Updated on 2026/03/10

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写真a

 
Sam-Yong Park
 
Organization
Graduate School of Medical Life Science Department of Medical Life Science Professor
School of Science Department of Science
Title
Professor
Homepage
http://www.tsurumi.yokohama-cu.ac.jp/pdl/index.html
Other name(s)
PS000028
Profile
1995年大阪大学大学院 基礎工学研究科博士課程修了、博士（工学）。1995年より理化学研究所、播磨研究所 研究員。2001年4月より現職。
研究内容：疾患由来タンパク質の構造生物学研究を行っている。
External link

Degree

  • (BLANK) ( Osaka University )

Research Interests

  • 構造創薬化学

  • 構造生物学

  • Biology

  • Structural Biology

  • Biophysical

Research Areas

  • Life Science / Biophysics

  • Life Science / Structural biochemistry

  • Life Science / Biodiversity and systematics

Research History

  • Yokohama City University

    2010

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  • Yokohama City University International College of Arts and Sciences Medical Life Science Graduate School of Medical Life Science Department of Medical Life Science   Professor

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Professional Memberships

Committee Memberships

  • 日本生物物理学会   会員  

    1990   

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    Committee type：Academic society

    日本生物物理学会

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Papers

  • Crystal and Cryo-EM structure of PPL, a novel hexameric R-type lectin from the poisonous mushroom Pleurocybella porrigens. International journal

    Daisuke Adachi, Naito Ishimoto, Kenji Mizutani, Katsuya Takahashi, Reiji Kubota, Haruka Kawabata, Sam-Yong Park, Laurens Vandebroek, Arnout R D Voet, Masao Yamada, Yasuhiro Ozeki, Yuki Fujii, Hideaki Fujita, Jeremy R H Tame, Kenichi Kamata

    Glycobiology   2025.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    Pleurocybella porrigens is a mushroom that grows widely around the temperate northern hemisphere, and was once considered edible, especially in Japan. Following a number of deaths in 2004, investigations revealed the presence of various toxins, including a lectin (PPL) that apparently survives cooking and enters the bloodstream via the stomach. We have cloned PPL and solved its structure by X-ray crystallography and cryo-EM. We report the sugar binding properties of this β-trefoil lectin, which has a novel hexameric structure.

    DOI： 10.1093/glycob/cwaf082

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  • Structural basis for hepatitis B virus restriction by a viral receptor homologue. International journal

    Kaho Shionoya, Jae-Hyun Park, Toru Ekimoto, Junko S Takeuchi, Junki Mifune, Takeshi Morita, Naito Ishimoto, Haruka Umezawa, Kenichiro Yamamoto, Chisa Kobayashi, Atsuto Kusunoki, Norimichi Nomura, So Iwata, Masamichi Muramatsu, Jeremy R H Tame, Mitsunori Ikeguchi, Sam-Yong Park, Koichi Watashi

    Nature communications   15 ( 1 )   9241 - 9241   2024.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    Macaque restricts hepatitis B virus (HBV) infection because its receptor homologue, NTCP (mNTCP), cannot bind preS1 on viral surface. To reveal how mNTCP loses the viral receptor function, we here solve the cryo-electron microscopy structure of mNTCP. Superposing on the human NTCP (hNTCP)-preS1 complex structure shows that Arg158 of mNTCP causes steric clash to prevent preS1 from embedding onto the bile acid tunnel of NTCP. Cell-based mutation analysis confirms that only Gly158 permitted preS1 binding, in contrast to robust bile acid transport among mutations. As the second determinant, Asn86 on the extracellular surface of mNTCP shows less capacity to restrain preS1 from dynamic fluctuation than Lys86 of hNTCP, resulting in unstable preS1 binding. Additionally, presence of long-chain conjugated-bile acids in the tunnel induces steric hindrance with preS1 through their tailed-chain. This study presents structural basis in which multiple sites in mNTCP constitute a molecular barrier to strictly restrict HBV.

    DOI： 10.1038/s41467-024-53533-6

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  • Structural basis of CXC chemokine receptor 1 ligand binding and activation. International journal

    Naito Ishimoto, Jae-Hyun Park, Kouki Kawakami, Michiko Tajiri, Kenji Mizutani, Satoko Akashi, Jeremy R H Tame, Asuka Inoue, Sam-Yong Park

    Nature communications   14 ( 1 )   4107 - 4107   2023.7

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    Neutrophil granulocytes play key roles in innate immunity and shaping adaptive immune responses. They are attracted by chemokines to sites of infection and tissue damage, where they kill and phagocytose bacteria. The chemokine CXCL8 (also known as interleukin-8, abbreviated IL-8) and its G-protein-coupled receptors CXCR1 and CXCR2 are crucial elements in this process, and also the development of many cancers. These GPCRs have therefore been the target of many drug development campaigns and structural studies. Here, we solve the structure of CXCR1 complexed with CXCL8 and cognate G-proteins using cryo-EM, showing the detailed interactions between the receptor, the chemokine and Gαi protein. Unlike the closely related CXCR2, CXCR1 strongly prefers to bind CXCL8 in its monomeric form. The model shows that steric clashes would form between dimeric CXCL8 and extracellular loop 2 (ECL2) of CXCR1. Consistently, transplanting ECL2 of CXCR2 onto CXCR1 abolishes the selectivity for the monomeric chemokine. Our model and functional analysis of various CXCR1 mutants will assist efforts in structure-based drug design targeting specific CXC chemokine receptor subtypes.

    DOI： 10.1038/s41467-023-39799-2

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  • X-ray fluorescence holography of biological metal sites: Application to myoglobin

    Ayana Sato-Tomita, Artoni Kevin R. Ang, Koji Kimura, Riho Marumi, Naohisa Happo, Tomohiro Matsushita, Sam-Yong Park, Naoya Shibayama, Yuji C. Sasaki, Kouichi Hayashi

    Biochemical and Biophysical Research Communications   635   277 - 282   2022.12

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.bbrc.2022.10.003

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  • Structural insights into the HBV receptor and bile acid transporter NTCP. International journal

    Jae-Hyun Park, Masashi Iwamoto, Ji-Hye Yun, Tomomi Uchikubo-Kamo, Donghwan Son, Zeyu Jin, Hisashi Yoshida, Mio Ohki, Naito Ishimoto, Kenji Mizutani, Mizuki Oshima, Masamichi Muramatsu, Takaji Wakita, Mikako Shirouzu, Kehong Liu, Tomoko Uemura, Norimichi Nomura, So Iwata, Koichi Watashi, Jeremy R H Tame, Tomohiro Nishizawa, Weontae Lee, Sam-Yong Park

    Nature   606 ( 7916 )   1027 - 1031   2022.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    Roughly 250 million people are infected with hepatitis B virus (HBV) worldwide1, and perhaps 15 million also carry the satellite virus HDV, which confers even greater risk of severe liver disease2. Almost ten years ago the HBV receptor was identified as NTCP (sodium taurocholate co-transporting polypeptide), which interacts directly with the first 48 amino acid residues of the N-myristoylated N-terminal preS1 domain of the viral large (L) protein3. Despite the pressing need for therapeutic agents to counter HBV, the structure of NTCP remains unsolved. This 349-residue protein is closely related to human apical sodium-dependent bile acid transporter (ASBT), another member of the solute carrier family SLC10. Crystal structures have been reported of similar bile acid transporters from bacteria4, 5, and these models with ten transmembrane helices are believed to resemble strongly both NTCP and ASBT. Using cryo-electron microscopy we have solved the structure of NTCP bound to an antibody, clearly showing the transporter has no equivalent to the first transmembrane helix of other SLC10 models, leaving the N-terminus exposed on the extracellular face. Comparison of the different structures indicates a common mechanism of bile acid transport, but the NTCP structure also displays a pocket formed by residues known to interact with preS1, presenting new and enticing opportunities for structure-based drug design.

    DOI： 10.1038/s41586-022-04857-0

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  • 感染受容体NTCPの多量体化が導くB型肝炎ウイルス細胞内侵入機構の解明

    深野 顕人, 大嶋 美月, 九十田 千子, 相崎 英樹, 大木 規央, 朴 三用, 脇田 隆字, 若江 亨祥, 渡士 幸一, 村松 正道

    日本薬学会年会要旨集   142年会   26M - pm15   2022.3

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    Language：Japanese   Publisher：(公社)日本薬学会  

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  • SLC10A1/NTCP多量体形成が制御するB型肝炎ウイルス細胞内侵入機構の解析

    深野 顕人, 大嶋 美月, 九十田 千子, 相崎 英樹, 大木 規央, 朴 三用, 脇田 隆字, 若江 亨祥, 渡士 幸一, 村松 正道

    日本生化学会大会プログラム・講演要旨集   94回   [P - 382]   2021.11

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    Language：Japanese   Publisher：(公社)日本生化学会  

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  • スプライシングタンパク質U2AF1によるイントロン認識機構のX線結晶構造解析

    吉田 尚史, 朴 三用, 成相 裕子, 坂下 暁介, 桑迫 香奈子, 武藤 裕, 浦野 健, 尾林 栄治

    日本生化学会大会プログラム・講演要旨集   94回   [1T15m - 195)]   2021.11

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  • NTCP oligomerization occurs downstream of the NTCP-EGFR interaction during hepatitis B virus internalization

    Kento Fukano, Mizuki Oshima, Senko Tsukuda, Hideki Aizaki, Mio Ohki, Sam-Yong Park, Takaji Wakita, Kousho Wakae, Koichi Watashi, Masamichi Muramatsu

    Journal of Virology   2021.10

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    Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

    Sodium taurocholate cotransporting polypeptide (NTCP) is a receptor that is essential for hepatitis B virus (HBV) entry into the host cell. A number of HBV entry inhibitors targeting NTCP have been reported to date; these inhibitors have facilitated a mechanistic analysis of the viral entry process. However, the mechanism of HBV internalization into host cells after interaction of virus with NTCP remains largely unknown. Recently, we reported that troglitazone, a thiazolidinedione derivative, specifically inhibits both HBV internalization and NTCP oligomerization, resulting in inhibition of HBV infection. Here, using troglitazone as a chemical probe to investigate entry process, the contribution of NTCP oligomerization to HBV internalization was evaluated. Using surface plasmon resonance and transporter kinetics, we found that troglitazone directly interacts with NTCP and non-competitively interferes with NTCP-mediated bile acid uptake, suggesting that troglitazone allosterically binds to NTCP, rather than to the bile acid-binding pocket. Additionally, alanine scanning mutagenesis showed that a mutation at phenylalanine 274 of NTCP (F274A) caused a loss of HBV susceptibility and disrupted both the oligomerization of NTCP and HBV internalization without affecting viral attachment to the cell surface. An inhibitor of the interaction between NTCP and epidermal growth factor receptor (EGFR), another host cofactor essential for HBV internalization, impeded NTCP oligomerization. Meanwhile, co-immunoprecipitation analysis revealed that neither troglitazone nor the F274A mutation in NTCP affect the NTCP-EGFR interaction. These findings suggest that NTCP oligomerization is initiated downstream of the NTCP-EGFR interaction, and then triggers HBV internalization. This study provides significant insight into the HBV entry mechanisms.



    <bold>Importance</bold>



    Hepatitis B virus (HBV) infection is mediated by a specific interaction with sodium taurocholate cotransporting polypeptide (NTCP), a viral entry receptor. Although the virus-receptor interactions are believed to trigger viral internalization into host cells, the exact molecular mechanisms of HBV internalization are not understood. In this study, we revealed the mode of action whereby troglitazone, a specific inhibitor of HBV internalization, impedes NTCP oligomerization, and identified NTCP phenylalanine 274 as a residue essential for this oligomerization. We further analyzed the association between NTCP oligomerization and HBV internalization, a process that is mediated by epidermal growth factor receptor (EGFR), another essential host cofactor for HBV internalization. Our study provides critical information on the mechanism of HBV entry, and suggests that oligomerization of the viral receptor serves as an attractive target for drug discovery.

