Trust, London, NW3 2PF, UK
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10
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Assessing the Heterogeneity of the Fc-Glycan of a Therapeutic Antibody Using an engineered FcγReceptor IIIa-Immobilized Column. Sci Rep 2018; 8:3955. [PMID: 29500371 PMCID: PMC5834517 DOI: 10.1038/s41598-018-22199-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/13/2018] [Indexed: 12/26/2022] Open
Abstract
The N-glycan moiety of IgG-Fc has a significant impact on multifaceted properties of antibodies such as in their effector function, structure, and stability. Numerous studies have been devoted to understanding its biological effect since the exact composition of the Fc N-glycan modulates the magnitude of effector functions such as the antibody-dependent cell mediated cytotoxicity (ADCC), and the complement-dependent cytotoxicity (CDC). To date, systematic analyses of the properties and influence of glycan variants have been of great interest. Understanding the principles on how N-glycosylation modulates those properties is important for the molecular design, manufacturing, process optimization, and quality control of therapeutic antibodies. In this study, we have separated a model therapeutic antibody into three fractions according to the composition of the N-glycan by using a novel FcγRIIIa chromatography column. Notably, Fc galactosylation was a major factor influencing the affinity of IgG-Fc to the FcγRIIIa immobilized on the column. Each antibody fraction was employed for structural, biological, and physicochemical analysis, illustrating the mechanism by which galactose modulates the affinity to FcγRIIIa. In addition, we discuss the benefits of the FcγRIIIa chromatography column to assess the heterogeneity of the N-glycan.
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11
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Nakano K, Chigira T, Miyafusa T, Nagatoishi S, Caaveiro JMM, Tsumoto K. Discovery and characterization of natural tropolones as inhibitors of the antibacterial target CapF from Staphylococcus aureus. Sci Rep 2015; 5:15337. [PMID: 26471247 PMCID: PMC5393024 DOI: 10.1038/srep15337] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/23/2015] [Indexed: 01/01/2023] Open
Abstract
The rapid spread of antibiotic-resistance among pathogenic bacteria poses a serious risk for public health. The search for novel therapeutic strategies and antimicrobial compounds is needed to ameliorate this menace. The bifunctional metalloenzyme CapF is an antibacterial target produced by certain pathogenic bacteria essential in the biosynthetic route of capsular polysaccharide, a mucous layer on the surface of bacterium that facilitates immune evasion and infection. We report the first inhibitor of CapF from Staphylococcus aureus, which was identified by employing fragment-based methodologies. The hit compound 3-isopropenyl-tropolone inhibits the first reaction catalyzed by CapF, disrupting the synthesis of a key precursor of capsular polysaccharide. Isothermal titration calorimetry demonstrates that 3-isopropenyl-tropolone binds tightly (KD = 27 ± 7 μM) to the cupin domain of CapF. In addition, the crystal structure of the enzyme-inhibitor complex shows that the compound engages the essential Zn2+ ion necessary for the first reaction catalyzed by the enzyme, explaining its inhibitory effect. Moreover, the tropolone compound alters the coordination sphere of the metal, leading to the overall destabilization of the enzyme. We propose 3-isopropenyl-tropolone as a precursor to develop stronger inhibitors for this family of enzymes to impair the synthesis of capsular polysaccharide in Staphylococcus aureus.
