1
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Imamura K, Akagi KI, Miyanoiri Y, Tsujimoto H, Hirokawa T, Ashida H, Murakami K, Inoue A, Suno R, Ikegami T, Sekiyama N, Iwata S, Kobayashi T, Tochio H. Interaction modes of human orexin 2 receptor with selective and nonselective antagonists studied by NMR spectroscopy. Structure 2024; 32:352-361.e5. [PMID: 38194963 DOI: 10.1016/j.str.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 08/17/2023] [Accepted: 12/13/2023] [Indexed: 01/11/2024]
Abstract
Orexin neuropeptides have many physiological roles in the sleep-wake cycle, feeding behavior, reward demands, and stress responses by activating cognitive receptors, the orexin receptors (OX1R and OX2R), distributed in the brain. There are only subtle differences between OX1R and OX2R in the orthosteric site, which has hindered the rational development of subtype-selective antagonists. In this study, we utilized solution-state NMR to capture the structural plasticity of OX2R labeled with 13CH3-ε-methionine in complex with antagonists. Mutations in the orthosteric site allosterically affected the intracellular tip of TM6. Ligand exchange experiments with the subtype-selective EMPA and the nonselective suvorexant identified three methionine residues that were substantially perturbed. The NMR spectra suggested that the suvorexant-bound state exhibited more structural plasticity than the EMPA-bound state, which has not been foreseen from the close similarity of their crystal structures, providing insights into dynamic features to be considered in understanding the ligand recognition mode.
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Affiliation(s)
- Kayo Imamura
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ken-Ichi Akagi
- Section of Laboratory Equipment, National Institute of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hirokazu Tsujimoto
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takatsugu Hirokawa
- Division of Biomedical Science, Faculty of Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Hideo Ashida
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kaori Murakami
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ryoji Suno
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Takahisa Ikegami
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - So Iwata
- Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Hirakata 573-1010, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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2
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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3
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Hou XN, Sekiyama N, Ohtani Y, Yang F, Miyanoiri Y, Akagi KI, Su XC, Tochio H. Conformational Space Sampled by Domain Reorientation of Linear Diubiquitin Reflected in Its Binding Mode for Target Proteins. Chemphyschem 2021; 22:1505-1517. [PMID: 33928740 DOI: 10.1002/cphc.202100187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Indexed: 11/06/2022]
Abstract
Linear polyubiquitin chains regulate diverse signaling proteins, in which the chains adopt various conformations to recognize different target proteins. Thus, the structural plasticity of the chains plays an important role in controlling the binding events. Herein, paramagnetic NMR spectroscopy is employed to explore the conformational space sampled by linear diubiquitin, a minimal unit of linear polyubiquitin, in its free state. Rigorous analysis of the data suggests that, regarding the relative positions of the ubiquitin units, particular regions of conformational space are preferentially sampled by the molecule. By combining these results with further data collected for charge-reversal derivatives of linear diubiquitin, structural insights into the factors underlying the binding events of linear diubiquitin are obtained.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Naotaka Sekiyama
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yasuko Ohtani
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Feng Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Yohei Miyanoiri
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ken-Ichi Akagi
- NIBIOHN, Section of Laboratory Equipment, Osaka, 567-0085, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, No.94 Weijin Road, Nankai District, Tianjin, 300071, P. R. China
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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4
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Igarashi R, Sugi T, Sotoma S, Genjo T, Kumiya Y, Walinda E, Ueno H, Ikeda K, Sumiya H, Tochio H, Yoshinari Y, Harada Y, Shirakawa M. Tracking the 3D Rotational Dynamics in Nanoscopic Biological Systems. J Am Chem Soc 2020; 142:7542-7554. [DOI: 10.1021/jacs.0c01191] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ryuji Igarashi
- Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- National Institute for Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1,
Inage-ku, Chiba 263-8555, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Takuma Sugi
- Division of Integrated Sciences for Life, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Shingo Sotoma
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
- Institute for Protein Research (IPR), Osaka University, 3-2 Yamadaoka,
Suita-shi, Osaka 565-0871, Japan
| | - Takuya Genjo
- Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Yuta Kumiya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Hiroshi Ueno
- Department of Applied Chemistry, Graduate School of Engineering, University of Tokyo, Tokyo 113-8656, Japan
| | - Kazuhiro Ikeda
- Advanced Materials Laboratory, Sumitomo Electric Industries, Ltd., 1-1-1, Koyakita, Itami, Hyogo 664-0016, Japan
| | - Hitoshi Sumiya
- Advanced Materials Laboratory, Sumitomo Electric Industries, Ltd., 1-1-1, Koyakita, Itami, Hyogo 664-0016, Japan
| | - Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502, Japan
| | - Yohsuke Yoshinari
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshie Harada
- Institute for Protein Research (IPR), Osaka University, 3-2 Yamadaoka,
Suita-shi, Osaka 565-0871, Japan
- Center for Quantum Information and Quantum Biology, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka 565-0871, Japan
| | - Masahiro Shirakawa
- Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba 263-8555, Japan
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-Ku, Kyoto 615-8510, Japan
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5
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Fujita H, Tokunaga A, Shimizu S, Whiting AL, Aguilar-Alonso F, Takagi K, Walinda E, Sasaki Y, Shimokawa T, Mizushima T, Ohki I, Ariyoshi M, Tochio H, Bernal F, Shirakawa M, Iwai K. Cooperative Domain Formation by Homologous Motifs in HOIL-1L and SHARPIN Plays A Crucial Role in LUBAC Stabilization. Cell Rep 2019; 23:1192-1204. [PMID: 29694895 PMCID: PMC6044281 DOI: 10.1016/j.celrep.2018.03.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/19/2018] [Accepted: 03/25/2018] [Indexed: 01/06/2023] Open
Abstract
The linear ubiquitin chain assembly complex (LUBAC) participates in inflammatory and oncogenic signaling by conjugating linear ubiquitin chains to target proteins. LUBAC consists of the catalytic HOIP subunit and two accessory subunits, HOIL-1L and SHARPIN. Interactions between the ubiquitin-associated (UBA) domains of HOIP and the ubiquitin-like (UBL) domains of two accessory subunits are involved in LUBAC stabilization, but the precise molecular mechanisms underlying the formation of stable trimeric LUBAC remain elusive. We solved the co-crystal structure of the binding regions of the trimeric LUBAC complex and found that LUBAC-tethering motifs (LTMs) located N terminally to the UBL domains of HOIL-1L and SHARPIN heterodimerize and fold into a single globular domain. This interaction is resistant to dissociation and plays a critical role in stabilizing trimeric LUBAC. Inhibition of LTM-mediated HOIL-1L/SHARPIN dimerization profoundly attenuated the function of LUBAC, suggesting LTM as a superior target of LUBAC destabilization for anticancer therapeutics. Fujita et al. report a crystal structure of the trimeric LUBAC core and show that motifs in HOIL-1L and SHARPIN fold into a single domain critical for LUBAC stabilization. The authors also develop an inhibitor of this interaction that destabilizes LUBAC and kills cancer cells.
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Affiliation(s)
- Hiroaki Fujita
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto 606-8501, Japan
| | - Akira Tokunaga
- Department of Molecular Engineering, Kyoto University School of Engineering, Kyoto 615-8510, Japan
| | - Satoshi Shimizu
- Department of Anesthesia, Kyoto University Hospital, Kyoto 606-8507, Japan
| | - Amanda L Whiting
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Francisco Aguilar-Alonso
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kenji Takagi
- Department of Picobiology, University of Hyogo School of Life Science, Hyogo 678-1297, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto 606-8501, Japan
| | - Yoshiteru Sasaki
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto 606-8501, Japan
| | - Taketo Shimokawa
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto 606-8501, Japan
| | - Tsunehiro Mizushima
- Department of Picobiology, University of Hyogo School of Life Science, Hyogo 678-1297, Japan
| | - Izuru Ohki
- Department of Molecular Engineering, Kyoto University School of Engineering, Kyoto 615-8510, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Kyoto University School of Engineering, Kyoto 615-8510, Japan
| | - Hidehito Tochio
- Department of Biophysics, Kyoto University School of Science, Kyoto 606-8502, Japan
| | - Federico Bernal
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Kyoto University School of Engineering, Kyoto 615-8510, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto 606-8501, Japan.