    DOI： 10.1128/jvi.00938-21

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  • Crystal structure of Nanoarchaeum equitans tyrosyl-tRNA synthetase and its aminoacylation activity toward tRNATyr with an extra guanosine residue at the 5ʹ-terminus

    Tatsuya Horikoshi, Hiroki Noguchi, Takuya Umehara, Hiromi Mutsuro-Aoki, Ryodai Kurihara, Ryohei Noguchi, Takahiro Hashimoto, Yuki Watanabe, Tadashi Ando, Kenichi Kamata, Sam-Yong Park, Koji Tamura

    Biochemical and Biophysical Research Communications   575   90 - 95   2021.10

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier {BV}  

    DOI： 10.1016/j.bbrc.2021.08.070

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  • Early-stage dynamics of chloride ion–pumping rhodopsin revealed by a femtosecond X-ray laser

    Ji-Hye Yun, Xuanxuan Li, Jianing Yue, Jae-Hyun Park, Zeyu Jin, Chufeng Li, Hao Hu, Yingchen Shi, Suraj Pandey, Sergio Carbajo, Sébastien Boutet, Mark S. Hunter, Mengning Liang, Raymond G. Sierra, Thomas J. Lane, Liang Zhou, Uwe Weierstall, Nadia A. Zatsepin, Mio Ohki, Jeremy R.H. Tame, Sam-Yong Park, John C.H. Spence, Wenkai Zhang, Marius Schmidt, Weontae Lee, Haiguang Liu

    Proceedings of the National Academy of Sciences of the United States of America   118 ( 13 )   2021.3

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：National Academy of Sciences  

    DOI： 10.1073/pnas.2020486118

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  • Photoactivated adenylyl cyclases: Fundamental properties and applications

    Mineo Iseki, Sam-Yong Park

    Advances in Experimental Medicine and Biology   1293   129 - 139   2021

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    Language：English   Publishing type：Part of collection (book)   Publisher：Springer  

    DOI： 10.1007/978-981-15-8763-4_7

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  • The structure of SeviL, a GM1b/asialo-GM1 binding R-type lectin from the mussel Mytilisepta virgata. International journal

    Kenichi Kamata, Kenji Mizutani, Katsuya Takahashi, Roberta Marchetti, Alba Silipo, Christine Addy, Sam-Yong Park, Yuki Fujii, Hideaki Fujita, Tsuyoshi Konuma, Takahisa Ikegami, Yasuhiro Ozeki, Jeremy R H Tame

    Scientific reports   10 ( 1 )   22102 - 22102   2020.12

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    SeviL is a recently isolated lectin found to bind to the linear saccharides of the ganglioside GM1b (Neu5Ac[Formula: see text](2-3)Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc) and its precursor, asialo-GM1 (Gal[Formula: see text](1-3)GalNAc[Formula: see text](1-4)Gal[Formula: see text](1-4)Glc). The crystal structures of recombinant SeviL have been determined in the presence and absence of ligand. The protein belongs to the [Formula: see text]-trefoil family, but shows only weak sequence similarity to known structures. SeviL forms a dimer in solution, with one binding site per subunit, close to the subunit interface. Molecular details of glycan recognition by SeviL in solution were analysed by ligand- and protein-based NMR techniques as well as ligand binding assays. SeviL shows no interaction with GM1 due to steric hindrance with the sialic acid branch that is absent from GM1b. This unusual specificity makes SeviL of great interest for the detection and control of certain cancer cells, and cells of the immune system, that display asialo-GM1.

    DOI： 10.1038/s41598-020-78926-7

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  • Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner

    Naomi Nakayama, Gyosuke Sakashita, Takashi Nagata, Naohiro Kobayashi, Hisashi Yoshida, Sam-Yong Park, Yuko Nariai, Hiroaki Kato, Eiji Obayashi, Kentaro Nakayama, Satoru Kyo, Takeshi Urano

    Biomedicines   8 ( 12 )   608 - 608   2020.12

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    Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

    Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.

    DOI： 10.3390/biomedicines8120608

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  • Elucidation of the aberrant 3′ splice site selection by cancer-associated mutations on the U2AF1 Reviewed International journal

    Hisashi Yoshida, Sam-Yong Park, Gyosuke Sakashita, Yuko Nariai, Kanako Kuwasako, Yutaka Muto, Takeshi Urano, Eiji Obayashi

    Nature Communications   11 ( 1 )   4744 - 4744   2020.12

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    Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

    <title>Abstract</title>
    The accurate exclusion of introns by RNA splicing is critical for the production of mature mRNA. U2AF1 binds specifically to the 3´ splice site, which includes an essential AG dinucleotide. Even a single amino acid mutation of U2AF1 can cause serious disease such as certain cancers or myelodysplastic syndromes. Here, we describe the first crystal structures of wild-type and pathogenic mutant U2AF1 complexed with target RNA, revealing the mechanism of 3´ splice site selection, and how aberrant splicing results from clinically important mutations. Unexpected features of this mechanism may assist the future development of new treatments against diseases caused by splicing errors.

    DOI： 10.1038/s41467-020-18559-6

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    Other Link： http://www.nature.com/articles/s41467-020-18559-6

  • Structure-Based Functional Modification Study of a Cyanobacterial Chloride Pump for Transporting Multiple Anions Reviewed

    Ji-Hye Yun, Jae-Hyun Park, Zeyu Jin, Mio Ohki, Yang Wang, Cecylia Severin Lupala, Haiguang Liu, Sam-Yong Park, Weontae Lee

    Journal of Molecular Biology   432 ( 19 )   5273 - 5286   2020.9

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    Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

    DOI： 10.1016/j.jmb.2020.07.016

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  • Direct observation of ligand migration within human hemoglobin at work Reviewed

    Naoya Shibayama, Ayana Sato-Tomita, Mio Ohki, Kouhei Ichiyanagi, Sam-Yong Park

    Proceedings of the National Academy of Sciences   117 ( 9 )   4741 - 4748   2020.3

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    Publishing type：Research paper (scientific journal)   Publisher：Proceedings of the National Academy of Sciences  

    Hemoglobin is one of the best-characterized proteins with respect to structure and function, but the internal ligand diffusion pathways remain obscure and controversial. Here we captured the CO migration processes in the tense (T), relaxed (R), and second relaxed (R2) quaternary structures of human hemoglobin by crystallography using a high-repetition pulsed laser technique at cryogenic temperatures. We found that in each quaternary structure, the photodissociated CO molecules migrate along distinct pathways in the α and β subunits by hopping between the internal cavities with correlated side chain motions of large nonpolar residues, such as α14Trp(A12), α105Leu(G12), β15Trp(A12), and β71Phe(E15). We also observe electron density evidence for the distal histidine [α58/β63His(E7)] swing-out motion regardless of the quaternary structure, although less evident in α subunits than in β subunits, suggesting that some CO molecules have escaped directly through the E7 gate. Remarkably, in T-state Fe(II)-Ni(II) hybrid hemoglobins in which either the α or β subunits contain Ni(II) heme that cannot bind CO, the photodissociated CO molecules not only dock at the cavities in the original Fe(II) subunit, but also escape from the protein matrix and enter the cavities in the adjacent Ni(II) subunit even at 95 K, demonstrating the high gas permeability and porosity of the hemoglobin molecule. Our results provide a comprehensive picture of ligand movements in hemoglobin and highlight the relevance of cavities, nonpolar residues, and distal histidines in facilitating the ligand migration.

    DOI： 10.1073/pnas.1913663117

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    Other Link： https://syndication.highwire.org/content/doi/10.1073/pnas.1913663117

  • B型肝炎ウイルス内在化機構における感染受容体多量体化の関与

    深野 顕人, 九十田 千子, 大嶋 美月, 大木 規央, 朴 三用, 若江 亨祥, 相崎 英樹, 脇田 隆字, 渡士 幸一, 村松 正道

    日本薬学会年会要旨集   140年会   26J - pm03   2020.3

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  • Pumping mechanism of NM-R3, a light-driven bacterial chloride importer in the rhodopsin family Reviewed

    Ji-Hye Yun, Mio Ohki, Jae-Hyun Park, Naito Ishimoto, Ayana Sato-Tomita, Wonbin Lee, Zeyu Jin, Jeremy R. H. Tame, Naoya Shibayama, Sam-Yong Park, Weontae Lee

    Science Advances   6 ( 6 )   eaay2042 - eaay2042   2020.2

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    Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

    A newly identified microbial rhodopsin, NM-R3, from the marine flavobacterium<italic>Nonlabens marinus</italic>, was recently shown to drive chloride ion uptake, extending our understanding of the diversity of mechanisms for biological energy conversion. To clarify the mechanism underlying its function, we characterized the crystal structures of NM-R3 in both the dark state and early intermediate photoexcited states produced by laser pulses of different intensities and temperatures. The displacement of chloride ions at five different locations in the model reflected the detailed anion-conduction pathway, and the activity-related key residues—Cys<sup>105</sup>, Ser<sup>60</sup>, Gln<sup>224</sup>, and Phe<sup>90</sup>—were identified by mutation assays and spectroscopy. Comparisons with other proteins, including a closely related outward sodium ion pump, revealed key motifs and provided structural insights into light-driven ion transport across membranes by the NQ subfamily of rhodopsins. Unexpectedly, the response of the retinal in NM-R3 to photostimulation appears to be substantially different from that seen in bacteriorhodopsin.

    DOI： 10.1126/sciadv.aay2042

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  • The machinery for endocytosis of epidermal growth factor receptor coordinates the transport of incoming hepatitis B virus to the endosomal network. Reviewed International journal

    Iwamoto M, Saso W, Nishioka K, Ohashi H, Sugiyama R, Ryo A, Ohki M, Yun JH, Park SY, Ohshima T, Suzuki R, Aizaki H, Muramatsu M, Matano T, Iwami S, Sureau C, Wakita T, Watashi K

    The Journal of biological chemistry   295 ( 3 )   800 - 807   2019.12

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    Sodium taurocholate cotransporting polypeptide (NTCP) is expressed at the surface of human hepatocytes and functions as an entry receptor of hepatitis B virus (HBV). Recently, we have reported that epidermal growth factor receptor (EGFR) is involved in NTCP-mediated viral internalization during the cell entry process. Here, we analyzed which function of EGFR is essential for mediating HBV internalization. In contrast to the reported crucial function of EGFR-downstream signaling for the entry of hepatitis C virus (HCV), blockade of EGFR-downstream signaling proteins, including mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and signal transducer and activator of transcription (STAT), had no or only minor effects on HBV infection. Instead, deficiency of EGFR endocytosis resulting from either a deleterious mutation in EGFR or genetic knockdown of endocytosis adaptor molecules abrogated internalization of HBV via NTCP and prevented viral infection. EGFR activation triggered a time-dependent relocalization of HBV preS1 to the early and late endosomes and to lysosomes in concert with EGFR transport. Suppression of EGFR ubiquitination by site-directed mutagenesis or by knocking down two EGFR-sorting molecules, signal-transducing adaptor molecule (STAM) and lysosomal protein transmembrane 4β (LAPTM4B), suggested that EGFR transport to the late endosome is critical for efficient HBV infection. Cumulatively, these results support the idea that the EGFR endocytosis/sorting machinery drives the translocation of NTCP-bound HBV from the cell surface to the endosomal network, which eventually enables productive viral infection.

    DOI： 10.1074/jbc.AC119.010366

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  • Glycyl-tRNA synthetase from Nanoarchaeum equitans: The first crystal structure of archaeal GlyRS and analysis of its tRNA glycylation Reviewed

    Alma Fujisawa, Risako Toki, Hideaki Miyake, Tomoko Shoji, Hiromi Doi, Hiromi Hayashi, Rina Hanabusa, Hiromi Mutsuro-Aoki, Takuya Umehara, Tadashi Ando, Hiroki Noguchi, Arnout Voet, Sam-Yong Park, Koji Tamura

    BIOCHEM BIOPH RES CO   511   228 - 233   2019.4

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    DOI： 10.1016/j.bbrc.2019.01.142

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  • Epidermal growth factor receptor is a host-entry cofactor triggering hepatitis B virus internalization. Reviewed International journal

    Iwamoto M, Saso W, Sugiyama R, Ishii K, Ohki M, Nagamori S, Suzuki R, Aizaki H, Ryo A, Yun JH, Park SY, Ohtani N, Muramatsu M, Iwami S, Tanaka Y, Sureau C, Wakita T, Watashi K, g, A

    Proceedings of the National Academy of Sciences of the United States of America   116 ( 17 )   8487 - 8492   2019.4

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    Sodium taurocholate cotransporting polypeptide (NTCP) is a host cell receptor required for hepatitis B virus (HBV) entry. However, the susceptibility of NTCP-expressing cells to HBV is diverse depending on the culture condition. Stimulation with epidermal growth factor (EGF) was found to potentiate cell susceptibility to HBV infection. Here, we show that EGF receptor (EGFR) plays a critical role in HBV virion internalization. In EGFR-knockdown cells, HBV or its preS1-specific fluorescence peptide attached to the cell surface, but its internalization was attenuated. PreS1 internalization and HBV infection could be rescued by complementation with functional EGFR. Interestingly, the HBV/preS1-NTCP complex at the cell surface was internalized concomitant with the endocytotic relocalization of EGFR. Molecular interaction between NTCP and EGFR was documented by immunoprecipitation assay. Upon dissociation from functional EGFR, NTCP no longer functioned to support viral infection, as demonstrated by either (i) the introduction of NTCP point mutation that disrupted its interaction with EGFR, (ii) the detrimental effect of decoy peptide interrupting the NTCP-EGFR interaction, or (iii) the pharmacological inactivation of EGFR. Together, these data support the crucial role of EGFR in mediating HBV-NTCP internalization into susceptible cells. EGFR thus provides a yet unidentified missing link from the cell-surface HBV-NTCP attachment to the viral invasion beyond the host cell membrane.