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Affiliation(s)
- Koichiro Nakano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Takeru Chigira
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takamitsu Miyafusa
- Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jose M M Caaveiro
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kouhei Tsumoto
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan.,Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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12
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Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10. J Virol 2015; 89:11975-89. [PMID: 26378169 PMCID: PMC4645341 DOI: 10.1128/jvi.01793-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/10/2015] [Indexed: 12/16/2022] Open
Abstract
The 4E10 antibody recognizes the membrane-proximal external region (MPER) of the HIV-1 Env glycoprotein gp41 transmembrane subunit, exhibiting one of the broadest neutralizing activities known to date. The neutralizing activity of 4E10 requires solvent-exposed hydrophobic residues at the apex of the complementarity-determining region (CDR) H3 loop, but the molecular basis for this requirement has not been clarified. Here, we report the cocrystal structures and the energetic parameters of binding of a peptide bearing the 4E10-epitope sequence (4E10ep) to nonneutralizing versions of the 4E10 Fab. Nonneutralizing Fabs were obtained by shortening and decreasing the hydrophobicity of the CDR-H3 loop (termed ΔLoop) or by substituting the two tryptophan residues of the CDR-H3 apex with Asp residues (termed WDWD), which also decreases hydrophobicity but preserves the length of the loop. The analysis was complemented by the first crystal structure of the 4E10 Fab in its ligand-free state. Collectively, the data ruled out major conformational changes of CDR-H3 at any stage during the binding process (equilibrium or transition state). Although these mutations did not impact the affinity of wild-type Fab for the 4E10ep in solution, the two nonneutralizing versions of 4E10 were deficient in binding to MPER inserted in the plasma membrane (mimicking the environment faced by the antibody in vivo). The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear α-helical epitope and likely constrained by the viral membrane lipids. IMPORTANCE The broadly neutralizing anti-HIV-1 4E10 antibody blocks infection caused by nearly all viral strains and isolates examined thus far. However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination. Impediments to the design of successful 4E10 immunogens are partly attributed to an incomplete understanding of the structural and binding characteristics of this class of antibodies. Since the broadly neutralizing activity of 4E10 is abrogated by mutations of the tip of the CDR-H3, we investigated their impact on binding of the MPER-epitope at the atomic and energetic levels. We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes. Our findings strengthen the idea that to elicit similar neutralizing antibodies, the suitable MPER vaccine must be “delivered” in a membrane environment.
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13
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Structural basis for binding of human IgG1 to its high-affinity human receptor FcγRI. Nat Commun 2015; 6:6866. [PMID: 25925696 PMCID: PMC4423232 DOI: 10.1038/ncomms7866] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 03/08/2015] [Indexed: 12/12/2022] Open
Abstract
Cell-surface Fcγ receptors mediate innate and adaptive immune responses. Human Fcγ receptor I (hFcγRI) binds IgGs with high affinity and is the only Fcγ receptor that can effectively capture monomeric IgGs. However, the molecular basis of hFcγRI's interaction with Fc has not been determined, limiting our understanding of this major immune receptor. Here we report the crystal structure of a complex between hFcγRI and human Fc, at 1.80 Å resolution, revealing an unique hydrophobic pocket at the surface of hFcγRI perfectly suited for residue Leu235 of Fc, which explains the high affinity of this complex. Structural, kinetic and thermodynamic data demonstrate that the binding mechanism is governed by a combination of non-covalent interactions, bridging water molecules and the dynamic features of Fc. In addition, the hinge region of hFcγRI-bound Fc adopts a straight conformation, potentially orienting the Fab moiety. These findings will stimulate the development of novel therapeutic strategies involving hFcγRI. FcγRs are cell-surface receptors for IgGs that play key roles in the humoral and cellular immune response to infection. Here, the authors present a high-resolution crystal structure of the hFcγRI-Fc complex to reveal the molecular mechanisms underlying the high specificity of this important immunological interaction.
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14
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Kiyoshi M, Caaveiro JMM, Miura E, Nagatoishi S, Nakakido M, Soga S, Shirai H, Kawabata S, Tsumoto K. Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex. PLoS One 2014; 9:e87099. [PMID: 24475232 PMCID: PMC3903617 DOI: 10.1371/journal.pone.0087099] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 12/19/2013] [Indexed: 12/18/2022] Open
Abstract
The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM) for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1). We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101) is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody). Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu). The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier) benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.