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6
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Polat OK, Uno M, Maruyama T, Tran HN, Imamura K, Wong CF, Sakaguchi R, Ariyoshi M, Itsuki K, Ichikawa J, Morii T, Shirakawa M, Inoue R, Asanuma K, Reiser J, Tochio H, Mori Y, Mori MX. Contribution of Coiled-Coil Assembly to Ca 2+/Calmodulin-Dependent Inactivation of TRPC6 Channel and its Impacts on FSGS-Associated Phenotypes. J Am Soc Nephrol 2019; 30:1587-1603. [PMID: 31266820 DOI: 10.1681/asn.2018070756] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 04/23/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND TRPC6 is a nonselective cation channel, and mutations of this gene are associated with FSGS. These mutations are associated with TRPC6 current amplitude amplification and/or delay of the channel inactivation (gain-of-function phenotype). However, the mechanism of the gain-of-function in TRPC6 activity has not yet been clearly solved. METHODS We performed electrophysiologic, biochemical, and biophysical experiments to elucidate the molecular mechanism underlying calmodulin (CaM)-mediated Ca2+-dependent inactivation (CDI) of TRPC6. To address the pathophysiologic contribution of CDI, we assessed the actin filament organization in cultured mouse podocytes. RESULTS Both lobes of CaM helped induce CDI. Moreover, CaM binding to the TRPC6 CaM-binding domain (CBD) was Ca2+-dependent and exhibited a 1:2 (CaM/CBD) stoichiometry. The TRPC6 coiled-coil assembly, which brought two CBDs into adequate proximity, was essential for CDI. Deletion of the coiled-coil slowed CDI of TRPC6, indicating that the coiled-coil assembly configures both lobes of CaM binding on two CBDs to induce normal CDI. The FSGS-associated TRPC6 mutations within the coiled-coil severely delayed CDI and often increased TRPC6 current amplitudes. In cultured mouse podocytes, FSGS-associated channels and CaM mutations led to sustained Ca2+ elevations and a disorganized cytoskeleton. CONCLUSIONS The gain-of-function mechanism found in FSGS-causing mutations in TRPC6 can be explained by impairments of the CDI, caused by disruptions of TRPC's coiled-coil assembly which is essential for CaM binding. The resulting excess Ca2+ may contribute to structural damage in the podocytes.
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Affiliation(s)
- Onur K Polat
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Masatoshi Uno
- Department of Biophysics, Graduate School of Science.,Department of Molecular Engineering, Graduate School of Engineering
| | - Terukazu Maruyama
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Ha Nam Tran
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Department of Technology and Ecology, Laboratory of Environmental Systems Biology, Graduate School of Global Environmental Studies
| | - Kayo Imamura
- Department of Biophysics, Graduate School of Science
| | - Chee Fah Wong
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, Perak, Malaysia
| | - Reiko Sakaguchi
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering.,Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Graduate School of Engineering
| | - Kyohei Itsuki
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Jun Ichikawa
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | | | - Ryuji Inoue
- Department of Physiology, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Katsuhiko Asanuma
- Department of Nephrology, School of Medicine, Chiba University, Chiba, Japan
| | - Jochen Reiser
- Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois
| | | | - Yasuo Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering
| | - Masayuki X Mori
- Laboratory of Molecular Biology, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering,
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7
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Uno M, Watanabe-Nakayama T, Konno H, Akagi KI, Tsutsumi N, Fukao T, Shirakawa M, Ohnishi H, Tochio H. Intramolecular interaction suggests an autosuppression mechanism for the innate immune adaptor protein MyD88. Chem Commun (Camb) 2018; 54:12318-12321. [DOI: 10.1039/c8cc06480f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An autosupression of MyD88 is regulated by the intramolecular interaction between TIRMyD88 and DDMyD88.
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Affiliation(s)
- Masatoshi Uno
- Department of Biophysics
- Kyoto University
- Kyoto
- Japan
- Department of Molecular Engineering
| | | | - Hiroki Konno
- Nano Life Science Institute (WPI NanoLSI)
- Kanazawa University
- Kanazawa
- Japan
| | | | - Naotaka Tsutsumi
- Department of Biophysics
- Kyoto University
- Kyoto
- Japan
- Department of Molecular Engineering
| | - Toshiyuki Fukao
- Department of Pediatrics
- Graduate School of Medicine
- Gifu University
- Gifu
- Japan
| | | | - Hidenori Ohnishi
- Department of Pediatrics
- Graduate School of Medicine
- Gifu University
- Gifu
- Japan
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8
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Higashino T, Nakatsuji H, Fukuda R, Okamoto H, Imai H, Matsuda T, Tochio H, Shirakawa M, Tkachenko NV, Hashida M, Murakami T, Imahori H. Cover Picture: Hexaphyrin as a Potential Theranostic Dye for Photothermal Therapy and 19
F Magnetic Resonance Imaging (ChemBioChem 10/2017). Chembiochem 2017. [DOI: 10.1002/cbic.201700217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tomohiro Higashino
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Nishikyo-ku Kyoto 615-8510 Japan
| | - Hirotaka Nakatsuji
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Nishikyo-ku Kyoto 615-8510 Japan
| | - Ryosuke Fukuda
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Nishikyo-ku Kyoto 615-8510 Japan
| | - Haruki Okamoto
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Sakyo-ku Kyoto 615-8510 Japan
| | - Hirohiko Imai
- Department of Systems Science; Graduate School of Informatics; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Tetsuya Matsuda
- Department of Systems Science; Graduate School of Informatics; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Hidehito Tochio
- Department of Biophysics; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Nishikyo-ku Kyoto 615-8510 Japan
| | - Nikolai V. Tkachenko
- Department of Chemistry and Bioengineering; Tampere University of Technology; P. O. Box 541 33101 Tampere Finland
| | - Mitsuru Hashida
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Sakyo-ku Kyoto 615-8510 Japan
- Department of Drug Delivery Research; Graduate School of Pharmaceutical Sciences; Kyoto University; Sakyo-ku Kyoto 606-8501 Japan
| | - Tatsuya Murakami
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Sakyo-ku Kyoto 615-8510 Japan
- Current address: Department of Biotechnology; Faculty of Engineering; Toyama Prefectural University; 5180 Kurokawa Imizu Toyama 939-0398 Japan
| | - Hiroshi Imahori
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Nishikyo-ku Kyoto 615-8510 Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS); Kyoto University; Sakyo-ku Kyoto 615-8510 Japan
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9
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Hirasaka K, Mills EM, Haruna M, Bando A, Ikeda C, Abe T, Kohno S, Nowinski SM, Lago CU, Akagi KI, Tochio H, Ohno A, Teshima-Kondo S, Okumura Y, Nikawa T. UCP3 is associated with Hax-1 in mitochondria in the presence of calcium ion. Biochem Biophys Res Commun 2016; 472:108-13. [PMID: 26915802 DOI: 10.1016/j.bbrc.2016.02.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/18/2016] [Indexed: 10/22/2022]
Abstract
Uncoupling protein 3 (UCP3) is known to regulate energy dissipation, proton leakage, fatty acid oxidation, and oxidative stress. To identify the putative protein regulators of UCP3, we performed yeast two-hybrid screens. Here we report that UCP3 interacted with HS-1 associated protein X-1 (Hax-1), an anti-apoptotic protein that was localized in the mitochondria, and is involved in cellular responses to Ca(2+). The hydrophilic sequences within loop 2, and the matrix-localized hydrophilic domain of mouse UCP3, were necessary for binding to Hax-1 at the C-terminal domain, adjacent to the mitochondrial inner membrane. Interestingly, interaction of these proteins occurred in a calcium-dependent manner. Moreover, the NMR spectrum of the C-terminal domain of Hax-1 was dramatically changed by removal of Ca(2+), suggesting that the C-terminal domain of Hax-1 underwent a Ca(2+)-induced conformational change. In the Ca(2+)-free state, the C-terminal Hax-1 tended to unfold, suggesting that Ca(2+) binding may induce protein folding of the Hax-1 C-terminus. These results suggested that the UCP3-Hax-1 complex may regulate mitochondrial functional changes caused by mitochondrial Ca(2+).
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Affiliation(s)
- Katsuya Hirasaka
- Graduate School of Fisheries and Environmental Sciences, Nagasaki University, Nagasaki, Japan; Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan.
| | - Edward M Mills
- Division of Pharmacology/Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Marie Haruna
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Aki Bando
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Chika Ikeda
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Tomoki Abe
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Shohei Kohno
- Division of Pharmacology/Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Sara M Nowinski
- Division of Pharmacology/Toxicology, University of Texas at Austin, Austin, TX, USA
| | - Cory U Lago
- Translational Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ken-Ichi Akagi
- Section of Laboratory Equipment, National Institute of Biomedical Innovation, Osaka, Japan
| | - Hidehito Tochio
- Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Ayako Ohno
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Shigetada Teshima-Kondo
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
| | - Yuushi Okumura
- Department of Nutrition and Health, Sagami Woman's University, Kanagawa, Japan
| | - Takeshi Nikawa
- Department of Nutritional Physiology, Institute of Health Biosciences, University of Tokushima, Tokushima, Japan
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10
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Tsuchiya M, Isogai S, Taniguchi H, Tochio H, Shirakawa M, Morohashi KI, Hiraoka Y, Haraguchi T, Ogawa H. Selective autophagic receptor p62 regulates the abundance of transcriptional coregulator ARIP4 during nutrient starvation. Sci Rep 2015; 5:14498. [PMID: 26412716 PMCID: PMC4585976 DOI: 10.1038/srep14498] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/01/2015] [Indexed: 12/13/2022] Open
Abstract
Transcriptional coregulators contribute to several processes involving nuclear receptor transcriptional regulation. The transcriptional coregulator androgen receptor-interacting protein 4 (ARIP4) interacts with nuclear receptors and regulates their transcriptional activity. In this study, we identified p62 as a major interacting protein partner for ARIP4 in the nucleus. Nuclear magnetic resonance analysis demonstrated that ARIP4 interacts directly with the ubiquitin-associated (UBA) domain of p62. ARIP4 and ubiquitin both bind to similar amino acid residues within UBA domains; therefore, these proteins may possess a similar surface structure at their UBA-binding interfaces. We also found that p62 is required for the regulation of ARIP4 protein levels under nutrient starvation conditions. We propose that p62 is a novel binding partner for ARIP4, and that its binding regulates the cellular protein level of ARIP4 under conditions of metabolic stress.