    DOI： 10.1073/pnas.1811064116

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  • Troglitazone Impedes the Oligomerization of Sodium Taurocholate Cotransporting Polypeptide and Entry of Hepatitis B Virus Into Hepatocytes. Reviewed

    Fukano K, Tsukuda S, Oshima M, Suzuki R, Aizaki H, Ohki M, Park SY, Muramatsu M, Wakita T, Sureau C, Ogasawara Y, Watashi K, g, A

    Frontiers in microbiology   9   3257   2019.1

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  • A new strategy to identify hepatitis B virus entry inhibitors by AlphaScreen technology targeting the envelope-receptor interaction. Reviewed

    Saso W, Tsukuda S, Ohashi H, Fukano K, Morishita R, Matsunaga S, Ohki M, Ryo A, Park SY, Suzuki R, Aizaki H, Muramatsu M, Sureau C, Wakita T, Matano T, Watashi K

    Biochemical and biophysical research communications   501 ( 2 )   374 - 379   2018.6

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  • Saturated Fatty Acids Undergo Intracellular Crystallization and Activate the NLRP3 Inflammasome in Macrophages Reviewed

    Tadayoshi Karasawa, Akira Kawashima, Fumitake Usui-Kawanishi, Sachiko Watanabe, Hiroaki Kimura, Ryo Kamata, Koumei Shirasuna, Yutaro Koyama, Ayana Sato-Tomita, Takashi Matsuzaka, Hiroshi Tomoda, Sam-Yong Park, Naoya Shibayama, Hitoshi Shimano, Tadashi Kasahara, Masafumi Takahashi

    Arteriosclerosis, Thrombosis, and Vascular Biology   38 ( 4 )   744 - 756   2018.4

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    DOI： 10.1161/ATVBAHA.117.310581

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  • Chemical array system, a platform to identify novel hepatitis B virus entry inhibitors targeting sodium taurocholate cotransporting polypeptide. Reviewed International journal

    Kaneko M, Futamura Y, Tsukuda S, Kondoh Y, Sekine T, Hirano H, Fukano K, Ohashi H, Saso W, Morishita R, Matsunaga S, Kawai F, Ryo A, Park SY, Suzuki R, Aizaki H, Ohtani N, Sureau C, Wakita T, Osada H, Watashi K

    Scientific reports   8 ( 1 )   2769 - 2769   2018.2

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    Current anti-hepatitis B virus (HBV) agents including interferons and nucleos(t)ide analogs efficiently suppress HBV infection. However, as it is difficult to eliminate HBV from chronically infected liver, alternative anti-HBV agents targeting a new molecule are urgently needed. In this study, we applied a chemical array to high throughput screening of small molecules that interacted with sodium taurocholate cotransporting polypeptide (NTCP), an entry receptor for HBV. From approximately 30,000 compounds, we identified 74 candidates for NTCP interactants, and five out of these were shown to inhibit HBV infection in cell culture. One of such compound, NPD8716, a coumarin derivative, interacted with NTCP and inhibited HBV infection without causing cytotoxicity. Consistent with its NTCP interaction capacity, this compound was shown to block viral attachment to host hepatocytes. NPD8716 also prevented the infection with hepatitis D virus, but not hepatitis C virus, in agreement with NPD8716 specifically inhibiting NTCP-mediated infection. Analysis of derivative compounds showed that the anti-HBV activity of compounds was apparently correlated with the affinity to NTCP and the capacity to impair NTCP-mediated bile acid uptake. These results are the first to show that the chemical array technology represents a powerful platform to identify novel viral entry inhibitors.

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  • Direct observation of conformational population shifts in crystalline human hemoglobin Reviewed

    Naoya Shibayama, Mio Ohki, Jeremy R. H. Tame, Sam-Yong Park

    JOURNAL OF BIOLOGICAL CHEMISTRY   292 ( 44 )   18258 - 18269   2017.11

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    DOI： 10.1074/jbc.M117.781146

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  • Molecular mechanism of photoactivation of a light-regulated adenylate cyclase Reviewed

    Mio Ohki, Ayana Sato-Tomita, Shigeru Matsunaga, Mineo Iseki, Jeremy R. H. Tame, Naoya Shibayama, Sam-Yong Park

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   114 ( 32 )   8562 - 8567   2017.8

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    DOI： 10.1073/pnas.1704391114

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  • Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis Reviewed

    Chang Hwa Jo, Jonghyeon Son, Sulhee Kim, Takashi Oda, Jaehoon Kim, Myoung-Ro Lee, Mamoru Sato, Hyun Tae Kim, Satoru Unzai, Sam-Yong Park, Kwang Yeon Hwang

    SCIENTIFIC REPORTS   7 ( 1 )   1764   2017.5

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    DOI： 10.1038/s41598-017-02044-0

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  • Cyclosporin derivatives inhibit hepatitis B virus entry without interfering with NTCP transporter activity. Reviewed

    Shimura S, Watashi K, Fukano K, Peel M, Sluder A, Kawai F, Iwamoto M, Tsukuda S, Takeuchi JS, Miyake T, Sugiyama M, Ogasawara Y, Park SY, Tanaka Y, Kusuhara H, Mizokami M, Sureau C, Wakita T

    Journal of hepatology   66 ( 4 )   685 - 692   2017.4

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  • Crystal structure of the overlapping dinucleosome composed of hexasome and octasome Reviewed

    Daiki Kato, Akihisa Osakabe, Yasuhiro Arimura, Yuka Mizukami, Naoki Horikoshi, Kazumi Saikusa, Satoko Akashi, Yoshifumi Nishimura, Sam-Yong Park, Jumpei Nogami, Kazumitsu Maehara, Yasuyuki Ohkawa, Atsushi Matsumoto, Hidetoshi Kono, Rintaro Inoue, Masaaki Sugiyama, Hitoshi Kurumizaka

    SCIENCE   356 ( 6334 )   205 - 208   2017.4

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    DOI： 10.1126/science.aak9867

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  • G196 epitope tag system: a novel monoclonal antibody, G196, recognizes the small, soluble peptide DLVPR with high affinity

    Kasumi Tatsumi, Gyosuke Sakashita, Yuko Nariai, Kosuke Okazaki, Hiroaki Kato, Eiji Obayashi, Hisashi Yoshida, Kanako Sugiyama, Sam-Yong Park, Joji Sekine, Takeshi Urano

    SCIENTIFIC REPORTS   7   2017.3

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    DOI： 10.1038/srep43480

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  • Crystal structure of MytiLec, a galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types Reviewed

    Daiki Terada, Fumihiro Kawai, Hiroki Noguchi, Satoru Unzai, Imtiaj Hasan, Yuki Fujii, Sam-Yong Park, Yasuhiro Ozeki, Jeremy R. H. Tame

    SCIENTIFIC REPORTS   6   28344   2016.6

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    DOI： 10.1038/srep28344

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  • Development of an X-ray fluorescence holographic measurement system for protein crystals. Reviewed

    Sato-Tomita A, Shibayama N, Happo N, Kimura K, Okabe T, Matsushita T, Park SY, Sasaki YC, Hayashi K

    The Review of scientific instruments   87 ( 6 )   063707   2016.6

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    DOI： 10.1063/1.4953453

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  • Structural insight into photoactivation of an adenylate cyclase from a photosynthetic cyanobacterium Reviewed

    Mio Ohki, Kanako Sugiyama, Fumihiro Kawai, Hitomi Tanaka, Yuuki Nihei, Satoru Unzai, Masumi Takebe, Shigeru Matsunaga, Shin-ichi Adachi, Naoya Shibayama, Zhiwen Zhou, Ryuta Koyama, Yuji Ikegaya, Tetsuo Takahashi, Jeremy R. H. Tame, Mineo Iseki, Sam-Yong Park

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   113 ( 24 )   6659 - 6664   2016.6

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    DOI： 10.1073/pnas.1517520113

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  • A Novel Tricyclic Polyketide, Vanitaracin A, Specifically Inhibits the Entry of Hepatitis B and D Viruses by Targeting Sodium Taurocholate Cotransporting Polypeptide Reviewed

    Manabu Kaneko, Koichi Watashi, Shinji Kamisuki, Hiroki Matsunaga, Masashi Iwamoto, Fumihiro Kawai, Hirofumi Ohashi, Senko Tsukuda, Satomi Shimura, Ryosuke Suzuki, Hideki Aizaki, Masaya Sugiyama, Sam-Yong Park, Takayoshi Ito, Naoko Ohtani, Fumio Sugawara, Yasuhito Tanaka, Masashi Mizokami, Camille Sureau, Takaji Wakita

    JOURNAL OF VIROLOGY   89 ( 23 )   11945 - 11953   2015.12

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    DOI： 10.1128/JVI.01855-15

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  • A novel 3 ' splice site recognition by the two zinc fingers in the U2AF small subunit Reviewed

    Hisashi Yoshida, Sam-Yong Park, Takashi Oda, Taeko Akiyoshi, Mamoru Sato, Mikako Shirouzu, Kengo Tsuda, Kanako Kuwasako, Satoru Unzai, Yutaka Muto, Takeshi Urano, Eiji Obayashi

    GENES & DEVELOPMENT   29 ( 15 )   1649 - 1660   2015.8

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    DOI： 10.1101/gad.267104.115

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  • The structure and conformational switching of Rap1B Reviewed

    Hiroki Noguchi, Takahisa Ikegami, Aritaka Nagadoi, Yuji O. Kamatari, Sam-Yong Park, Jeremy R. H. Tame, Satoru Unzai

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   462 ( 1 )   46 - 51   2015.6

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    DOI： 10.1016/j.bbrc.2015.04.103

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  • Structure-based analysis of domain function of chitin oligosaccharide deacetylase from Vibrio parahaemolyticus Reviewed

    Takako Hirano, Kanako Sugiyama, Yuta Sakaki, Wataru Hakamata, Sam-Yong Park, Toshiyuki Nishio

    FEBS LETTERS   589 ( 1 )   145 - 151   2015.1

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    DOI： 10.1016/j.febslet.2014.11.039

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  • Computational design of a self-assembling symmetrical beta-propeller protein Reviewed

    Arnout R. D. Voet, Hiroki Noguchi, Christine Addy, David Simoncini, Daiki Terada, Satoru Unzai, Sam-Yong Park, Kam Y. J. Zhang, Jeremy R. H. Tame

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   111 ( 42 )   15102 - 15107   2014.10

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    DOI： 10.1073/pnas.1412768111

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  • The Crystal Structure of the Active Domain of Anopheles Anti-platelet Protein, a Powerful Anti-coagulant, in Complex with an Antibody Reviewed

    Kanako Sugiyama, Mitsuhiro Iyori, Asuka Sawaguchi, Satoko Akashi, Jeremy R. H. Tame, Sam-Yong Park, Shigeto Yoshida

    JOURNAL OF BIOLOGICAL CHEMISTRY   289 ( 23 )   16303 - 16312   2014.6

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    DOI： 10.1074/jbc.M114.564526

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  • Capturing the Hemoglobin Allosteric Transition in a Single Crystal Form Reviewed

    Naoya Shibayama, Kanako Sugiyama, Jeremy R. H. Tame, Sam-Yong Park

    JOURNAL OF THE AMERICAN CHEMICAL SOCIETY   136 ( 13 )   5097 - 5105   2014.4

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    DOI： 10.1021/ja500380e

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  • 3P036 X-ray crystal structures of carbonmonoxy hemoglobin photolysis intermediates(01B. Protein: Structure & Function,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

    Tomita Ayana, Sato Tokushi, Noguchi Hiroki, Nozawa Shunsuke, Koshihara Shin-ya, Park Sam-Yong, Shibayama Naoya, Adachi Shin-ichi

    Seibutsu Butsuri   54 ( 1 )   S254   2014

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    DOI： 10.2142/biophys.54.S254_6

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  • Homopiperazine derivatives as a novel class of proteasome inhibitors with a unique mode of proteasome binding. Reviewed International journal

    Kikuchi J, Shibayama N, Yamada S, Wada T, Nobuyoshi M, Izumi T, Akutsu M, Kano Y, Sugiyama K, Ohki M, Park SY, Furukawa Y

    PloS one   8 ( 4 )   e60649   2013.4

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    The proteasome is a proteolytic machinery that executes the degradation of polyubiquitinated proteins to maintain cellular homeostasis. Proteasome inhibition is a unique and effective way to kill cancer cells because they are sensitive to proteotoxic stress. Indeed, the proteasome inhibitor bortezomib is now indispensable for the treatment of multiple myeloma and other intractable malignancies, but is associated with patient inconvenience due to intravenous injection and emerging drug resistance. To resolve these problems, we attempted to develop orally bioavailable proteasome inhibitors with distinct mechanisms of action and identified homopiperazine derivatives (HPDs) as promising candidates. Biochemical and crystallographic studies revealed that some HPDs inhibit all three catalytic subunits (ß 1, ß 2 and ß 5) of the proteasome by direct binding, whereas bortezomib and other proteasome inhibitors mainly act on the ß5 subunit. Proteasome-inhibitory HPDs exhibited cytotoxic effects on cell lines from various hematological malignancies including myeloma. Furthermore, K-7174, one of the HPDs, was able to inhibit the growth of bortezomib-resistant myeloma cells carrying a ß5-subunit mutation. Finally, K-7174 had additive effects with bortezomib on proteasome inhibition and apoptosis induction in myeloma cells. Taken together, HPDs could be a new class of proteasome inhibitors, which compensate for the weak points of conventional ones and overcome the resistance to bortezomib.