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Affiliation(s)
- Masato Kiyoshi
- Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Jose M. M. Caaveiro
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Eri Miura
- Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Satoru Nagatoishi
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Makoto Nakakido
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Shinji Soga
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, Japan
| | - Hiroki Shirai
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, Japan
| | - Shigeki Kawabata
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Ibaraki, Japan
| | - Kouhei Tsumoto
- Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Laboratory of Medical Proteomics, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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15
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Kobe A, Caaveiro JMM, Tashiro S, Kajihara D, Kikkawa M, Mitani T, Tsumoto K. Incorporation of Rapid Thermodynamic Data in Fragment-Based Drug Discovery. J Med Chem 2013; 56:2155-9. [DOI: 10.1021/jm301603n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Akihiro Kobe
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Jose M. M. Caaveiro
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Shinya Tashiro
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
| | - Daisuke Kajihara
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Masato Kikkawa
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Tomoya Mitani
- Life Science Division, GE Healthcare Japan, 3-25-1 Hyakuninicho, Shinjuku,
Tokyo 169-0073, Japan
| | - Kouhei Tsumoto
- Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
- Department of Medical Genome
Science, School of Frontier Sciences, The University of Tokyo, Kashiwa 277-8562, Japan
- Department
of Chemistry and
Biotechnology, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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16
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Rich RL, Myszka DG. Survey of the 2009 commercial optical biosensor literature. J Mol Recognit 2012; 24:892-914. [PMID: 22038797 DOI: 10.1002/jmr.1138] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We took a different approach to reviewing the commercial biosensor literature this year by inviting 22 biosensor users to serve as a review committee. They set the criteria for what to expect in a publication and ultimately decided to use a pass/fail system for selecting which papers to include in this year's reference list. Of the 1514 publications in 2009 that reported using commercially available optical biosensor technology, only 20% passed their cutoff. The most common criticism the reviewers had with the literature was that "the biosensor experiments could have been done better." They selected 10 papers to highlight good experimental technique, data presentation, and unique applications of the technology. This communal review process was educational for everyone involved and one we will not soon forget.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT, USA
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17
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Yanaka S, 谷 中, Sano E, 佐 野, Naruse N, 成 瀬, Miura KI, 三 浦, Futatsumori-Sugai M, 二 ツ, Caaveiro JMM, Tsumoto K, 津 本. Non-core region modulates interleukin-11 signaling activity: generation of agonist and antagonist variants. J Biol Chem 2010; 286:8085-8093. [PMID: 21138838 DOI: 10.1074/jbc.m110.152561] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human interleukin-11 (hIL-11) is a pleiotropic cytokine administered to patients with low platelet counts. From a structural point of view hIL-11 belongs to the long-helix cytokine superfamily, which is characterized by a conserved core motif consisting of four α-helices. We have investigated the region of hIL-11 that does not belong to the α-helical bundle motif, and that for the purpose of brevity we have termed "non-core region." The primary sequence of the interleukin was altered at various locations within the non-core region by introducing glycosylation sites. Functional consequences of these modifications were examined in cell-based as well as biophysical assays. Overall, the data indicated that the non-core region modulates the function of hIL-11 in two ways. First, the majority of muteins displayed enhanced cell-stimulatory properties (superagonist behavior) in a glycosylation-dependent manner, suggesting that the non-core region is biologically designed to limit the full potential of hIL-11. Second, specific modification of a predicted mini α-helix led to cytokine inactivation, demonstrating that this putative structural element belongs to site III engaging a second copy of cell-receptor gp130. These findings have unveiled new and unexpected elements modulating the biological activity of hIL-11, which may be exploited to develop more versatile medications based on this important cytokine.
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Affiliation(s)
- Saeko Yanaka
- From the Department of Medical Genome Science, School of Frontier Sciences, and
| | - 中冴子 谷
- From the Department of Medical Genome Science, School of Frontier Sciences, and
| | - Emiko Sano
- From the Department of Medical Genome Science, School of Frontier Sciences, and; The Institute of Medical Science, The University of Tokyo, Kashiwa 277-8562 and
| | - 野恵海子 佐
- From the Department of Medical Genome Science, School of Frontier Sciences, and; The Institute of Medical Science, The University of Tokyo, Kashiwa 277-8562 and
| | | | - 瀬紀男 成
- Proteios Inc., Kamakura, 248-8555, Japan
| | - Kin-Ichiro Miura
- From the Department of Medical Genome Science, School of Frontier Sciences, and
| | - 浦謹一郎 三
- From the Department of Medical Genome Science, School of Frontier Sciences, and
| | | | - ツ森ー菅井睦美 二
- From the Department of Medical Genome Science, School of Frontier Sciences, and
| | - Jose M M Caaveiro
- From the Department of Medical Genome Science, School of Frontier Sciences, and; The Institute of Medical Science, The University of Tokyo, Kashiwa 277-8562 and
| | - Kouhei Tsumoto
- From the Department of Medical Genome Science, School of Frontier Sciences, and; The Institute of Medical Science, The University of Tokyo, Kashiwa 277-8562 and.
| | - 本浩平 津
- From the Department of Medical Genome Science, School of Frontier Sciences, and; The Institute of Medical Science, The University of Tokyo, Kashiwa 277-8562 and
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