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Affiliation(s)
- Megumi Tsuchiya
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan
| | - Shin Isogai
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroaki Taniguchi
- Laboratory for Genetic Code, Graduate School of Life and Medical Sciences, Doshisha University, 1-3 Tatara Miyakodani, Kyotanabe 610-0394, Japan
| | - Hidehito Tochio
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | | | - Ken-Ichirou Morohashi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita 565-0871, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
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11
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Tochio H, Murayama S, Inomata K, Morimoto D, Ohno A, Shirakawa M. [Non-invasive analysis of proteins in living cells using NMR spectroscopy]. YAKUGAKU ZASSHI 2015; 135:391-8. [PMID: 25759048 DOI: 10.1248/yakushi.14-00240-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
NMR spectroscopy enables structural analyses of proteins and has been widely used in the structural biology field in recent decades. NMR spectroscopy can be applied to proteins inside living cells, allowing characterization of their structures and dynamics in intracellular environments. The simplest "in-cell NMR" approach employs bacterial cells; in this approach, live Escherichia coli cells overexpressing a specific protein are subjected to NMR. The cells are grown in an NMR active isotope-enriched medium to ensure that the overexpressed proteins are labeled with the stable isotopes. Thus the obtained NMR spectra, which are derived from labeled proteins, contain atomic-level information about the structure and dynamics of the proteins. Recent progress enables us to work with higher eukaryotic cells such as HeLa and HEK293 cells, for which a number of techniques have been developed to achieve isotope labeling of the specific target protein. In this review, we describe successful use of electroporation for in-cell NMR. In addition, (19)F-NMR to characterize protein-ligand interactions in cells is presented. Because (19)F nuclei rarely exist in natural cells, when (19)F-labeled proteins are delivered into cells and (19)F-NMR signals are observed, one can safely ascertain that these signals originate from the delivered proteins and not other molecules.
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Affiliation(s)
- Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
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12
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Sotoma S, Igarashi R, Iimura J, Kumiya Y, Tochio H, Harada Y, Shirakawa M. Suppression of Nonspecific Protein–Nanodiamond Adsorption Enabling Specific Targeting of Nanodiamonds to Biomolecules of Interest. CHEM LETT 2015. [DOI: 10.1246/cl.141036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Shingo Sotoma
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
| | - Ryuji Igarashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
| | - Jun Iimura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
| | - Yuta Kumiya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University
| | - Yoshie Harada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
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13
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Yoshinari Y, Mori S, Igarashi R, Sugi T, Yokota H, Ikeda K, Sumiya H, Mori I, Tochio H, Harada Y, Shirakawa M. Optically Detected Magnetic Resonance of Nanodiamonds In Vivo; Implementation of Selective Imaging and Fast Sampling. J Nanosci Nanotechnol 2015; 15:1014-1021. [PMID: 26353607 DOI: 10.1166/jnn.2015.9739] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Single-molecule fluorescence measurements of biological samples frequently suffer from background autofluorescence originating from fluorescent materials pre-existing in living samples, and from unstable photo-physical properties of fluorescent labeling molecules. In this study, we first describe our method of selective imaging of nanodiamonds containing nitrogen-vacancy centers, promising fluorescent color centers, by a combination of optically detected magnetic resonance. The resultant images exhibit perfect elimination of extraneous fluorescence in real-time microscope observations. As the practical example applied to an in vivo system, we measured the resonance spectrum of nanodiamonds introduced into the intestine of Caenorhabditis elegans in the clear background and compared the spectral profile over time. The observed evolution strongly suggests that the rotation of the nanodiamond was detected. We also report our recent progress in the development of a spectrometer equipped with an avalanche photo-diode for fast sampling of photons, which can be used while observing the selective image of a field of view in a real-time manner. This apparatus is suitable for exploring dynamics through the measurement of fluctuation in fluorescence intensity caused by a rotating nanodiamond.
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14
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Yamada H, Hasegawa Y, Imai H, Takayama Y, Sugihara F, Matsuda T, Tochio H, Shirakawa M, Sando S, Kimura Y, Toshimitsu A, Aoyama Y, Kondo T. Magnetic Resonance Imaging of Tumor with a Self-Traceable Phosphorylcholine Polymer. J Am Chem Soc 2015; 137:799-806. [DOI: 10.1021/ja510479v] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hisatsugu Yamada
- Advanced
Biomedical Engineering Research Unit, Center for the Promotion of
Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
| | - Yoshinori Hasegawa
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hirohiko Imai
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yuki Takayama
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Fuminori Sugihara
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tetsuya Matsuda
- Department
of Systems Science, Graduate School of Informatics, Kyoto University, Yoshida-honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hidehito Tochio
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Masahiro Shirakawa
- Department
of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shinsuke Sando
- Department of Chemistry & Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Kimura
- Research
and Educational Unit of Leaders for Integrated Medical System, Center
for the Promotion of Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Akio Toshimitsu
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Division
of Multidisciplinary Chemistry, Institute for Chemical Research, Kyoto University, Gokanosho, Uji, Kyoto 611-0011, Japan
| | - Yasuhiro Aoyama
- Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
| | - Teruyuki Kondo
- Advanced
Biomedical Engineering Research Unit, Center for the Promotion of
Interdisciplinary Education and Research, Kyoto University, Katsura, Nishikyo-ku,
Kyoto 615-8510, Japan
- Department
of Energy and Hydrocarbon Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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15
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Sotoma S, Akagi K, Hosokawa S, Igarashi R, Tochio H, Harada Y, Shirakawa M. Comprehensive and quantitative analysis for controlling the physical/chemical states and particle properties of nanodiamonds for biological applications. RSC Adv 2015. [DOI: 10.1039/c4ra16482b] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The physical/chemical states and properties of nanodiamonds subjected to thermal annealing and air oxidation, which are indispensable processes for the preparation of fluorescent nanodiamonds, were investigated.
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Affiliation(s)
- S. Sotoma
- Department of Molecular Engineering
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - K. Akagi
- Section of Laboratory Equipment
- National Institute of Biomedical Innovation
- Osaka
- Japan
| | - S. Hosokawa
- Department of Molecular Engineering
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - R. Igarashi
- Department of Molecular Engineering
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
| | - H. Tochio
- Department of Biophysics
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502
- Japan
| | - Y. Harada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - M. Shirakawa
- Department of Molecular Engineering
- Graduate School of Engineering
- Kyoto University
- Kyoto 615-8510
- Japan
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16
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Tsutsumi N, Kimura T, Arita K, Ariyoshi M, Ohnishi H, Yamamoto T, Zuo X, Maenaka K, Park EY, Kondo N, Shirakawa M, Tochio H, Kato Z. The structural basis for receptor recognition of human interleukin-18. Nat Commun 2014; 5:5340. [PMID: 25500532 PMCID: PMC4275594 DOI: 10.1038/ncomms6340] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/20/2014] [Indexed: 12/25/2022] Open
Abstract
Interleukin (IL)-18 is a proinflammatory cytokine that belongs to the IL-1 family and plays an important role in inflammation. The uncontrolled release of this cytokine is associated with severe chronic inflammatory disease. IL-18 forms a signalling complex with the IL-18 receptor α (Rα) and β (Rβ) chains at the plasma membrane, which induces multiple inflammatory cytokines. Here, we present a crystal structure of human IL-18 bound to the two receptor extracellular domains. Generally, the receptors' recognition mode for IL-18 is similar to IL-1β; however, certain notable differences were observed. The architecture of the IL-18 receptor second domain (D2) is unique among the other IL-1R family members, which presumably distinguishes them from the IL-1 receptors that exhibit a more promiscuous ligand recognition mode. The structures and associated biochemical and cellular data should aid in developing novel drugs to neutralize IL-18 activity.