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  • The structure of the deacetylase domain of Escherichia coli PgaB, an enzyme required for biofilm formation: a circularly permuted member of the carbohydrate esterase 4 family Reviewed

    Takashi Nishiyama, Hiroki Noguchi, Hisashi Yoshida, Sam-Yong Park, Jeremy R. H. Tame

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   69 ( Pt 1 )   44 - 51   2013.1

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    DOI： 10.1107/S0907444912042059

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  • Structures of haemoglobin from woolly mammoth in liganded and unliganded states Reviewed

    Hiroki Noguchi, Kevin L. Campbell, Chien Ho, Satoru Unzai, Sam-Yong Park, Jeremy R. H. Tame

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   68 ( Pt 11 )   1441 - 1449   2012.11

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  • Crystal Structures of Penicillin-Binding Protein 3 (PBP3) from Methicillin-Resistant Staphylococcus aureus in the Apo and Cefotaxime-Bound Forms Reviewed

    Hisashi Yoshida, Fumihiro Kawai, Eiji Obayashi, Satoko Akashi, David I. Roper, Jeremy R. H. Tame, Sam-Yong Park

    JOURNAL OF MOLECULAR BIOLOGY   423 ( 3 )   351 - 364   2012.10

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    DOI： 10.1016/j.jmb.2012.07.012

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  • Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle. Reviewed International journal

    Hansman GS, Taylor DW, McLellan JS, Smith TJ, Georgiev I, Tame JR, Park SY, Yamazaki M, Gondaira F, Miki M, Katayama K, Murata K, Kwong PD

    Journal of virology   86 ( 7 )   3635 - 3646   2012.4

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  • Structures and Oxygen Affinities of Crystalline Human Hemoglobin C (beta 6 Glu -&gt; Lys) in the R and R2 Quaternary Structures Reviewed

    Naoya Shibayama, Kanako Sugiyama, Sam-Yong Park

    JOURNAL OF BIOLOGICAL CHEMISTRY   286 ( 38 )   33661 - 33668   2011.9

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    DOI： 10.1074/jbc.M111.266056

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  • Crystal structure of the human centromeric nucleosome containing CENP-A. Reviewed International journal

    Tachiwana H, Kagawa W, Shiga T, Osakabe A, Miya Y, Saito K, Hayashi-Takanaka Y, Oda T, Sato M, Park SY, Kimura H, Kurumizaka H

    Nature   476 ( 7359 )   232 - 235   2011.7

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    In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate α-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the αN helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome. A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg 80 and Gly 81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.

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  • Structure-Based Drug Design Targeting a Subunit Interaction of Influenza Virus RNA Polymerase

    SUGIYAMA Kanako, OBAYASHI Eiji, YOSHIDA Hisashi, PARK Sam-Yong

    X-RAYS   52 ( 6 )   271 - 278   2010.12

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    Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. Influenza virus reproduces rapidly, mutates frequently, and occasionally crosses species barriers. The recent emergence of swine-origin influenza H1N1 and avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. Here, we describe two crystal structures of complexes made by fragments of PA and PB1, and PB1 and PB2. These novel interfaces are surprisingly small, yet they play a crucial role in regulating the 250 kDa polymerase complex, and are completely conserved among swine, avian and human influenza viruses. Given their importance to viral replication and strict conservation, the PA/PB1 and PB1/PB2 interfaces appear to be promising targets for novel anti-influenza drugs of use against all strains of influenza A virus. It is hoped that the structures presented here will assist the search for such compounds.

    DOI： 10.5940/jcrsj.52.271

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  • Role of domains within the autotransporter Hbp/Tsh Reviewed

    Kaoru Nishimura, Young-Ho Yoon, Atsushi Kurihara, Satoru Unzai, Joen Luirink, Sam-Yong Park, Jeremy R. H. Tame

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   66   1295 - 1300   2010.12

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  • Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography. Reviewed

    Kovalevsky A, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher SZ, Langan P, Morimoto Y

    Acta crystallographica. Section D, Biological crystallography   66   1144 - 1152   2010.11

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  • A Novel Intein-Like Autoproteolytic Mechanism in Autotransporter Proteins Reviewed

    Nami Tajima, Fumihiro Kawai, Sam-Yong Park, Jeremy R. H. Tame

    JOURNAL OF MOLECULAR BIOLOGY   402 ( 4 )   645 - 656   2010.10

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    DOI： 10.1016/j.jmb.2010.06.068

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  • Crystallization and preliminary crystallographic studies of the butyrolactone autoregulator receptor protein (BarA) from Streptomyces virginiae Reviewed

    Young-Ho Yoon, Fumihiro Kawai, Kanako Sugiyama, Sam-Yong Park, Takuya Nihira, Sun-Uk Choi, Yong-Il Hwang

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   66 ( 6 )   662 - 664   2010.6

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    DOI： 10.1107/S1744309110009930

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  • Expression, purification, physicochemical characterization and structural analysis of cytochrome C554 from Vibrio parahaemolyticus strain RIMD2210633 Reviewed

    Hideharu Akazaki, Fumihiro Kawai, Hirotaka Chida, Takako Hirano, Wataru Hakamata, Sam-Yong Park, Toshiyuki Nishio, Tadatake Oku

    Biosci. Biotechnol. Biochem   74 ( 5 )   1113-1115   2010.5

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  • Direct determination of protonation states of histidine residues in a 2 A neutron structure of deoxy-human normal adult hemoglobin and implications for the Bohr effect. Reviewed

    Kovalevsky AY, Chatake T, Shibayama N, Park SY, Ishikawa T, Mustyakimov M, Fisher Z, Langan P, Morimoto Y

    Journal of molecular biology   398   276 - 291   2010.4

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  • Structure Basis for an Subunit Interaction of Influenza Virus RNA Polymerase for Drug Design

    PARK Sam-Yong

    Seibutsu Butsuri   50 ( 2 )   74 - 79   2010.3

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    Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. Influenza virus reproduces rapidly, mutates frequently, and occasionally crosses species barriers. The recent emergence of swine-origin influenza H1N1 and avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. I describe two crystal structures of complexes made by fragments of PA and PB1, and PB1 and PB2. These novel interfaces are surprisingly small, yet they play a crucial role in regulating the 250 kDa polymerase complex, and are completely conserved among swine, avian and human influenza viruses. Given their importance to viral replication and strict conservation, the PA/PB1 and PB1/PB2 interfaces appear to be promising targets for novel anti-influenza drugs of use against all strains of influenza A virus. It is hoped that the structures presented here will assist the search for such compounds.<br>

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  • Crystal Structures of Penicillin-Binding Proteins 4 and 5 from Haemophilus influenzae Reviewed

    Fumihiro Kawai, Thomas B. Clarke, David I. Roper, Gab-Jo Han, Kwang Yeon Hwang, Satoru Unzai, Eiji Obayashi, Sam-Yong Park, Jeremy R. H. Tame

    JOURNAL OF MOLECULAR BIOLOGY   396 ( 3 )   634 - 645   2010.2

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  • Mitotic regulation of the stability of microtubule plus-end tracking protein EB3 by ubiquitin ligase SIAH-1 and Aurora mitotic kinases. International journal

    Reiko Ban, Hideki Matsuzaki, Tomohiro Akashi, Gyosuke Sakashita, Hisaaki Taniguchi, Sam-Yong Park, Hirofumi Tanaka, Koichi Furukawa, Takeshi Urano

    The Journal of biological chemistry   284 ( 41 )   28367 - 81   2009.10

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    Microtubule plus-end tracking proteins (+TIPs) control microtubule dynamics in fundamental processes such as cell cycle, intracellular transport, and cell motility, but how +TIPs are regulated during mitosis remains largely unclear. Here we show that the endogenous end-binding protein family EB3 is stable during mitosis, facilitates cell cycle progression at prometaphase, and then is down-regulated during the transition to G(1) phase. The ubiquitin-protein isopeptide ligase SIAH-1 facilitates EB3 polyubiquitination and subsequent proteasome-mediated degradation, whereas SIAH-1 knockdown increases EB3 stability and steady-state levels. Two mitotic kinases, Aurora-A and Aurora-B, phosphorylate endogenous EB3 at Ser-176, and the phosphorylation triggers disruption of the EB3-SIAH-1 complex, resulting in EB3 stabilization during mitosis. Our results provide new insight into a regulatory mechanism of +TIPs in cell cycle transition.

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  • Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase Reviewed

    Sugiyama K, Obayashi E, Kawaguchi A, Suzuki Y, Tame JRH, Nagata K, Park SY

    EMBO Journal   28 ( 12 )   1803 - 1811   2009.6

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  • RNA and protein complexes of trp RNA-binding attenuation protein characterized by mass spectrometry. Reviewed

    Akashi S, Watanabe M, Heddle JG, Unzai S, Park SY, Tame JR

    Analytical chemistry   81 ( 6 )   2218 - 2226   2009.3

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  • Mutational Analysis of the Substrate Specificity of Escherichia coli Penicillin Binding Protein 4 Reviewed

    Thomas B. Clarke, Fumihiro Kawai, Sam-Yong Park, Jeremy R. H. Tame, Christopher G. Dowson, David I. Roper

    BIOCHEMISTRY   48 ( 12 )   2675 - 2683   2009.3

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    DOI： 10.1021/bi801993x

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  • Biophysical Techniques for Detecting Ligand Binding to Pharmaceutical Targets

    HUBBARD Roderick E., KAWAKAMI Yoshiyuki, AKASHI Satoko, WATANABE Masahiro, HEDDLE Jonathan G., UNZAI Satoru, PARK Sam-Yong, TAME Jeremy R. H.

    X-RAYS   51 ( 1 )   104 - 105   2009.2

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    DOI： 10.5940/jcrsj.51.104

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  • Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin. Reviewed International journal

    Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park SY, Tsuduki T, Yamato T, Koshihara SY, Adachi S

    Proceedings of the National Academy of Sciences of the United States of America   106 ( 8 )   2612 - 2616   2009.2

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    Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.

    DOI： 10.1073/pnas.0807774106

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  • The nature of the TRAP-Anti-TRAP complex. Reviewed

    Watanabe M, Heddle JG, Kikuchi K, Unzai S, Akashi S, Park SY, Tame JR

    Proceedings of the National Academy of Sciences of the United States of America   106 ( 7 )   2176 - 2181   2009.2

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  • The Structural Basis for an Essential Subunit Interaction in Influenza Virus RNA Polymerase

    OBAYASHI Eiji, YOSHIDA Hisashi, PARK Sam-Yong

    X-RAYS   50 ( 6 )   329 - 334   2009.1

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    Influenza A virus is a major human and animal pathogen with the potential to cause catastrophic loss of life. The virus reproduces rapidly, mutates frequently, and occasionally crosses species barriers. The recent emergence in Asia of avian influenza related to highly pathogenic forms of the human virus has highlighted the urgent need for new effective treatments. No current medication targets this heterotrimeric polymerase complex. All three subunits, PB1, PB2, and PA are required for both transcription and replication. PB1 carries the polymerise active site, PB2 includes the capped-RNA recognition domain, and PA is involved in assembly of the functional complex, but so far very little structural information has been reported for any of them. We describe the crystal structure of a large fragment of one subunit (PA) of influenza A RNA polymerise bound to a fragment of another subunit (PB1) . The C terminal domain of PA forms a novel fold, and forms a deep, highly hydrophobic groove into which the N-terminal residues of PB1 can fit by forming a 3<SUB>10</SUB> helix.

    DOI： 10.5940/jcrsj.50.329

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    Other Link： https://jlc.jst.go.jp/DN/JALC/00325072645?from=CiNii

  • 1SA3-01 Structural insight into essential subunit contacts of the influenza virus RNA polymerase(1SA3 Novel findings of influenza A virus RNA dependent RNA polymerase,The 47th Annual Meeting of the Biophysical Society of Japan)

    Obayashi Eiji, Sugiyama Kanako, Yoshida Hisashi, Kawai Fumihiro, Kawaguchi Atsushi, Suzuki Yukari, Tame Jeremy, Nagata Kyosuke, Park Sam-Yong

    Seibutsu Butsuri   49   S5   2009

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    DOI： 10.2142/biophys.49.S5_2

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  • 3ECZ: Carbonmonoxy Sperm Whale Myoglobin at 120 K: Laser on [30 min] Reviewed

    Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park S-Y, Koshihara S, Adachi S

    2009

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  • 2ZSO: Carbonmonoxy Sperm Whale Myoglobin at 100 K: Laser on [450 min] Reviewed

    Tomita A, Sato T, Ichiyanagi K, Nozawa S, Ichikawa H, Chollet M, Kawai F, Park S-Y, Koshihara S, Adachi S

    2009

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  • Physicochemical properties of diheme cytochrome c4 of unknown function from Vibrio parahaemolyticus strain RIMD2210633. Reviewed

    Akazaki H, Futami Y, Shibayama N, Shirasaki I, Nakade H, Chida H, Hakamata W, Park SY, Nishio T, Oku T

    Bioscience, biotechnology, and biochemistry   72 ( 10 )   2791 - 2794   2008.10

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    To characterize a diheme cytochrome <I>c</I><SUB>4</SUB> of unknown functional of the <I>Vibrio</I> genus for the first time, the <I>Vibrio parahaemolyticus</I> cytochrome <I>c</I><SUB>4</SUB> was overexpressed in <I>Escherichia coli</I> periplasm using the endogenous signal sequence. The physicochemical properties of the purified recombinant protein, <I>viz.</I>, molecular mass, UV/Vis, and CD spectra, and the redox potentials of the N- and C-terminal domain hemes were determined.

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  • The structural basis for an essential subunit interaction in influenza virus RNA polymerase Reviewed

    Obayashi E, Yoshida H, Kawai F, Shibayama N, Kawaguchi A, Nagata K, Tame JRH, Park SY

    Nature   454 ( 7208 )   1127 - 0   2008.8

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    DOI： 10.1038/nature07225

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  • Intersubunit linker length as a modifier of protein stability: crystal structures and thermostability of mutant TRAP. Reviewed

    Watanabe M, Mishima Y, Yamashita I, Park SY, Tame JR, Heddle JG

    Protein science : a publication of the Protein Society   17 ( 3 )   518 - 526   2008.3

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  • A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. Reviewed

    Ozaki, S, Kawakami, H, Nakamura, K, Fujikawa, N, Kagawa, W, Park, SY, Yokoyama, S, Kurumizaka, H

    The Journal of biological chemistry   283 ( 13 )   8351 - 8362   2008.3

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  • Crystal structures of the clock protein EA4 from the silkworm Bombyx mori. Reviewed

    Hiraki T, Shibayama N, Akashi S, Park SY

    Journal of molecular biology   377   630 - 635   2008.3

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  • Cloning,expressionand purification of cytochrome c6 from the brown alga Hizikia fusiformis and complete X-ray diffraction analysis of the structure Reviewed

    Hideharu Akazaki, Fumihiro Kawai, Hirotaka Chida, Yuichirou Matsumoto, Mao Hirayama, Ken Hoshikawa, Satoru Unzai, Wataru Hakamata, Toshiyuki Nishio, Sam-Yong Park, Tadatake OKu

    Acta Crystallographica Section D   F64   674-680   2008

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  • Protonation states of buried histidine residues in human deoxyhemoglobin revealed by neutron crystallography. Reviewed

    Chatake T, Shibayama N, Park SY, Kurihara K, Tamada T, Tanaka I, Niimura N, Kuroki R, Morimoto Y

    Journal of the American Chemical Society   129 ( 48 )   14840 - 14841   2007.12

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  • Effect of N-terminal residues on the structural stability of recombinant horse L-chain apoferritin in an acidic environment Reviewed

    Keiko Yoshizawa, Yumiko Mishima, Sam-Yong Park, Jonathan G. Heddle, Jeremy R. H. Tame, Kenji Iwahori, Mime Kobayashi, Ichiro Yamashita

    JOURNAL OF BIOCHEMISTRY   142 ( 6 )   707 - 713   2007.12

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    DOI： 10.1093/jb/mvm187

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  • Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: catalytic mechanism of tRNA intron-splicing endonucleases Reviewed

    Kim YK, Mizutani K, Rhee KH, Nam KH, Lee WH, Lee EH, Kim EE, Park SY, Hwang KY

    J Bacteriol.   189 ( 22 )   8339 - 8346   2007.11

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    DOI： 10.1128/JB.00713-07

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  • Crystallization and preliminary crystallographic studies of the metalloglycoprotein esterase A4 using a baculovirus expression system. Reviewed

    Hiraki T, Shibayama N, Yoon YH, Yun KM, Hamamoto T, Tame JR, Park SY

    Acta crystallographica. Section F, Structural biology and crystallization communications   63   734 - 736   2007.9

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  • Dynamic allostery in the ring protein TRAP Reviewed

    Jonathan G. Heddle, Tomoyuki Okajima, David J. Scott, Satoko Akashi, Sam-Yong Park, Jeremy R. H. Tame

    JOURNAL OF MOLECULAR BIOLOGY   371 ( 1 )   154 - 167   2007.8

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    DOI： 10.1016/j.jmb.2007.05.013

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  • Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli Reviewed

    Atsushi Izumi, Dean Rea, Tomoko Adachi, Satoru Unzai, Sam-Yong Park, David I. Roper, Jeremy R. H. Tame

    JOURNAL OF MOLECULAR BIOLOGY   370 ( 5 )   899 - 911   2007.7

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    DOI： 10.1016/j.jmb.2007.05.006

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  • Nickel binding to NikA: an additional binding site reconciles spectroscopy, calorimetry and crystallography. Reviewed

    Addy C, Ohara M, Kawai F, Kidera A, Ikeguchi M, Fuchigami S, Osawa M, Shimada I, Park SY, Tame JR, Heddle JG

    Acta crystallographica. Section D, Biological crystallography   63 ( Pt 2 )   221 - 229   2007.2

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  • 1P016 EA4 is a protein with a built-in self-timer(Proteins-structure and structure-function relationship,Oral Presentations)

    Shibayama Naoya, Hiraki Toshiki, Akashi Satoko, Tame Jeremy R. H., Park Sam-Yong

    Seibutsu Butsuri   47   S27   2007

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    DOI： 10.2142/biophys.47.S27_3

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  • Expression, purification and crystallization of 2-oxo-hept-4-ene-1,7-dioate hydratase (HpcG) from Escherichia coli C

    Dean Rea, Tomoko Adachi, Atsushi Izumi, Sam-Yong Park, Jeremy R. H. Tame, David I. Roper

    Acta Crystallographica Section F: Structural Biology and Crystallization Communications   62 ( 10 )   1010 - 1012   2006.10

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    DOI： 10.1107/S1744309106035901

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  • 1.25 A resolution crystal structures of human haemoglobin in the oxy, deoxy and carbonmonoxy forms. Reviewed

    Park SY, Yokoyama T, Shibayama N, Shiro Y, Tame JR

    Journal of molecular biology   360   690 - 701   2006.7

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  • Rounding up: Engineering 12-membered rings from the cyclic 11-mer TRAP Reviewed

    JG Heddle, T Yokoyama, Yamashita, I, SY Park, JRH Tame

    STRUCTURE   14 ( 5 )   925 - 933   2006.5

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    DOI： 10.1016/j.str.2006.03.013

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  • Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics Reviewed

    H Kishida, S Unzai, DI Roper, A Lloyd, SY Park, JRH Tame

    BIOCHEMISTRY   45 ( 3 )   783 - 792   2006.1

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    DOI： 10.1021/bi051533t

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  • Crystal structure of hemoglobin protease, a heme binding autotransporter protein from pathogenic Escherichia coli Reviewed

    BR Otto, R Sijbrandi, J Luirink, B Oudega, JG Heddle, K Mizutani, SY Park, JRH Tame

    JOURNAL OF BIOLOGICAL CHEMISTRY   280 ( 17 )   17339 - 17345   2005.4

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    DOI： 10.1074/jbc.M412885200

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  • Crystal structure of a novel polyisoprenoid-binding protein from Thermus thermophilus HB8 Reviewed

    Noriko Handa, Takaho Terada, Yukiko Doi-Katayama, Hiroshi Hirota, Jeremy R. H. Tame, Sam-Yong Park, Seiki Kuramitsu, Mikako Shirouzu, Shigeyuki Yokoyama

    Protein Science   14 ( 4 )   1004 - 1010   2005.4

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    DOI： 10.1110/ps.041183305

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  • 1P018 Crystal structure of esterase A4 that acts alone as a molecular clock

    Hiraki T., Shibayama N., Tame Jeremy R.H., Park S.-Y.

    Seibutsu Butsuri   45   S36   2005

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    DOI： 10.2142/biophys.45.S36_2

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  • 3P328 Functional and structural analysis of recombinant Horse Spleen ferritin with N-terminal amino-acid deletion

    Mishima Y., Iwahori K., Park S.-Y., Heddle Jonathan, Tame Jeremy R.H., Yamashita I.

    Seibutsu Butsuri   45   S285   2005

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    DOI： 10.2142/biophys.45.S285_4

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  • Multi-wavelength anomalous diffraction method for I and Xe atoms using ultra-high-energy X-rays from SPring-8 Reviewed

    K Takeda, H Miyatake, SY Park, M Kawamoto, N Kamiya, K Miki

    JOURNAL OF APPLIED CRYSTALLOGRAPHY   37 ( 6 )   925 - 933   2004.12

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    DOI： 10.1107/S0021889804023076

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  • Crystal structure of a conserved hypothetical protein TT1751 from Thermus thermophilus HB8 Reviewed

    S Kishishita, A Tatsuguchi, R Ushikoshi-Nakayama, T Terada, S Kuramitsu, SY Park, JRH Tame, M Shirouzu, S Yokoyama

    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS   57 ( 4 )   883 - 887   2004.12

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    DOI： 10.1002/prot.20282

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  • Crystal structures of unliganded and half-liganded human hemoglobin derivatives cross-linked between Lys 82beta1 and Lys 82beta2. Reviewed

    Park SY, Shibayama N, Hiraki T, Tame JR

    Biochemistry   43   8711 - 8717   2004.7

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  • Novel mechanisms of pH sensitivity in tuna hemoglobin - A structural explanation of the root effect Reviewed

    T Yokoyama, KT Chong, G Miyazaki, H Morimoto, DTB Shih, S Unzai, JRH Tame, SY Park

    JOURNAL OF BIOLOGICAL CHEMISTRY   279 ( 27 )   28632 - 28640   2004.7

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    DOI： 10.1074/jbc.M401740200

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  • Crystal Structure of the Conserved Hypothetical Protein TT1380 from Thermus thermophilus HB8 Reviewed

    Takashi Wada, Mikako Shirouzu, Takaho Terada, Yuki Kamewari, Sam-Yong Park, Jeremy R.H. Tame, Seiki Kuramitsu, Shigeyuki Yokoyama

    Proteins: Structure, Function and Genetics   55 ( 3 )   778 - 780   2004.5

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    DOI： 10.1002/prot.20122

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  • Crystal structures of the catalytic domains of pseudouridine synthases RluC and RluD from Escherichia coli Reviewed

    K Mizutani, Y Machida, S Unzai, SY Park, JRH Tame

    BIOCHEMISTRY   43 ( 15 )   4454 - 4463   2004.4

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    DOI： 10.1021/bi036079c

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  • 2P006 Neutron Structure analysis of Human Hemoglobin Reviewed

    Morimoto Y., Park S.Y., Shibayama N., Kurihara K., Tanaka I., Tamada T., Kuroki R., Niimura N.

    Seibutsu Butsuri   44 ( 0 )   S111   2004

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    DOI： 10.2142/biophys.44.S111_2

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  • 2P005 Crystal structure of heme binding protein P46 from Bacteroides fragilis

    Izumi A., Otto Ben, Heddle Jonathan, Park S.Y., Tame Jeremy R.H.

    Seibutsu Butsuri   44   S111   2004

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    DOI： 10.2142/biophys.44.S111_1

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  • 2P099 Crystal Structures of the Catalytic Domains of Pseudouridine Synthases RluC and RluD from Eschericia coli

    Mizutani K., Machida Y., Unzai S., Park S.-Y., Tame Jeremy R.H.

    Seibutsu Butsuri   44   S134   2004

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    DOI： 10.2142/biophys.44.S134_3

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  • 3SB04 Direct observation of photolysis-induced structural changes in hemoglobin

    Adachi S., Shiro Y., Park S.-Y., Tame Jeremy R. H., Shibayama N.

    Seibutsu Butsuri   44   S20   2004

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    DOI： 10.2142/biophys.44.S20_4

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  • Crystal structures of the liganded and unliganded nickel-binding protein NikA from Escherichia coli Reviewed

    J Heddle, DJ Scott, S Unzai, SY Park, JRH Tame

    JOURNAL OF BIOLOGICAL CHEMISTRY   278 ( 50 )   50322 - 50329   2003.12

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    DOI： 10.1074/jbc.M307941200

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  • Infrared spectroscopic and mutational studies on putidaredoxin-induced conformational changes in ferrous CO-P450cam Reviewed

    S Nagano, H Shimada, A Tarumi, T Hishiki, Y Kimata-Ariga, T Egawa, M Suematsu, SY Park, S Adachi, Y Shiro, Y Ishimura

    BIOCHEMISTRY   42 ( 49 )   14507 - 14514   2003.12

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    DOI： 10.1021/bi035410p

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  • Crystal structure of the human centromere protein B (CENP-B) dimerization domain at 1.65-A resolution

    Tawaramoto, MS, Park SY, Tanaka, Y, Nureki, O, Kurumizaka, H, Yokoyama, S

    The Journal of Biological Chemistry   278 ( 51 )   51454 - 51461   2003.12

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    DOI： 10.1074/jbc.M310388200

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  • Crystal structure of 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Reviewed

    Wada T, Kuzuyama T, Satoh S, Kuramitsu S, Yokoyama S, Unzai S, Tame JR, Park SY

    The Journal of biological chemistry   278 ( 32 )   30022 - 30027   2003.8

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  • Crystal structure of the conserved protein TT1542 from Thermus thermophilus HB8. Reviewed

    Handa N, Terada T, Kamewari Y, Hamana H, Tame JR, Park SY, Kinoshita K, Ota M, Nakamura H, Kuramitsu S, Shirouzu M, Yokoyama S

    Protein science : a publication of the Protein Society   12 ( 8 )   1621 - 1632   2003.8

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  • Structure of a conserved CoA-binding protein synthesized by a cell-free system Reviewed

    T Wada, M Shirouzu, T Terada, Y Ishizuka, T Matsuda, T Kigawa, S Kuramitsu, SY Park, JRH Tame, S Yokoyama

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   59   1213 - 1218   2003.7

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    DOI： 10.1107/S0907444903011028

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  • Direct observation of photolysis-induced tertiary structural changes in hemoglobin. Reviewed

    Adachi S, Park SY, Tame JR, Shiro Y, Shibayama N

    Proceedings of the National Academy of Sciences of the United States of America   100   7039 - 7044   2003.6