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Affiliation(s)
- Naotaka Tsutsumi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Kimura
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Kyohei Arita
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama Kanagawa 230-0045, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Takahiro Yamamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Xiaobing Zuo
- X-Ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, USA
| | - Katsumi Maenaka
- Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, , Kita-12, Nishi-6, Kita-ki, Sapporo 060-0812, Japan
| | - Enoch Y. Park
- Research Institute of Green Science and Technology, Department of Bioscience, Graduate school of Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
- Heisei College of Health Sciences, 180 Kurono, Gifu 501-1131, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
- Core Research of Evolution Science (CREST), Japan Sciences and Technology Agency, Tokyo 102-0076, Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8502, Japan
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
- Biomedical Informatics, Medical Information Sciences Division, The United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu 501-1194, Japan
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17
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Kimura T, Tsutsumi N, Arita K, Ariyoshi M, Ohnishi H, Kondo N, Shirakawa M, Kato Z, Tochio H. Purification, crystallization and preliminary X-ray crystallographic analysis of human IL-18 and its extracellular complexes. Acta Crystallogr F Struct Biol Commun 2014; 70:1351-6. [PMID: 25286938 DOI: 10.1107/s2053230x14016926] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 07/22/2014] [Indexed: 01/21/2023]
Abstract
Interleukin-18 (IL-18), a pro-inflammatory cytokine belonging to the interleukin-1 (IL-1) family, is involved in the pathogenesis of autoimmune/autoinflammatory and allergic diseases such as juvenile idiopathic arthritis and bronchial asthma. IL-18 forms a signalling complex with the IL-18 receptor α (IL-18Rα) and β (IL-18Rβ) chains; however, the detailed activation mechanism remains unclear. Here, the IL-18-IL-18Rα binary and IL-18-IL-18Rα-IL-18Rβ ternary complexes were purified and crystallized as well as IL-18 alone. An X-ray diffraction data set for IL-18 was collected to 2.33 Å resolution from a crystal belonging to space group P21, with unit-cell parameters a = 68.15, b = 79.51, c = 73.46 Å, β = 100.97°. Crystals of both the IL-18 binary and ternary complexes belonging to the orthorhombic space groups P21212 and P212121, respectively, diffracted to 3.10 Å resolution. Unit-cell parameters were determined as a = 135.49, b = 174.81, c = 183.40 Å for the binary complex and a = 72.56, b = 111.56, c = 134.57 Å for the ternary complex.
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Affiliation(s)
- Takeshi Kimura
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Naotaka Tsutsumi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho,Tsurumi-ku, Yokohama, Japan
| | - Mariko Ariyoshi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
| | - Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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18
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Arita K, Ariyoshi M, Sugita K, Tochio H, Shirakawa M. Structure study of UHRF1, recoginition of epigenetic marks. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314084095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Two major epigenetic traits, histone modifications and DNA methylation, regulate various chromatin-template processes in mammals. The pattern of these epigenetic traits is cooperatively established in early embryogenesis and cell development, and inherited during the cell cycle. UHRF1 (also known as Np95 or ICBP90) is believed to play an important role in linking the two major epigenetic traits. UHRF1 has five functional domains, UBL, Tandem Tudor (TTD), pland homeo domain (PHD), SET and RING-associated doain (SRA) and RING finger. To maintain DNA methylation pattern, UHRF1 recognizes hemi-methylated DNA generated during DNA replication through interactions with its SRA domain, and recruit maintenance of DNA methyltransferase Dnmt1 to the site [1], [2]. UHRF1 also recognizes histone H3 containing tri-methylated Lys9 (H3K9me3) via its TTD-PHD moiety. [3]. To obtain the structural basis for recognition of epigenetic marks by UHRF1, we determined the crystal structure of the SRA domain in complex with hemi-methylated DNA. The structure showed that the DNA binding caused a loop and an N-terminal tail of the SRA domain. Interestingly, the methyl-cytosine base at the hemi-methylation site was flipped out from the DNA helix, which has not observed in other DNA binding proteins. These results suggest that the Base flip out mechanism is important event for maintenance of DNA methylation. We also determined the crystal structure of TTD-PHD region of UHRF1 in complex with H3K9me3 peptide. To our surprise, the linker region between the reader modules, which is predicted as an intrinsically disorder, was formed a stable structure with binding to the groove of TTD and plays an essential role in the formation of histone H3 binding hole between the reader modules. The structure revealed how multiple histone modifications were simultaneously decoded by the linked histone reader modules of UHRF1.
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19
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Tsutsumi N, Kimura T, Arita K, Ariyoshi M, Ohnishi H, Yamamoto T, Zuo X, Kondo N, Shirakawa M, Kato Z, Tochio H. Crystal structure of the extracellular signaling complex of interleukin-18. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314097423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Interleukin (IL)-18 [1], a proinflammatory cytokine belonging to the IL-1 superfamily, plays important roles in both innate and adaptive immune system, which is involved in not only the function of host defense mechanism but also allergic reactions. IL-18 is secreted by various types of cells and strongly augments the production of interferon-γ. IL-18 is synthesized as a biologically inactive precursor (proIL-18), which is matured by the action of caspase-1 in the cell upon stimulation. The matured IL-18 is subsequently secreted extracellularly and binds to IL-18 receptor α (Rα) and IL-18 receptor β (Rβ) in a stepwise manner, forming the IL-18/Rα/Rβ ternary complex. The complex initiates the signaling that finally activates NF-κB via the MyD88 dependent pathway [2]. Here, we show the crystal structure of IL-18 (Fig a), the IL-18/Rα binary complex (Fig b) and the IL-18/Rα/Rβ signaling ternary complex (Fig c, d) at 2.33, 3.10 and 3.10 Å resolution, respectively. Overall, the recognition manner of IL-18 by the receptors was similar to that of IL-1β [3], although some remarkable differences such as the orientation of Ig-like domains of IL-18Rβ were revealed. We also demonstrate that carbohydrate chains on IL-18Rα contributes to the recognition of IL-18. Biochemical experiments based on the structure identify amino acid residues that are important in forming the ternary complex and the signal transduction. Our results not only show the common extracellular signaling architecture of IL-1 family cytokines but also unveil unique recognition mechanism of IL-18 with the detailed atomic structures. The structure of the signaling ternary complex of IL-18 would contribute to both understanding the pathogeneses of the IL-18 related diseases and designing new efficient therapeutic agents.
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20
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Tochio H, Sotoma S, Harada Y. [Application of nitrogen-vacancy centers of diamonds to biological imaging]. Seikagaku 2014; 86:145-153. [PMID: 24864440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
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21
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Walinda E, Morimoto D, Sugase K, Konuma T, Tochio H, Shirakawa M. Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin. J Biol Chem 2014; 289:13890-902. [PMID: 24692539 DOI: 10.1074/jbc.m114.555441] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
NBR1 (neighbor of BRCA1 gene 1) is a protein commonly found in ubiquitin-positive inclusions in neurodegenerative diseases. Due to its high architectural similarity to the well studied autophagy receptor protein p62/SQSTM1, NBR1 has been thought to analogously bind to ubiquitin-marked autophagic substrates via its C-terminal ubiquitin-associated (UBA) domain and deliver them to autophagosomes for degradation. Unexpectedly, we find that NBR1 differs from p62 in its UBA structure and accordingly in its interaction with ubiquitin. Structural differences are observed on helix α-3, which is tilted farther from helix α-2 and extended by approximately one turn in NBR1. This results not only in inhibition of a p62-type self-dimerization of NBR1 UBA but also in a significantly higher affinity for monoubiquitin as compared with p62 UBA. Importantly, the NBR1 UBA-ubiquitin complex structure shows that the negative charge of the side chain in front of the conserved MGF motif in the UBA plays an integral role in the recognition of ubiquitin. In addition, NMR and isothermal titration calorimetry experiments show that NBR1 UBA binds to each monomeric unit of polyubiquitin with similar affinity and by the same surface used for binding to monoubiquitin. This indicates that NBR1 lacks polyubiquitin linkage-type specificity, in good agreement with the nonspecific linkages observed in intracellular ubiquitin-positive inclusions. Consequently, our results demonstrate that the structural differences between NBR1 UBA and p62 UBA result in a much higher affinity of NBR1 for ubiquitin, which in turn suggests that NBR1 may form intracellular inclusions with ubiquitylated autophagic substrates more efficiently than p62.
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Affiliation(s)
- Erik Walinda
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Daichi Morimoto
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Kenji Sugase
- the Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
| | - Tsuyoshi Konuma
- the Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
| | - Hidehito Tochio
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Masahiro Shirakawa
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
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22
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Danielsson J, Inomata K, Murayama S, Tochio H, Lang L, Shirakawa M, Oliveberg M. Pruning the ALS-associated protein SOD1 for in-cell NMR. J Am Chem Soc 2013; 135:10266-9. [PMID: 23819500 DOI: 10.1021/ja404425r] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
To efficiently deliver isotope-labeled proteins into mammalian cells poses a main challenge for structural and functional analysis by in-cell NMR. In this study we have employed cell-penetrating peptides (CPPs) to deliver the ALS-associated protein superoxide dismutase (SOD1) into HeLa cells. Our results show that, although full-length SOD1 cannot be efficiently internalized, a variant in which the active-site loops IV and VII have been truncated (SOD1(ΔIVΔVII)) yields high cytosolic delivery. The reason for the enhanced delivery of SOD1(ΔIVΔVII) seems to be the elimination of negatively charged side chains, which alters the net charge of the CPP-SOD1 complex from neutral to +4. The internalized SOD1(ΔIVΔVII) protein displays high-resolution in-cell NMR spectra similar to, but not identical to, those of the lysate of the cells. Spectral differences are found mainly in the dynamic β strands 4, 5, and 7, triggered by partial protonation of the His moieties of the Cu-binding site. Accordingly, SOD1(ΔIVΔVII) doubles here as an internal pH probe, revealing cytosolic acidification under the experimental treatment. Taken together, these observations show that CPP delivery, albeit inefficient at first trials, can be tuned by protein engineering to allow atomic-resolution NMR studies of specific protein structures that have evaded other in-cell NMR approaches: in this case, the structurally elusive apoSOD1 barrel implicated as precursor for misfolding in ALS.