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  • Substrate recognition and molecular mechanism of fatty acid hydroxylation by cytochrome P450 from Bacillus subtilis - Crystallographic, spectroscopic, and mutational studies

    DS Lee, A Yamada, H Sugimoto, Matsunaga, I, H Ogura, K Ichihara, S Adachi, SY Park, Y Shiro

    JOURNAL OF BIOLOGICAL CHEMISTRY   278 ( 11 )   9761 - 9767   2003.3

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    DOI： 10.1074/jbc.M211575200

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  • Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. Reviewed

    Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY

    Acta crystallographica. Section D, Biological crystallography   59 ( Pt 1 )   23 - 31   2003.1

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  • Crystal structure of horse carbonmonoxyhemoglobin-bezafibrate complex at 1.55-A resolution. A novel allosteric binding site in R-state hemoglobin. Reviewed

    Shibayama N, Miura S, Tame JR, Yonetani T, Park SY

    The Journal of biological chemistry   277   38791 - 38796   2002.10

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  • Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties Reviewed

    SY Park, K Yamane, S Adachi, Y Shiro, KE Weiss, SA Maves, SG Sligar

    JOURNAL OF INORGANIC BIOCHEMISTRY   91 ( 4 )   491 - 501   2002.9

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  • Crystal structures of deoxy- and carbonmonoxyhemoglobin F1 from the hagfish Eptatretus burgeri Reviewed

    M Mito, KT Chong, G Miyazaki, S Adachi, SY Park, JRH Tame, H Morimoto

    JOURNAL OF BIOLOGICAL CHEMISTRY   277 ( 24 )   21898 - 21905   2002.6

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    DOI： 10.1074/jbc.M111492200

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  • Crystallization and preliminary X-ray diffraction analysis of fatty-acid hydroxylase cytochrome P450BS beta from Bacillus subtilis Reviewed

    DS Lee, A Yamada, Matsunaga, I, K Ichihara, S Adachi, SY Park, Y Shiro

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   58   687 - 689   2002.4

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    DOI： 10.1107/S0907444902001762

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  • X-ray structure of nitric oxide reductase (cytochrome P450nor) at atomic resolution

    H Shimizu, SY Park, Y Shiro, S Adachi

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   58   81 - 89   2002.1

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    DOI： 10.1107/S0907444901017383

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  • 2J1630 Crystal sturcture of photolysed intermediates of T- and R-state lmman carbonmonoxy heamoglobin at 25 K

    Adachi S., Park S. -Y., Tame Jeremy, Shiro Y., Shibayama N.

    Seibutsu Butsuri   42 ( 2 )   S128   2002

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    DOI： 10.2142/biophys.42.S128_4

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  • Molecular mechanism of nitric oxide reduction catalyzed by fungal nitric oxide reductase Reviewed

    E Obayashi, H Shimizu, S Park, H Nakamura, S Takahashi, H Shoun, Y Shiro

    OXYGEN AND LIFE: OXYGENASES, OXIDASE AND LIPID MEDIATORS   1233   59 - 62   2002

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  • Characterization of the oxygenated intermediate of the thermophilic cytochrome P450 CYP119 Reviewed

    Ilia G. Denisov, Shao-Ching Hung, Kara E. Weiss, Mark A. McLean, Yoshitsugu Shiro, Sam-Yong Park, Paul M. Champion, Stephen G. Sligar

    Journal of Inorganic Biochemistry   87 ( 4 )   215 - 226   2001.12

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    DOI： 10.1016/S0162-0134(01)00328-2

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  • Crystallization and preliminary X-ray diffraction analysis of the light-harvesting protein phycocyanin from the thermophilic cyanobacterium Synechococcus elongatus Reviewed

    Y Toriumi, SY Park, H Hashimoto, H Shimizu, M Hirano, N Kamiya

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   57   1326 - 1328   2001.9

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  • The RIKEN structural biology beamline II (BL44B2) at the SPring-8 Reviewed

    S Adachi, T Oguchi, H Tanida, SY Park, H Shimizu, H Miyatake, N Kamiya, Y Shiro, Y Inoue, T Ueki, T Iizuka

    NUCLEAR INSTRUMENTS & METHODS IN PHYSICS RESEARCH SECTION A-ACCELERATORS SPECTROMETERS DETECTORS AND ASSOCIATED EQUIPMENT   467   711 - 714   2001.7

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  • The functional similarity and structural diversity of human and cartilaginous fish hemoglobins Reviewed

    Y Naoi, KT Chong, K Yoshimatsu, G Miyazaki, JRH Tame, SY Park, S Adachi, H Morimoto

    JOURNAL OF MOLECULAR BIOLOGY   307 ( 1 )   259 - 270   2001.3

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  • Structures and stabilities of interspecies chimeric cytochromes c

    Yamamoto E., Shibayama N., Saigo S.

    Seibutsu Butsuri   41   S45   2001

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    DOI： 10.2142/biophys.41.S45_2

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  • Oxygen affinity of R-state hemoglobin can be altered by drug binding

    Shibayama N., Tame Jeremy, Yonetani T., Park S.-Y.

    Seibutsu Butsuri   41   S112   2001

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    DOI： 10.2142/biophys.41.S112_1

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  • X-ray crystal structure and catalytic properties of Thr252Ile mutant of cytochrome P450cam: Roles of Thr252 and water in the active center Reviewed

    T Hishiki, H Shimada, S Nagano, T Egawa, Y Kanamori, R Makino, SY Park, S Adachi, Y Shiro, Y Ishimura

    JOURNAL OF BIOCHEMISTRY   128 ( 6 )   965 - 974   2000.12

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  • Crystallization and preliminary X-ray diffraction analysis of a cytochrome P450 (CYP119) from Sulfolobus solfataricus Reviewed

    SY Park, K Yamane, S Adachi, Y Shiro, KE Weiss, SG Sligar

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   56   1173 - 1175   2000.9

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  • Crystal structure of nitric oxide reductase cytochrome P-450(nor) Fusarium oxysporum Reviewed

    SY Park, H Shimizu, SI Adachi, Y Shiro, T Iizuka, H Shoun

    OXYGEN HOMEOSTASIS AND ITS DYNAMICS   1   147 - 155   1998

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  • Crystallization, preliminary diffraction and electron paramagnetic resonance studies of a single crystal of cytochrome P450nor Reviewed

    SY Park, H Shimizu, S Adachi, Y Shiro, T Iizuka, A Nakagawa, Tanaka, I, H Shoun, H Hori

    FEBS LETTERS   412 ( 2 )   346 - 350   1997.7

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    DOI： 10.1016/S0014-5793(97)00795-3

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  • Functional and structural comparison of nitric oxide reductases from denitrifying fungi Cylindrocarpon tonkinense and Fusarium oxysporum Reviewed

    N Toritsuka, H Shoun, UP Singh, SY Park, T Iizuka, Y Shiro

    BIOCHIMICA ET BIOPHYSICA ACTA-PROTEIN STRUCTURE AND MOLECULAR ENZYMOLOGY   1338 ( 1 )   93 - 99   1997.3

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  • High-resolution crystal structure of magnesium (MgII)-iron (FeII) hybrid hemoglobin with liganded beta subunits Reviewed

    SY Park, A Nakagawa, H Morimoto

    JOURNAL OF MOLECULAR BIOLOGY   255 ( 5 )   726 - 734   1996.2

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    DOI： 10.1006/jmbi.1996.0059

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    Other Link： http://orcid.org/0000-0002-1700-7861

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  • スプライシングタンパク質U2AF1によるイントロン認識機構のX線結晶構造解析

    吉田尚史, 吉田尚史, 朴三用, 成相裕子, 坂下暁介, 桑迫香奈子, 武藤裕, 浦野健, 尾林栄治

    日本生化学会大会(Web)   94th   2021

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  • スプライシングタンパク質U2AF1によるイントロン認識機構の解明

    吉田尚史, 朴三用, 坂下暁介, 成相裕子, 桑迫香奈子, 武藤裕, 浦野健, 尾林栄治

    生体分子科学討論会講演要旨集   47th   2021

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  • Structural and Functional Insights into a Photoactivated Adenylyl Cyclase

    59 ( 2 )   102 - 107   2017.6

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  • Seeing the light with BLUF proteins

    Sam-Yong Park, Jeremy R. H. Tame

    Biophysical Reviews   9 ( 2 )   169 - 176   2017.4

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    Language：English   Publishing type：Book review, literature introduction, etc.   Publisher：Springer Verlag  

    DOI： 10.1007/s12551-017-0258-6

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  • X-Ray Fluorescence Holography for Proteins: Application to Hemoglobin and Myoglobin

    Ayana Sato-Tomita, Naohisa Happo, Sam-Yong Park, Koichi Hayashi, Yuji C. Sasaki, Naoya Shibayama

    BIOPHYSICAL JOURNAL   112 ( 3 )   579A - 579A   2017.2

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  • New Structural Analysis Methods for Hemoglobin Crystals. Time-Resolved Cryogenic X-Ray Crystallography with Extended Pulsed-Laser Pumping and 3D Imaging by X-Ray Fluorescence Holography

    Ayana Sato-Tomita, Shin-ichi Adachi, Sam-Yong Park, Yuji C. Sasaki, Koichi Hayashi, Naoya Shibayama

    BIOPHYSICAL JOURNAL   110 ( 3 )   160A - 160A   2016.2

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  • 特殊なヌクレオソームの立体構造解析

    加藤大貴, 越阪部晃永, 足立風水也, 水上優夏, 有村泰宏, 七種和美, 七種和美, 明石知子, 西村善文, 朴三用, 松本淳, 河野秀俊, 井上倫太郎, 杉山正明, 胡桃坂仁志

    日本分子生物学会年会プログラム・要旨集(Web)   39th   2016

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  • Chitin Oligosaccharide Deacetylase from Marine Bacteria : Enzymological Characters, Three-dimensional Structure, and the Roles of Its Product

    Hirano Takako, Sugiyama Kanako, Sakaki Yuta, Uehara Rie, Shiraishi Haruka, Hakamata Wataru, Park Sam-Yong, Nishio Toshiyuki

    Bulletin of applied glycoscience   5 ( 2 )   113 - 119   2015.5

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    一般に,海洋細菌であるVibrio属細菌は,キチナーゼを分泌してN,N&#039;-diacetylchitobiose[(GlcNAc)_2]を生産することが知られている。しかし,一部の菌はさらにキチンオリゴ糖脱アセチル化酵素(COD)を分泌し,菌体外最終産物としてβ-N-acetyl-D-glucosaminyl-(1,4)-D-glucosamine(GlcNAc-GlcN)を生産する。CODは,Carbohydrate esterase family 4に分類され(GlcNAc)_2に特異性の高い脱アセチル化酵素として2010年にEC 3.5.1.105が付された酵素である。CODの酵素化学的性質については,数種のVibrio属細菌由来の酵素で報告されている。最近,我々はVibrio parahaemolyticus由来CODが1つの活性ドメイン(PDD)と2つのキチン結合ドメイン(CBD)から成ることを立体構造から確認した。また,各ドメインがそれぞれ独立して機能することも解明した。さらにGlcNAc-GlcNは,COD生産性Vibrio属細菌に特異的なキチナーゼ生産誘導因子および遊走性因子であることも明らかにした。これらのことから,CODは一部のVibrio属細菌にとってはキチン利用のためのシグナル分子生産に必須な酵素であることがわかった。

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  • S3-4 海洋細菌のキチンオリゴ糖脱アセチル化酵素に関する研究(応用糖質科学シンポジウム,日本応用糖質科学会平成26年度大会(第63回))

    平野 貴子, 杉山 佳奈子, 坂木 祐太, 上原 理絵, 白石 晴香, 袴田 航, 朴 三用, 西尾 俊幸

    応用糖質科学 : 日本応用糖質科学会誌   4 ( 3 )   2014.8

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  • Aa-8 Vibrio parahaemolyticus由来キチンオリゴ糖デアセチラーゼのキチン結合ドメインの機能解析(キチナーゼ・キチン関連酵素,一般講演,日本応用糖質科学会平成25年度大会(第62回))

    坂木 祐太, 平野 貴子, 杉山 佳奈子, 袴田 航, 朴 三用, 西尾 俊幸

    応用糖質科学 : 日本応用糖質科学会誌   3 ( 3 )   B26   2013.8

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  • Ba2-5 Vibrio属細菌由来キチンオリゴ糖デアセチラーゼの構造解析および諸性質調査(バイオマス関連酵素(キチナーゼ・キトサナーゼ他),一般講演,日本応用糖質科学会平成24年度大会(第61回))

    前原 佑哉, 杉山 佳奈子, 坂木 祐太, 上原 理絵, 平野 貴子, 袴田 航, 朴 三用, 西尾 俊幸

    応用糖質科学 : 日本応用糖質科学会誌   2 ( 3 )   B52   2012.8

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  • Enzyme chemistry of chitin oligosaccharide deacetylase from Vibrios

    HIRANO Takako, SUGIYAMA Kanako, MAEBARA Yuya, SAKAKI Yuta, UEHARA Rie, HAKAMATA Wataru, PARK Sam-Yong, NISHIO Toshiyuki

    18 ( 2 )   140 - 141   2012.7

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  • Structure of PB1-PB2 subunit interface of inflenza A virus RNA polymerase

    Kanako Sugiyama, Eiji Obayashi, Atsushi Kawaguchi, Yukari Suzuki, Jeremy R. H. Tame, Kyosuke Nagata, Sam-Yong Park

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   67   C411 - C412   2011

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    DOI： 10.1107/S0108767311089677

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  • The structural basis for the essential PA-PB1 subunit interaction in influenza RNA polymerase

    Hisashi Yoshida, Eiji Obayashi, Atsushi Kawaguchi, Kyosuke Nagata, Jeremy R. H. Tame, Sam-Yong Park

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   67   C413 - C413   2011

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    DOI： 10.1107/S0108767311089641

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  • Autotransporter passenger proteins: virulence factors with common structural themes

    Kaoru Nishimura, Nami Tajima, Young-Ho Yoon, Sam-Yong Park, Jeremy R. H. Tame

    JOURNAL OF MOLECULAR MEDICINE-JMM   88 ( 5 )   451 - 458   2010.5

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    DOI： 10.1007/s00109-010-0600-y

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  • Inhibition of Electron Acceptance from Ascorbate by the Specific N-carbethoxylations of Maize Cytochrome b_<561> : A Common Mechanism for the Transmembrane Electron Transfer in Cytochrome b_<561> Protein Family

    NAKANISHI Nobuyuki, RAHMAN Md Motiur, SAKAMOTO Yoichi, MIURA Masahiro, TAKEUCHI Fusako, PARK Sam-Yong, TSUBAKI Motonari

    Journal of Biochemistry   146 ( 6 )   857 - 866   2009.12

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  • Studies of Protein-Protein and Protein-RNA Complexes by Mass Spectrometry

    AKASHI Satoko, WATANABE Masahiro, HEDDLE Jonathan G., UNZAI Satoru, PARK Sam-Yong, TAME Jeremy R. H.