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Affiliation(s)
- Jens Danielsson
- Department of Biochemistry and Biophysics, Arrhenius Laboratories of Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden
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23
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Takaoka Y, Kioi Y, Morito A, Otani J, Arita K, Ashihara E, Ariyoshi M, Tochio H, Shirakawa M, Hamachi I. Quantitative comparison of protein dynamics in live cells and in vitro by in-cell (19)F-NMR. Chem Commun (Camb) 2013; 49:2801-3. [PMID: 23440262 DOI: 10.1039/c3cc39205h] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we describe how a (19)F-probe incorporated into an endogenous protein by a chemical biology method revealed protein dynamics. By explicit determination of ligand-bound and unbound structures with X-ray crystallography, the quantitative comparison of the protein's dynamics in live cells and in vitro is presented. These results clearly demonstrated the greater conformational fluctuations of the intracellular protein, partially due to macromolecular crowding effects.
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Affiliation(s)
- Yousuke Takaoka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto, Japan
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24
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Muraoka T, Adachi K, Ui M, Kawasaki S, Sadhukhan N, Obara H, Tochio H, Shirakawa M, Kinbara K. Back Cover: A Structured Monodisperse PEG for the Effective Suppression of Protein Aggregation (Angew. Chem. Int. Ed. 9/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/anie.201300347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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25
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Muraoka T, Adachi K, Ui M, Kawasaki S, Sadhukhan N, Obara H, Tochio H, Shirakawa M, Kinbara K. Rücktitelbild: A Structured Monodisperse PEG for the Effective Suppression of Protein Aggregation (Angew. Chem. 9/2013). Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Muraoka T, Adachi K, Ui M, Kawasaki S, Sadhukhan N, Obara H, Tochio H, Shirakawa M, Kinbara K. A structured monodisperse PEG for the effective suppression of protein aggregation. Angew Chem Int Ed Engl 2013; 52:2430-4. [PMID: 23361965 DOI: 10.1002/anie.201206563] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Indexed: 11/09/2022]
Abstract
Part of the solution: A PEG with a discrete triangular structure exhibits hydrophilicity/hydrophobicity switching upon increasing temperatures, and suppresses the thermal aggregation of lysozyme to retain nearly 80 % of the enzymatic activity. CD and NMR spectroscopic studies revealed that, with the structured PEG, the higher-order structures of lysozyme persist at high temperature, and the native conformation is recovered after cooling.
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Affiliation(s)
- Takahiro Muraoka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Sendai, Japan
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27
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Muraoka T, Adachi K, Ui M, Kawasaki S, Sadhukhan N, Obara H, Tochio H, Shirakawa M, Kinbara K. A Structured Monodisperse PEG for the Effective Suppression of Protein Aggregation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201206563] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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28
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Abstract
Isotope-assisted multi-dimensional NMR spectroscopy can now be applied to proteins inside living cells. The technique, called in-cell NMR, aims to investigate the structures, interactions and dynamics of proteins under their native conditions, ideally at an atomic resolution. The application has begun with bacterial cells but has now expanded to mammalian cultured cells, such as HeLa cells. The importance of the realization of such 'in-mammalian cell' NMR should be stressed, as these are the cells most often employed in cell biology. Hence, a substantially wide range of application would be possible in the near future once the technique has been well developed.
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Affiliation(s)
- Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.
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29
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Igarashi R, Yoshinari Y, Yokota H, Sugi T, Sugihara F, Ikeda K, Sumiya H, Tsuji S, Mori I, Tochio H, Harada Y, Shirakawa M. Real-time background-free selective imaging of fluorescent nanodiamonds in vivo. Nano Lett 2012; 12:5726-5732. [PMID: 23066639 DOI: 10.1021/nl302979d] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent developments of imaging techniques have enabled fluorescence microscopy to investigate the localization and dynamics of intracellular substances of interest even at the single-molecule level. However, such sensitive detection is often hampered by autofluorescence arising from endogenous molecules. Those unwanted signals are generally reduced by utilizing differences in either wavelength or fluorescence lifetime; nevertheless, extraction of the signal of interest is often insufficient, particularly for in vivo imaging. Here, we describe a potential method for the selective imaging of nitrogen-vacancy centers (NVCs) in nanodiamonds. This method is based on the property of NVCs that the fluorescence intensity sensitively depends on the ground state spin configuration which can be regulated by electron spin magnetic resonance. Because the NVC fluorescence exhibits neither photobleaching nor photoblinking, this protocol allowed us to conduct long-term tracking of a single nanodiamond in both Caenorhabditis elegans and mice, with excellent imaging contrast even in the presence of strong background autofluorescence.
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Affiliation(s)
- Ryuji Igarashi
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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30
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Arita K, Isogai S, Oda T, Unoki M, Sugita K, Sekiyama N, Kuwata K, Hamamoto R, Tochio H, Sato M, Ariyoshi M, Shirakawa M. Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1. Proc Natl Acad Sci U S A 2012; 109:12950-5. [PMID: 22837395 PMCID: PMC3420164 DOI: 10.1073/pnas.1203701109] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Multiple covalent modifications on a histone tail are often recognized by linked histone reader modules. UHRF1 [ubiquitin-like, containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1], an essential factor for maintenance of DNA methylation, contains linked two-histone reader modules, a tandem Tudor domain and a PHD finger, tethered by a 17-aa linker, and has been implicated to link histone modifications and DNA methylation. Here, we present the crystal structure of the linked histone reader modules of UHRF1 in complex with the amino-terminal tail of histone H3. Our structural and biochemical data provide the basis for combinatorial readout of unmodified Arg-2 (H3-R2) and methylated Lys-9 (H3-K9) by the tandem tudor domain and the PHD finger. The structure reveals that the intermodule linker plays an essential role in the formation of a histone H3-binding hole between the reader modules by making extended contacts with the tandem tudor domain. The histone H3 tail fits into the hole by adopting a compact fold harboring a central helix, which allows both of the reader modules to simultaneously recognize the modification states at H3-R2 and H3-K9. Our data also suggest that phosphorylation of a linker residue can modulate the relative position of the reader modules, thereby altering the histone H3-binding mode. This finding implies that the linker region plays a role as a functional switch of UHRF1 involved in multiple regulatory pathways such as maintenance of DNA methylation and transcriptional repression.
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Affiliation(s)
- Kyohei Arita
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Shin Isogai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Takashi Oda
- Division of Macromolecular Crystallography, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
| | - Motoko Unoki
- Division of Epigenomics, Department of Molecular Genetics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Kazuya Sugita
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Naotaka Sekiyama
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Keiko Kuwata
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Ryuji Hamamoto
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Mamoru Sato
- Division of Macromolecular Crystallography, Graduate School of Nanobioscience, Yokohama City University, Yokohama 230-0045, Japan
| | - Mariko Ariyoshi
- Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto 606-8501, Japan; and
- Precursory Research for Embryonic Science and Technology (PREST) and
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
- Core Research of Evolution Science (CREST), Japan Sciences and Technology Agency, Tokyo 102-0076, Japan
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Ohnishi H, Tochio H, Kato Z, Kawamoto N, Kimura T, Kubota K, Yamamoto T, Funasaka T, Nakano H, Wong RW, Shirakawa M, Kondo N. TRAM is involved in IL-18 signaling and functions as a sorting adaptor for MyD88. PLoS One 2012; 7:e38423. [PMID: 22685567 PMCID: PMC3369926 DOI: 10.1371/journal.pone.0038423] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/09/2012] [Indexed: 01/07/2023] Open
Abstract
MyD88, a Toll/interleukin-1 receptor homology (TIR) domain-containing adaptor protein, mediates signals from the Toll-like receptors (TLR) or IL-1/IL-18 receptors to downstream kinases. In MyD88-dependent TLR4 signaling, the function of MyD88 is enhanced by another TIR domain-containing adaptor, Mal/TIRAP, which brings MyD88 to the plasma membrane and promotes its interaction with the cytosolic region of TLR4. Hence, Mal is recognized as the “sorting adaptor” for MyD88. In this study, a direct interaction between MyD88-TIR and another membrane-sorting adaptor, TRAM/TICAM-2, was demonstrated in vitro. Cell-based assays including RNA interference experiments and TRAM deficient mice revealed that the interplay between MyD88 and TRAM in cells is important in mediating IL-18 signal transduction. Live cell imaging further demonstrated the co-localized accumulation of MyD88 and TRAM in the membrane regions in HEK293 cells. These findings suggest that TRAM serves as the sorting adaptor for MyD88 in IL-18 signaling, which then facilitates the signal transduction. The binding sites for TRAM are located in the TIR domain of MyD88 and actually overlap with the binding sites for Mal. MyD88, the multifunctional signaling adaptor that works together with most of the TLR members and with the IL-1/IL-18 receptors, can interact with two distinct sorting adaptors, TRAM and Mal, in a conserved manner in a distinct context.
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MESH Headings
- Adaptor Proteins, Signal Transducing/chemistry
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Animals
- Binding Sites/genetics
- HEK293 Cells
- Humans
- Immunoprecipitation
- Interferon-gamma/metabolism
- Interleukin-12/pharmacology
- Interleukin-18/pharmacology
- Interleukin-18 Receptor beta Subunit/genetics
- Interleukin-18 Receptor beta Subunit/metabolism
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microscopy, Confocal
- Models, Molecular
- Mutation
- Myeloid Differentiation Factor 88/genetics
- Myeloid Differentiation Factor 88/metabolism
- Protein Binding
- Protein Structure, Tertiary
- RNA Interference
- Receptors, Interleukin-1/genetics
- Receptors, Interleukin-1/metabolism
- Receptors, Interleukin-18/metabolism
- Signal Transduction
- Th1 Cells/drug effects
- Th1 Cells/metabolism
- Toll-Like Receptor 4/metabolism
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Affiliation(s)
- Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
- * E-mail: (HO); (HT)
| | - Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
- * E-mail: (HO); (HT)
| | - Zenichiro Kato
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Norio Kawamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takeshi Kimura
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Kazuo Kubota
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Takahiro Yamamoto
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Tatsuyoshi Funasaka
- Laboratory of Molecular and Cellular Biology, Department of Biology, School of Natural System, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Hiroshi Nakano
- Laboratory of Molecular and Cellular Biology, Department of Biology, School of Natural System, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Richard W. Wong
- Laboratory of Molecular and Cellular Biology, Department of Biology, School of Natural System, Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Naomi Kondo
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
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32
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Nada M, Ohnishi H, Tochio H, Kato Z, Kimura T, Kubota K, Yamamoto T, Kamatari YO, Tsutsumi N, Shirakawa M, Kondo N. Molecular analysis of the binding mode of Toll/interleukin-1 receptor (TIR) domain proteins during TLR2 signaling. Mol Immunol 2012; 52:108-16. [PMID: 22673208 DOI: 10.1016/j.molimm.2012.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 04/23/2012] [Accepted: 05/01/2012] [Indexed: 01/07/2023]
Abstract
Toll-like receptor (TLR) signaling is initiated by the binding of various adaptor proteins through ligand-induced oligomerization of the Toll/interleukin-1 receptor (TIR) domains of the TLRs. TLR2, which recognizes peptidoglycans, lipoproteins or lipopeptides derived from Gram-positive bacteria, is known to use the TIR domain-containing adaptor proteins myeloid differentiating factor 88 (MyD88) and MyD88 adaptor-like (Mal). Molecular analyses of the binding specificity of MyD88, Mal, and TLR2 are important for understanding the initial defenses mounted against Gram-positive bacterial infections such as Streptococcus pneumoniae. However, the detailed molecular mechanisms involved in the multiple interactions of these TIR domains remain unclear. Our study demonstrates that the TIR domain proteins MyD88, Mal, TLR1, and TLR2 directly bind to each other in vitro. We have also identified two binding interfaces of the MyD88 TIR domain for the TLR2 TIR domain. A residue at these interfaces has recently been found to be mutated in innate immune deficiency patients. These novel insights into the binding mode of TIR proteins will contribute to elucidation of the mechanisms underlying innate immune deficiency diseases, and to future structural studies of hetero-oligomeric TIR-TIR complexes.
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Affiliation(s)
- Masatoshi Nada
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu 501-1194, Japan
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33
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Sekiyama N, Jee J, Isogai S, Akagi KI, Huang TH, Ariyoshi M, Tochio H, Shirakawa M. NMR analysis of Lys63-linked polyubiquitin recognition by the tandem ubiquitin-interacting motifs of Rap80. J Biomol NMR 2012; 52:339-350. [PMID: 22350954 DOI: 10.1007/s10858-012-9614-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Accepted: 01/31/2012] [Indexed: 05/31/2023]
Abstract
Ubiquitin is a post-translational modifier that is involved in cellular functions through its covalent attachment to target proteins. Ubiquitin can also be conjugated to itself at seven lysine residues and at its amino terminus to form eight linkage-specific polyubiquitin chains for individual cellular processes. The Lys63-linked polyubiquitin chain is recognized by tandem ubiquitin-interacting motifs (tUIMs) of Rap80 for the regulation of DNA repair. To understand the recognition mechanism between the Lys63-linked diubiquitin (K63-Ub(2)) and the tUIMs in solution, we determined the solution structure of the K63-Ub(2):tUIMs complex by using NOE restraints and RDC data derived from NMR spectroscopy. The structure showed that the tUIMs adopts a nearly straight and single continuous α-helix, and the two ubiquitin units of the K63-Ub(2) separately bind to each UIM motif. The interfaces are formed between Ile44-centered patches of the two ubiquitin units and the hydrophobic residues of the tUIMs. We also showed that the linker region between the two UIM motifs possesses a random-coil conformation in the free state, but undergoes the coil-to-helix transition upon complex formation, which simultaneously fixes the relative position of ubiquitin subunits. These data suggest that the relative position of ubiquitin subunits in the K63-Ub(2):tUIMs complex is essential for linkage-specific binding of Rap80 tUIMs.
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Affiliation(s)
- Naotaka Sekiyama
- Graduate School of Engineering, Kyoto University, Kyoto daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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34
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Yamada H, Mizusawa K, Igarashi R, Tochio H, Shirakawa M, Tabata Y, Kimura Y, Kondo T, Aoyama Y, Sando S. Substrate/Product-targeted NMR monitoring of pyrimidine catabolism and its inhibition by a clinical drug. ACS Chem Biol 2012; 7:535-42. [PMID: 22260358 DOI: 10.1021/cb2003972] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We report the application of one-dimensional triple-resonance NMR to metabolic analysis and thereon-based evaluation of drug activity. Doubly (13)C/(15)N-labeled uracil ([(15)N1,(13)C6]-uracil) was prepared. Its catabolic (degradative) conversion to [(13)C3,(15)N4]-β-alanine and inhibition thereof by gimeracil, a clinical co-drug used with the antitumor agent 5-fluorouracil, in mouse liver lysates were monitored specifically using one-dimensional triple-resonance ((1)H-{(13)C-(15)N}) NMR, but not double-resonance ((1)H-{(13)C}) NMR, in a ratiometric manner. The administration of labeled uracil to a mouse resulted in its non-selective distribution in various organs, with efficient catabolism to labeled β-alanine exclusively in the liver. The co-administration of gimeracil inhibited the catabolic conversion of uracil in the liver. In marked contrast to in vitro results, however, gimeracil had practically no effect on the level of uracil in the liver. The potentiality of triple-resonance NMR in the analysis of in vivo pharmaceutical activity of drugs targeting particular metabolic reactions is discussed.
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Affiliation(s)
- Hisatsugu Yamada
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | | | | - Yasuhiko Tabata
- Department of Biomaterials, Field
of Tissue Engineering, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawara-cho Shogoin, Sakyo-ku,
Kyoto 606-8507, Japan
| | - Yu Kimura
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Teruyuki Kondo
- Advanced Biomedical Engineering
Research Unit, Kyoto University, Katsura,
Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yasuhiro Aoyama
- Department
of Molecular Chemistry
and Biochemistry, Faculty of Science and Engineering, Doshisha University, Kyotanabe, Kyoto 610-0321, Japan
| | - Shinsuke Sando
- INAMORI Frontier Research Center, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395,
Japan
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35
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Tochio H, Shirakawa M. [Structural analysis of proteins in living eukaryotic cells using magnetic resonance spectroscopy]. YAKUGAKU ZASSHI 2012; 132:185-93. [PMID: 22293698 DOI: 10.1248/yakushi.132.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three-dimensional structures of proteins are often critical in understanding proteins functions. However, structures or states of proteins in cells undergo dynamical changes in response to interactions with other proteins and/or biological molecules. In addition, post-translational modification such as phosphorylation, methylation and ubiquitination can drastically change the structure and hence the properties of proteins. Therefore, to precisely correlate structure data of proteins with cell biology data, the structure information should be collected in living cells preferably at atomic level. In addition, as numerous biomolecules are packed into limited space, the concentration of macromolecules is substantially high in cells. Such crowded environment of the cell interior can markedly change proteins behavior, affecting biochemistry and biophysics of the proteins, which is so-called "Macromolecular Crowding Effect". To figure out protein behavior inside cells, which may be missed in in vitro studies, we are developing NMR and ESR methodologies to analyze protein structure and dynamics inside eukaryotic cultured cells. In this paper, in-cell NMR/ESR studies performed on HeLa cells and Xenopus oocytes are presented.
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Affiliation(s)
- Hidehito Tochio
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan.