    51 ( 1 )   105 - 106   2009.2

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  • ついに解明! インフルエンザウイルス増殖の謎--増殖に関与するRNAポリメラーゼの立体構造

    尾林 栄治, 朴 三用

    化学   64 ( 2 )   25 - 29   2009.2

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  • Crystallization and Structural Analysis of Cytochrome c_6 from the Diatom Phaeodactylum tricornutum at 1.5Å Resolution

    AKAZAKI Hideharu, KAWAI Fumihiro, HOSOKAWA Masaki, HAMA Toshiyuki, CHIDA Hirotaka, HIRANO Takako, LIM Boon-Keng, SAKURAI Nobuo, HAKAMATA Wataru, PARK Sam-Yong, NISHIO Toshiyuki, OKU Tadatake

    Agricultural and Biological Chemistry   73 ( 1 )   189 - 191   2009

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    Language：English   Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry  

    We determined for the first time the crystal structure of diatom cytochrome <I>c</I><SUB>6</SUB> from <I>Phaeodactylum tricornutum</I> at 1.5 Å resolution. The overall structure of the protein was classified as a class I <I>c</I>-type cytochrome. The physicochemical properties of the protein were examined by denaturation with guanidine hydrochloride and urea, and compared with those of other algal cytochrome <I>c</I><SUB>6</SUB>.

    DOI： 10.1271/bbb.80472

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    Other Link： https://jlc.jst.go.jp/DN/JALC/00324722886?from=CiNii

  • Slow ligand migration dynamics in carbonmonoxy myoglobin at cryogenic temperature

    Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Shin-ya Koshihara, Shin-ichi Adachi

    ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES   64   C358 - C358   2008

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    DOI： 10.1107/S0108767308088545

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  • パルス中性子源を用いたヒト由来デオキシヘモグロビンの中性子実験

    茶竹俊行, 石川卓哉, KOVALEVSKYI Andrii Y., 柴山修哉, PARK Sam-Yong, MUSTYAKIMOV Marat, LANGAN Paul, 森本幸生

    京都大学原子炉実験所学術講演会報文集   42nd   2008

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  • R-state haemoglobin with low oxygen affinity: Crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35

    T Yokoyama, S Neya, A Tsuneshige, T Yonetani, SY Park, JRH Tame

    JOURNAL OF MOLECULAR BIOLOGY   356 ( 3 )   790 - 801   2006.2

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  • Crystal structure of oxidised cytochrome c6A from Alabidopsis thaliana

    奥 忠武, Chida H, Yokoyama T, Kawai F, Nakazawa A, Akazaki H, Takayama Y, Hirano T, Suruga K, Satoh T, Yamada S, Kawachi R, Unzai S, Nishio T, Park SY, Oku T

    FEBS Letters   580 ( 15 )   3763 - 3768   2006

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  • デオキシヘモグロビンの中性子構造の精密化により明らかにされた,ヒスチジン残基のプロトネーション

    茶竹俊行, PARK Sam-Yong, 柴山修哉, 森本幸生

    日本中性子科学会年会講演概要集   6th   2006

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  • The crystal structures of the ferric and ferrous forms of the heme complex of HmuO, a heme oxygenase of Corynebacterium diphtheriae

    S Hirotsu, GC Chu, M Unno, DS Lee, T Yoshida, SY Park, Y Shiro, M Ikeda-Saito

    JOURNAL OF BIOLOGICAL CHEMISTRY   279 ( 12 )   11937 - 11947   2004.3

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  • MAD phasing at ultra-high energy region

    Miyatake H, Takeda K, Park S-Y, Kawamoto M, Kamiya N, Miki K

    Seibutsu Butsuri   43 ( 0 )   S2   2003

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    DOI： 10.2142/biophys.43.S2_2

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  • EXAFS analysis for heme ligands in CO-dependent transcriptional activator CooA

    H Nakajima, E Nakagawa, S Aono, SY Park, H Miyatake, Y Shiro

    JOURNAL OF INORGANIC BIOCHEMISTRY   86 ( 1 )   355 - 355   2001.8

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  • Structural characterization of n-butyl-isocyanide complexes of cytochromes P450nor and P450cam

    DS Lee, SY Park, K Yamane, E Obayashi, H Hori, Y Shiro

    BIOCHEMISTRY   40 ( 9 )   2669 - 2677   2001.3

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  • Crystal structure of rat biliverdin reductase

    A Kikuchi, SY Park, H Miyatake, DY Sun, M Sato, T Yoshida, Y Shiro

    NATURE STRUCTURAL BIOLOGY   8 ( 3 )   221 - 225   2001.3

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  • Redox properties and coordination structure of the heme in the CO-sensing transcriptional activator CooA

    H Nakajima, Y Honma, T Tawara, T Kato, SY Park, H Miyatake, Y Shiro, S Aono

    JOURNAL OF BIOLOGICAL CHEMISTRY   276 ( 10 )   7055 - 7061   2001.3

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  • A positively charged cluster formed in the heme-distal pocket of cytochrome P450nor is essential for interaction with NADH

    T Kudo, N Takaya, SY Park, Y Shiro, H Shoun

    JOURNAL OF BIOLOGICAL CHEMISTRY   276 ( 7 )   5020 - 5026   2001.2

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  • n-Butyl-isocyanide結合型P450のX線結晶構造解析

    40   2669 - 2677   2001

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  • 一酸化炭素センサータンパク質CooAの機能解析

    276   7055 - 7061   2001

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  • Rat Biliverdinの還元構造のX線結晶構造解析

    8   7055 - 7061   2001

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  • サメヘモグロビンのX線結晶構造解析

    307   259 - 270   2001

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  • Mechanism of Molecular Evolution of Vertebrate Hemoglobin Deduced from the Structural Comparison of Cartilaginous Fish hemoglobins with Human Hemoglobin

    Journal of molecular biology   307   259 - 270   2001

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  • NADH結合部位のX線結晶構造解析

    276   5020 - 5026   2001

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  • Structure of cytochrome c(6) from the red alga Porphyra yezoensis at 1.57 angstrom resolution

    S Yamada, SY Park, H Shimizu, Y Koshizuka, K Kadokura, T Satoh, K Suruga, M Ogawa, Y Isogai, T Nishio, Y Shiro, T Oku

    ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY   56   1577 - 1582   2000.12

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  • Mutation effects of a conserved threonine (Thr243) of cytochrome P450nor on its structure and function

    E Obayashi, H Shimizu, SY Park, H Shoun, Y Shiro

    JOURNAL OF INORGANIC BIOCHEMISTRY   82 ( 1-4 )   103 - 111   2000.11

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  • ヘム代謝系酵素ビリベルジンリダクターゼの構造

    菊地晶裕, 朴三用, 宮武秀行, 清水英明, 足立伸一, 城宜嗣, 孫丹宇, 佐藤道比古, 吉田匡

    生化学   72 ( 8 )   760   2000.8

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  • Sensory mechanism of oxygen sensor FixL from Rhizobium meliloti: Crystallographic, mutagenesis and resonance Raman spectroscopic studies

    H Miyatake, M Mukai, SY Park, S Adachi, K Tamura, H Nakamura, K Nakamura, T Tsuchiya, T Iizuka, Y Shiro

    JOURNAL OF MOLECULAR BIOLOGY   301 ( 2 )   415 - 431   2000.8

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  • Crystal structures of cytochrome P450nor and its mutants (Ser286 -&gt; Val, Thr) in the ferric resting state at cryogenic temperature: a comparative analysis with monooxygenase cytochrome P450s

    H Shimizu, SY Park, DS Lee, H Shoun, Y Shiro

    JOURNAL OF INORGANIC BIOCHEMISTRY   81 ( 3 )   191 - 205   2000.8

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  • Current Status of RIKEN beamline II (BL44B2)

    ADACHI Shin-ichi, MIYATAKE Hideyuki, PARK Sam-Yong, KAMIYA Nobuo, SHIRO Yoshitsugu, INOUE Yorinao, OGUCHI Takuyo, TANIDA Hajime, UEKI Tatzuo, IIZUKA Tetsutaro

    Journal of the Crystallographic Society of Japan   42 ( 1 )   106 - 113   2000.2

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    Language：Japanese   Publisher：日本結晶学会  

    RIKEN beamline II (BL44B2) is dedicated to macromolecular crystallography in white and monochromatic X-ray mode, and XAFS of diluted biological systems. The user run was started since April 1998, and lots of scientific applications including time-resolved (intermediate state) protein crystallography, protein crystallography at atomic resolution, phasing with anomalous scattering, membrane protein crystallography, and fluorescence XAFS of diluted metalloproteins have been emerging.

    DOI： 10.5940/jcrsj.42.106

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  • Proton delivery in NO reduction by fungal nitric-oxide reductase - Cryogenic crystallography, spectroscopy, and kinetics of ferric-NO complexes of wild-type and mutant enzymes

    H Shimizu, E Obayashi, Y Gomi, H Arakawa, SY Park, H Nakamura, S Adachi, H Shoun, Y Shiro

    JOURNAL OF BIOLOGICAL CHEMISTRY   275 ( 7 )   4816 - 4826   2000.2

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  • 一酸化窒素還元酵素P450norの機能解析

    275   4816 - 4826   2000

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  • Structure of Biliverdin Reductase

    Kikuchi A, Park S-Y, Miyatake H, Shiro Y, Sun D, Sato M, Yoshida T

    Seibutsu Butsuri   40 ( 0 )   S122   2000

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    Language：Japanese   Publisher：一般社団法人 日本生物物理学会  

    DOI： 10.2142/biophys.40.S122_3

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  • 酸素センサータンパク質FixLのX線構造解析

    301   415 - 431   2000

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  • Magnesium(II) and zinc(II)-protoporphyrin IX's stabilize the lowest oxygen affinity state of human hemoglobin even more strongly than deoxyheme

    G Miyazaki, H Morimoto, KM Yun, SY Park, A Nakagawa, H Minagawa, N Shibayama

    JOURNAL OF MOLECULAR BIOLOGY   292 ( 5 )   1121 - 1136   1999.10

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  • Crystallization and preliminary X-ray diffraction analysis of a recombinant bacterial heme oxygenase (Hmu O) from Corynebacterium diphtheriae

    GC Chu, SY Park, Y Shiro, T Yoshida, M Ikeda-Saito

    JOURNAL OF STRUCTURAL BIOLOGY   126 ( 2 )   171 - 174   1999.6

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  • Zn(II)混成ヘモグロビンの機能と構造解析

    292   1121 - 1136   1999

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  • Crystal Structure of Oxygen Sensor FixL.