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36
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Arita K, Sugita K, Unoki M, Oda T, Isogai S, Tochio H, Sato M, Ariyoshi M, Shirakawa M. Structure study of UHRF1. Acta Crystallogr A 2011. [DOI: 10.1107/s0108767311094335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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37
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Isogai S, Morimoto D, Arita K, Unzai S, Tenno T, Hasegawa J, Sou YS, Komatsu M, Tanaka K, Shirakawa M, Tochio H. Crystal structure of the ubiquitin-associated (UBA) domain of p62 and its interaction with ubiquitin. J Biol Chem 2011; 286:31864-74. [PMID: 21715324 DOI: 10.1074/jbc.m111.259630] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
p62/SQSTM1/A170 is a multimodular protein that is found in ubiquitin-positive inclusions associated with neurodegenerative diseases. Recent findings indicate that p62 mediates the interaction between ubiquitinated proteins and autophagosomes, leading these proteins to be degraded via the autophagy-lysosomal pathway. This ubiquitin-mediated selective autophagy is thought to begin with recognition of the ubiquitinated proteins by the C-terminal ubiquitin-associated (UBA) domain of p62. We present here the crystal structure of the UBA domain of mouse p62 and the solution structure of its ubiquitin-bound form. The p62 UBA domain adopts a novel dimeric structure in crystals, which is distinctive from those of other UBA domains. NMR analyses reveal that in solution the domain exists in equilibrium between the dimer and monomer forms, and binding ubiquitin shifts the equilibrium toward the monomer to form a 1:1 complex between the UBA domain and ubiquitin. The dimer-to-monomer transition is associated with a structural change of the very C-terminal end of the p62 UBA domain, although the UBA fold itself is essentially maintained. Our data illustrate that dimerization and ubiquitin binding of the p62 UBA domain are incompatible with each other. These observations reveal an autoinhibitory mechanism in the p62 UBA domain and suggest that autoinhibition plays a role in the function of p62.
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Affiliation(s)
- Shin Isogai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Kyoto 615-8510, Japan
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38
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Ohno A, Inomata K, Tochio H, Shirakawa M. Application of NMR spectroscopy in medicinal chemistry and drug discovery. Curr Top Med Chem 2011; 11:68-73. [PMID: 20809894 DOI: 10.2174/156802611793611878] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 02/12/2010] [Indexed: 11/22/2022]
Abstract
"In-cell nuclear magnetic resonance (NMR)" is a unique method for characterization of conformation, interaction and dynamics of proteins inside living cells at atomic level. Since the method was proposed by Dötch and co-workers in 2001 [1], its application had been limited to bacterial cells and oocytes of Xenopus laevis [2]. Recently, we reported a method for efficient delivery of (15)N-labeled proteins into human HeLa cells using cell-penetrating peptides, and measured high-resolution two-dimensional (1)H-(15)N correlation spectra of proteins in the cells. The in-cell NMR spectroscopy in human cells is capable of analyzing structures, interactions, dynamics and stability of proteins inside cells. Of its possible applications, we propose that in-cell NMR spectroscopy can be utilized as an effective step in protein-targeted drug development process, by demonstrating that interaction of FKBP12 with immunosuppressants administered extracellularly was successfully observed in living cells. This observation suggests that drug delivery and capability of target proteins inside cells for interaction with drugs can be investigated by in-cell NMR spectroscopy. More recently, an alternative way for intracellular delivery of labeled proteins for in-cell NMR was reported on 293F cells by Shimada and co-workers. Here, we review recent technical developments of in-cell NMR spectroscopy, and discuss potential usefulness for protein chemistry and drug screening process.
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Affiliation(s)
- Ayako Ohno
- Division of Nutritional physiology, Institute of Health Biosciences, The University of Tokushima Graduate School, 3-18-15 Kuramoto-cho, Tokushima, Japan
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Ohnishi H, Tochio H, Kato Z, Kimura T, Hiroaki H, Kondo N, Shirakawa M. 1H, 13C, and 15N resonance assignment of the TIR domain of human MyD88. Biomol NMR Assign 2010; 4:123-125. [PMID: 20354830 DOI: 10.1007/s12104-010-9222-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 03/10/2010] [Indexed: 05/29/2023]
Abstract
Myeloid differentiating factor 88 (MyD88) is one of a critical adaptor molecule in the Toll-like receptor (TLR) signaling pathway. The TIR domain of MyD88 serves as a protein-protein interaction module and interacts with other TIR-containing proteins such as Mal (MyD88 adaptor-like) and Toll-like receptor 4 to form signal initiation complexes. Here we report the (15)N, (13)C, and (1)H chemical shift assignments of the TIR domain of MyD88. The resonance assignments obtained in this work will contribute to the study of heteromeric TIR-TIR interactions between MyD88 and TIR-containing receptors or adaptors.
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Affiliation(s)
- Hidenori Ohnishi
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Yanagido 1-1, Gifu, 501-1194, Japan.
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Mizusawa K, Igarashi R, Uehira K, Takafuji Y, Tabata Y, Tochio H, Shirakawa M, Sando S, Aoyama Y. Turn-on Detection of Targeted Biochemical Reactions by Triple Resonance NMR Analysis Using Isotope-labeled Probe. CHEM LETT 2010. [DOI: 10.1246/cl.2010.926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Morimoto D, Isogai S, Tenno T, Tochio H, Shirakawa M, Ariyoshi M. Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:834-7. [PMID: 20606286 DOI: 10.1107/s1744309110018804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 05/20/2010] [Indexed: 11/11/2022]
Abstract
Post-translational modification of proteins by covalent attachment of ubiquitin regulates diverse cellular events. A Lys48-linked polyubiquitin chain is formed via an isopeptide bond between Lys48 and the C-terminal Gly76 of different ubiquitin molecules. The chain is attached to a lysine residue of a substrate protein, which leads to proteolytic degradation of the protein by the 26S proteasome. In order to reveal the chain-length-dependent higher order structures of polyubiquitin chains, Lys48-linked polyubiquitin chains were synthesized enzymatically on a large scale and the chains were separated according to chain length by cation-exchange column chromatography. Subsequently, crystallization screening was performed using the hanging-drop vapour-diffusion method, from which crystals of tetraubiquitin, hexaubiquitin and octaubiquitin chains were obtained. The crystals of the tetraubiquitin and hexaubiquitin chains diffracted to 1.6 and 1.8 A resolution, respectively. The tetraubiquitin crystals belonged to space group C222(1), with unit-cell parameters a = 58.795, b = 76.966, c = 135.145 A. The hexaubiquitin crystals belonged to space group P2(1), with unit-cell parameters a = 51.248, b = 102.668, c = 51.161 A. Structural analysis by molecular replacement is in progress.
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Affiliation(s)
- Daichi Morimoto
- Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8015, Japan
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Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M. Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45. Proteins 2010; 78:1491-502. [PMID: 20077568 DOI: 10.1002/prot.22667] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Post-translational modification by small ubiquitin-like modifier (SUMO) provides an important regulatory mechanism in diverse cellular processes. Modification of SUMO has been shown to target proteins involved in systems ranging from DNA repair pathways to the ubiquitin-proteasome degradation system by the action of SUMO-targeted ubiquitin ligases (STUbLs). STUbLs recognize target proteins modified with a poly-SUMO chain through their SUMO-interacting motifs (SIMs). STUbLs are also associated with RENi family proteins, which commonly have two SUMO-like domains (SLD1 and SLD2) at their C terminus. We have determined the crystal structures of SLD2 of mouse RENi protein, Nip45, in a free form and in complex with a mouse E2 sumoylation enzyme, Ubc9. While Nip45 SLD2 shares a beta-grasp fold with SUMO, the SIM interaction surface conserved in SUMO paralogues does not exist in SLD2. Biochemical data indicates that neither tandem SLDs or SLD2 of Nip45 bind to either tandem SIMs from either mouse STUbL, RNF4 or to those from SUMO-binding proteins, whose interactions with SUMO have been well characterized. On the other hand, Nip45 SLD2 binds to Ubc9 in an almost identical manner to that of SUMO and thereby inhibits elongation of poly-SUMO chains. This finding highlights a possible role of the RENi proteins in the modulation of Ubc9-mediated poly-SUMO formation.
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Igarashi R, Sakai T, Hara H, Tenno T, Tanaka T, Tochio H, Shirakawa M. Distance Determination in Proteins inside Xenopus laevis Oocytes by Double Electron−Electron Resonance Experiments. J Am Chem Soc 2010; 132:8228-9. [DOI: 10.1021/ja906104e] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryuji Igarashi
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Tomomi Sakai
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Hideyuki Hara
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Takeshi Tenno
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Toshiaki Tanaka
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Hidehito Tochio
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
| | - Masahiro Shirakawa
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan, CREST, JST, Saitama 332-0012, Japan, Mitsubishi Kagaku Institute of Life Sciences, Tokyo 194-8511, Japan, Bruker Biospin K.K., Kanagawa 221-0022, Japan, Graduate School of Medicine, Kobe University, Hyogo 650-0017, Japan, Faculty of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan, and RIKEN, Yokohama Institute, Kanagawa 230-0045, Japan
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Iwaya N, Kuwahara Y, Fujiwara Y, Goda N, Tenno T, Akiyama K, Mase S, Tochio H, Ikegami T, Shirakawa M, Hiroaki H. A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. J Biol Chem 2010; 285:16822-9. [PMID: 20339000 DOI: 10.1074/jbc.m110.108365] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Katanin p60 (kp60), a microtubule-severing enzyme, plays a key role in cytoskeletal reorganization during various cellular events in an ATP-dependent manner. We show that a single domain isolated from the N terminus of mouse katanin p60 (kp60-NTD) binds to tubulin. The solution structure of kp60-NTD was determined by NMR. Although their sequence similarities were as low as 20%, the structure of kp60-NTD revealed a striking similarity to those of the microtubule interacting and trafficking (MIT) domains, which adopt anti-parallel three-stranded helix bundle. In particular, the arrangement of helices 2 and 3 is well conserved between kp60-NTD and the MIT domain from Vps4, which is a homologous protein that promotes disassembly of the endosomal sorting complexes required for transport III membrane skeleton complex. Mutation studies revealed that the positively charged surface formed by helices 2 and 3 binds tubulin. This binding mode resembles the interaction between the MIT domain of Vps4 and Vps2/CHMP1a, a component of endosomal sorting complexes required for transport III. Our results show that both the molecular architecture and the binding modes are conserved between two AAA-ATPases, kp60 and Vps4. A common mechanism is evolutionarily conserved between two distinct cellular events, one that drives microtubule severing and the other involving membrane skeletal reorganization.
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Affiliation(s)
- Naoko Iwaya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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Jee J, Mizuno T, Kamada K, Tochio H, Chiba Y, Yanagi KI, Yasuda G, Hiroaki H, Hanaoka F, Shirakawa M. Structure and mutagenesis studies of the C-terminal region of licensing factor Cdt1 enable the identification of key residues for binding to replicative helicase Mcm proteins. J Biol Chem 2010; 285:15931-40. [PMID: 20335175 DOI: 10.1074/jbc.m109.075333] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In eukaryotes, DNA replication is fired once in a single cell cycle before cell division starts to maintain stability of the genome. This event is tightly controlled by a series of proteins. Cdt1 is one of the licensing factors and is involved in recruiting replicative DNA helicase Mcm2-7 proteins into the pre-replicative complex together with Cdc6. In Cdt1, the C-terminal region serves as a binding site for Mcm2-7 proteins, although the details of these interactions remain largely unknown. Here, we report the structure of the region and the key residues for binding to Mcm proteins. We determined the solution structure of the C-terminal fragment, residues 450-557, of mouse Cdt1 by NMR. The structure consists of a winged-helix domain and shows unexpected similarity to those of the C-terminal domain of Cdc6 and the central fragment of Cdt1, thereby implying functional and evolutionary relationships. Structure-based mutagenesis and an in vitro binding assay enabled us to pinpoint the region that interacts with Mcm proteins. Moreover, by performing in vitro binding and budding yeast viability experiments, we showed that approximately 45 residues located in the N-terminal direction of the structural region are equally crucial for recognizing Mcm proteins. Our data suggest the possibility that winged-helix domain plays a role as a common module to interact with replicative helicase in the DNA replication-licensing process.
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Affiliation(s)
- Jungoo Jee
- Center for Priority Areas, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, Tokyo 192-0397, Japan.
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Abstract
Poly-ADP-ribosylation is a unique post-translational modification that controls various nuclear events such as repair of DNA single-strand breaks. Recently, the protein containing the poly-ADP-ribose (pADPr)-binding zinc-finger (PBZ) domain was shown to be a novel AP endonuclease and involved in a cell cycle checkpoint. Here, we determined the three-dimensional structure of the PBZ domain from Drosophila melanogaster CG1218-PA using NMR spectroscopy. The domain folds into a C2H2-type zinc-finger structure in an S configuration, containing a characteristic loop between the zinc-coordinating cysteine and histidine residues. This is distinct from the structure of other C2H2-type zinc fingers. NMR signal changes that occur when pADPr binds to the PBZ domains from CG1218-PA and human checkpoint with FHA (forkhead-associated) and ring finger (CHFR) and mutagenesis suggest that a surface relatively well conserved among PBZ domains may serve as a major interface with pADPr.
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Affiliation(s)
- Shin Isogai
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Kyoto 615-8510, Japan
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Tateishi Y, Ariyoshi M, Igarashi R, Hara H, Mizuguchi K, Seto A, Nakai A, Kokubo T, Tochio H, Shirakawa M. Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2. J Biol Chem 2009; 284:2435-47. [DOI: 10.1074/jbc.m806392200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Kimura T, Kato Z, Ohnishi H, Tochio H, Shirakawa M, Kondo N. Expression, purification and structural analysis of human IL-18 binding protein: a potent therapeutic molecule for allergy. Allergol Int 2008; 57:367-76. [PMID: 18797176 DOI: 10.2332/allergolint.o-08-546] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 05/09/2008] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND While interleukin-18 (IL-18) plays an important role in the innate and adaptive immune responses, it can also cause severe allergic inflammatory reactions. Thus it is a molecule currently being targeted for therapy. The natural intrinsic inhibitor of IL-18 receptor activation, IL-18 binding protein (IL-18BP), shows a great potential for the treatment of allergy. METHODS Expression and purification of recombinant human IL-18BP (rhIL-18BP) were performed using the baculovirus system to develop a therapeutic molecule for the treatment of IL-18-related diseases and to investigate the structural basis of its inhibitory mechanism. RESULTS Purified rhIL-18BP potently inhibited the production of interferon-gamma by peripheral blood mononuclear cells in the presence of lipopolysaccharide and by human myelomonocytic KG-1 cells in the presence of IL-18 (IC50 = 0.4 nM). Surface plasmon resonance showed a high affinity (Kd = 0.46 nM) for rhIL-18BP in binding hIL-18. Structural analysis indicated that the stoichiometry between IL-18 and IL-18BP is 1 : 1 in solution and the model structure of the complex suggests that the key residues on IL-18 (L5, K53, S55) and the estimated key residues on IL-18BP (F93,Y97, F104) could have interactions. The structural mechanism of IL-18BP inhibition might be a competition for Site 2 on rIL-18 so that IL-18BP can prevent IL-18 receptor alpha from binding to Site 2 and inhibit IL-18 receptor activation. CONCLUSIONS IL-18BP has unique features with respect to its structure, binding mode and inhibitory mechanism. It is a molecule that has a great potential for the therapy of allergy.
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Affiliation(s)
- Takeshi Kimura
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
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Sekiyama N, Ikegami T, Yamane T, Ikeguchi M, Uchimura Y, Baba D, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M. Structure of the small ubiquitin-like modifier (SUMO)-interacting motif of MBD1-containing chromatin-associated factor 1 bound to SUMO-3. J Biol Chem 2008; 283:35966-75. [PMID: 18842587 DOI: 10.1074/jbc.m802528200] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Post-translational modification by small ubiquitin-like modifier (SUMO) proteins has been implicated in the regulation of a variety of cellular events. The functions of sumoylation are often mediated by downstream effector proteins harboring SUMO-interacting motifs (SIMs) that are composed of a hydrophobic core and a stretch of acidic residues. MBD1-containing chromatin-associated factor 1 (MCAF1), a transcription repressor, interacts with SUMO-2/3 and SUMO-1, with a preference for SUMO-2/3. We used NMR spectroscopy to solve the solution structure of the SIM of MCAF1 bound to SUMO-3. The hydrophobic core of the SIM forms a parallel beta-sheet pairing with strand beta2 of SUMO-3, whereas its C-terminal acidic stretch seems to mediate electrostatic interactions with a surface area formed by basic residues of SUMO-3. The significance of these electrostatic interactions was shown by mutations of both SUMO-3 and MCAF1. The present structural and biochemical data suggest that the acidic stretch of the SIM of MCAF1 plays an important role in the binding to SUMO-3.
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Affiliation(s)
- Naotaka Sekiyama
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M. Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Nature 2008; 455:818-21. [PMID: 18772891 DOI: 10.1038/nature07249] [Citation(s) in RCA: 354] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 07/09/2008] [Indexed: 12/27/2022]
Abstract
DNA methylation of CpG dinucleotides is an important epigenetic modification of mammalian genomes and is essential for the regulation of chromatin structure, of gene expression and of genome stability. Differences in DNA methylation patterns underlie a wide range of biological processes, such as genomic imprinting, inactivation of the X chromosome, embryogenesis, and carcinogenesis. Inheritance of the epigenetic methylation pattern is mediated by the enzyme DNA methyltransferase 1 (Dnmt1), which methylates newly synthesized CpG sequences during DNA replication, depending on the methylation status of the template strands. The protein UHRF1 (also known as Np95 and ICBP90) recognizes hemi-methylation sites via a SET and RING-associated (SRA) domain and directs Dnmt1 to these sites. Here we report the crystal structures of the SRA domain in free and hemi-methylated DNA-bound states. The SRA domain folds into a globular structure with a basic concave surface formed by highly conserved residues. Binding of DNA to the concave surface causes a loop and an amino-terminal tail of the SRA domain to fold into DNA interfaces at the major and minor grooves of the methylation site. In contrast to fully methylated CpG sites recognized by the methyl-CpG-binding domain, the methylcytosine base at the hemi-methylated site is flipped out of the DNA helix in the SRA-DNA complex and fits tightly into a protein pocket on the concave surface. The complex structure suggests that the successive flip out of the pre-existing methylated cytosine and the target cytosine to be methylated is associated with the coordinated transfer of the hemi-methylated CpG site from UHRF1 to Dnmt1.
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Affiliation(s)
- Kyohei Arita
- Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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