    Miyatake H, Park S-Y, Adachi S, Tamura K, Nakamura H, Tsuchiya T, Iizuka T, Shiro Y

    Seibutsu Butsuri   39 ( 0 )   S105   1999

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    Language：Japanese   Publisher：一般社団法人 日本生物物理学会  

    DOI： 10.2142/biophys.39.S105_4

    CiNii Books

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  • Ligand exchange on the heme in the transcriptional activator CooA regulated by CO

    Nakajima H, Aono S, Shiro Y, Miyatake H, Park S

    Biophysics   38 ( 2 )   S36   1998.9

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    Language：Japanese   Publisher：一般社団法人日本生物物理学会  

    CiNii Books

    J-GLOBAL

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  • Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum

    SY Park, H Shimizu, S Adachi, A Nakagawa, Tanaka, I, K Nakahara, H Shoun, E Obayashi, H Nakamura, T Iizuka, Y Shiro

    NATURE STRUCTURAL BIOLOGY   4 ( 10 )   827 - 832   1997.10

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  • Crystal structure of nitric oxide reductase cytochrome P450nor from Fusarium oxysporum

    SY Park, H Shimizu, S Adachi, H Shoun, T Iizuka, Y Shiro

    FASEB JOURNAL   11 ( 9 )   A795 - A795   1997.7

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    Language：English   Publishing type：Research paper, summary (international conference)  

    Web of Science

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  • Crystal structure and reaction mechanism of nitric oxide reductase cytochrome P450nor

    Y Shiro, SY Park, H Shoun

    FASEB JOURNAL   11 ( 9 )   A773 - A773   1997.7

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    Language：English   Publishing type：Research paper, summary (international conference)  

    Web of Science

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  • 一酸化窒素還元酵素P450norのX線結晶構造解析

    4   827 - 832   1997

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  • Crystal Structure of Nitric Oxide Reductase Cytochrome P450nor from Fusarium oxysporum

    PARK S.-Y., SHIMIZU H, ADACHI S, IIZUKA T., SHIRO Y., SHOUN H., NAKAGAWA A., TANAKA I.

    45   S64   1996.12

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    Language：English  

    CiNii Books

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  • 一酸化窒素還元酵素チトクロムP450norのX線結晶構造解析

    清水 英明, 足立 伸一, 朴 三用, 城 宜嗣, 飯塚 哲太郎, 祥雲 弘文

    日本分子生物学会年会プログラム・講演要旨集   19   151 - 151   1996.8

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    Language：Japanese  

    CiNii Books

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  • Crystallization of Nitric Oxide Reductase Cytochrome P450nor from Fusarium oxysporum

    Sam-Yong Park, Shin-ichi Adachi, Hideaki Shimizu, Tetsutaro Iizuka, Yoshitsugu Shiro, Hiroshi Shoun, Atsushi Nakagawa, Isao Tanaka

    Photon Factory Activity Report   13 ( Suppl )   66   1995

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    Language：English   Publishing type：Article, review, commentary, editorial, etc. (international conference proceedings)  

    DOI： 10.1107/S0108767396093762

    Web of Science

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Works

  • 高熱菌チトクロムCYP119のX線結晶構造解析

    1999 - 2001

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  • High Resolution Structural Origin of Thermostability

    1999 - 2001

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  • Crystal Structure of Mg(I)-Fe(II)Hydrid Hemoglobin

    1996 - 2001

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  • Mg(II)-Fe(II)混成ヘモグロビンのX線結晶構造解析

    1996 - 2001

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  • 一酸化窒素還元酵素P450norのX線結晶構造解析

    1996 - 2000

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  • Crystal Structure of Cytochrome P450nor

    1996 - 2000

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Awards

  • 日本生化学会論文賞

    2000  

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    Country：Japan

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Research Projects

  • Structure and functional analysis of the SARS-CoV-2 Nucleocapsid Protein

    Grant number：21H02449  2021.4 - 2024.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant amount：\17550000 （ Direct Cost: \13500000 、 Indirect Cost：\4050000 ）

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  • Structural analysis of various light-driven reaction mechanisms of light-sensitive proteins.

    Grant number：19H05779  2019.6 - 2024.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

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    Grant amount：\106470000 （ Direct Cost: \81900000 、 Indirect Cost：\24570000 ）

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  • Molecular mechanism of photoactivation of a light-regulated adenylate cyclase

    Grant number：18H02413  2018.4 - 2021.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Park Sam-Yong

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    Grant amount：\17680000 （ Direct Cost: \13600000 、 Indirect Cost：\4080000 ）

    Optogenetics is a rapidly growing field in which light is used to control biological systems. We show that OaPAC protein produces the fundamental second messenger cyclic-AMP (cAMP) in response to blue light, is stable and functional in human cells, and can therefore be used to trigger events by raising cAMP level. OaPAC consists of a catalytic domain controlled by a photosensitive BLUF domain. We have solved the crystal structure to show how activity is triggered by light, and guide mutagenesis experiments. Although the catalytic domain resembles known cyclases, the BLUF domains form an unusual intertwined structure. The protein activity is the same in solution as in the crystal, showing that the activation mechanism involves only very small molecular movements.

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  • Structural Study on Mental Disease Gene Product Protein

    Grant number：15K06980  2015.4 - 2018.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    UNZAI Satoru, PARK Sam-Yong, KOMIYAMA Noboru

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    Grant amount：\5200000 （ Direct Cost: \4000000 、 Indirect Cost：\1200000 ）

    The brain-specific synaptic GTPase activating protein (SynGAP) is important in synaptic plasticity. Mutations in SYNGAP1 gene cause epileptic encephalopathy, intellectual disability, and autism via haploinsufficiency. Basic research is needed to better understand the molecular functions of the SynGAP protein, which will lead to targets for therapeutic intervention. Structural biology methods were applied for the SynGAP function research. Recombinant SynGAP and Rap1B (SynGAP can enhance Rap1B GTPase activity) were prepared using e-coli expression system. We succeeded in solving high resolution crystal structure of the Rap1B protein and understanding its molecular switch mechanism. We established small volume GTPase activity measurement system using malachite green. Rap1B GTPase activity enhancement by SynGAP can be detected by this system.

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  • The mechanism analysis of influenza RNA polymerase

    Grant number：25291016  2013.4 - 2016.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    Park Sam-Yong, Sugiyama Kanako, Urano Takeshi

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    Grant amount：\18330000 （ Direct Cost: \14100000 、 Indirect Cost：\4230000 ）

    Influenza RNA polymerase plays vital roles in the virus life cycle and, since it is much more highly conserved than other influenza virus proteins, it is of great interest as a drug target. This laboratory has created monoclonal antibodies that bind to fragments of the polymerase and block viral replication. Antibody PA11.9 binds to the PA subunit carrying the RNA polymerisation active site.
    Two other antibodies were shown to bind to the RNA-binding PB2 subunit of the polymerase, including antibody PB2 3-1.6, which has notably high affinity for its target. This antibody has been patented as a research tool and diagnostic reagent (patent number 2014-068824).

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  • Molecular basis of host cell competency in virus infection

    Grant number：24115001  2012.6 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    NAGATA Kyosuke, Park Sam-Yong, Takeyasu Kunio, Takaori Akifumi, Arase Hisashi, Iba Hideo, Koyanagi Yoshio

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    Grant amount：\53950000 （ Direct Cost: \41500000 、 Indirect Cost：\12450000 ）

    In this research, we aimed to promote the research among groups and to support the new research concepts. Along with the collaborative research, we will understand the molecular basis of host-specific viral replication resulting in pathogenecity and antagonism between host defense system and infectious agents. Based on these findings, we aimed to establish general concepts, which determine tolerance / non-tolerance against infectious agents, .

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  • Host cell competnecy for negative-stranded RNA viruses

    Grant number：24115002  2012.6 - 2017.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    NAGATA Kyosuke, Kawaguchi Atsushi

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    Grant amount：\143130000 （ Direct Cost: \110100000 、 Indirect Cost：\33030000 ）

    This research aimed to identify host factors, which regulate influenza virus genome function, and to analyze the replicational and post-replicational regulation of influenza virus genome.
    We identified pp32/APRIL and Prp18 as stimulatory factors of viral RNA polymerase. Further, we found that newly synthesized viral genomes are recruited to the centrosome by YB-1, and the progeny viral genome is transported to the plasma membrane via cholesterol-enriched Rab11a-positive recycling endosomes. Cholesterol is thought to be a trigger for the virus assembly concomitantly with arrival of the virus genome beneath the plasma membrane.

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  • Elucidation of the true picture of the hemoglobin allosteric equilibrium

    Grant number：23570197  2011 - 2013

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    SHIBAYAMA Naoya, PARK Sam-yong

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    Grant amount：\5720000 （ Direct Cost: \4400000 、 Indirect Cost：\1320000 ）

    The molecular mechanisms of protein allostery have been attributed to the two-state transition between T (tense) and R (relaxed) states, based largely on the knowledge about hemoglobin (Hb). However, an equilibrium ensemble for solution Hb cannot be adequately described by just these two states. Here we report an unprecedented crystal form in which Hb is free to adopt any allosteric structure, depending on the conditions, and at the same time allows oxygen binding to be monitored directly in the crystal. We identify nine conformations including a new intermediate between T and R. Our findings give a comprehensive picture of the equilibrium conformers and transition pathway for Hb.

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  • Structural Study on neuron protein complex essential for memory and learning

    Grant number：23570145  2011 - 2013

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    UNZAI Satoru, PARK Sam-yong

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    Grant amount：\5460000 （ Direct Cost: \4200000 、 Indirect Cost：\1260000 ）

    In the vertebrate brain, nerve cells are managing memory and learning. The nerve cells are connected via synapses, which are real nature of the memory and learning. NMDA receptor and related proteins at the synapse are essential for the regulation of synaptic strength. The proteins form quite large complex and they communicate each other via interaction or chemical modification. Using structural biology technics, we try to understand how they communicate, how they form complexes, and how they work for the synaptic strength regulation. Rap1 molecule is a GTPase, a kind of molecular switch belongs to Ras super family. This molecule works as a signal transduction factor in a nerve cell and related with the NMDA receptor protein complex. We succeeded solving high-resolution crystal structure of the Rap1 molecule, GTP analogue bound form and GDP bound form.

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  • Analyses of centromeric chromatin structure

    Grant number：23770008  2011 - 2012

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Young Scientists (B)

    TACHIWANA Hiroaki, KURUMIZAKA Hitoshi, KAGAWA Wataru, KIMURA Hiroshi, PARK Sam-yong, SATO Mamoru, SHIBATA Takehiko, MASUMOTO Hiroshi, OHZEKI Jun-ichirou, OSAKABE Akihisa, HORIKOSHI Naoki, ARIMURA Yasuhiro, MIYA Yuta, MATSUMOTO Ryohei

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    Grant amount：\4680000 （ Direct Cost: \3600000 、 Indirect Cost：\1080000 ）

    Genomic DNA is duplicated during S phase, and is equally divided into two daughter cells during M phase. The detail mechanism of equal chromosome segregation is unknown. Centromeres are distinct regions in the chromosome, and plays important roles in chromosome segregation and centromeric chromatin is necessary to function. In this study, centromeric chromatin structure was analyzed.

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  • Analysis of the outer membrane BAM complex

    Grant number：22370044  2010 - 2012

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    J・R・H Tame, PARK Sam-yong, UNZAI Satoru

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    Grant amount：\18980000 （ Direct Cost: \14600000 、 Indirect Cost：\4380000 ）

    Gram negative bacteria require the BAM complex for the insertion of membrane proteins into the outer membrane. This essential complex consists of five proteins, the large transmembrane barrel being BamA. BamA carries five POTRA domains at its N terminus which interact with other proteins in the complex. Only BamA and BamD are essential, but the roles of these proteins is unknown. We have solved the crystal structure of an outer membrane protein, Hbp, and studied the interaction between BamC and BamD. The Hbp beta-barrel is a substrate of BAM, but the interactions between the two are unclear. We have shown that BamC and BamD interact to give a flexible complex.

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  • Structural basis for an essential subunit interaction in influenza virus RNA polymerase PB1-PB2

    Grant number：21370046  2009 - 2011

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    PARK Sam-yong, FUKUNISHI Yoshihumi

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    Grant amount：\19110000 （ Direct Cost: \14700000 、 Indirect Cost：\4410000 ）

    Influenza virus RNA-dependent RNA polymerase is a multi-functional heterotrimer, which uses a "cap-snatching" mechanism to produce viral mRNA. Host cell mRNA is cleaved to yield a cap-bearing oligonucleotide which can be extended using viral genomic RNA as a template. The cap binding and endonuclease activities are only activated once viral genomic RNA is bound. This requires signaling from the RNA-binding PB1 subunit to the cap-binding PB2 subunit, and the interface between these two subunits is essential for polymerase activity. We have defined this interaction surface by protein crystallography, and tested the effects of mutating contact residues on the function of the holo-enzyme. This novel interface is surprisingly small, yet it plays a crucial role in regulating the 250 kDa polymerase, and is completely conserved among avian and human influenza.

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  • The structural analysis of centromere specific nucleosome

    Grant number：21870038  2009 - 2010

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Research Activity Start-up

    TACHIWANA Hiroaki, KURUMIZAKA HITOSHI, KAGAWA Wataru, KIMURA Hiroshi, PARK Sam-Yong, SATO Mamoru, SHIGA Tatsuya, OSAKABE Akihisa, MIYA Yuta, MATSUMOTO Ryohei, ARIMURA Yasuhiro, HORIKOSHI Naoki

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    Grant amount：\2756000 （ Direct Cost: \2120000 、 Indirect Cost：\636000 ）

    In eukaryotes, genomic DNA is duplicated during S phase, and is equally divided into two daughter cells during M phase. Centromere, which is one of the distinct regions in chromosome, plays important rules in this division. Centromere formation is necessary for chromosome segregation. But, it is not known how centromere region is formed and distinguished from other region. Some proteins, which localize specifically at centromere region, are identified. CENP-A, a histone H3 variant, also localize specifically at centromere region. CENP-A is assembled into the chromatin of centromeres and is thought to generate unique chromatin features. In this study, we performed structural analysis of the CENP-A nucleosome and determined crystal structure of CENP-A nucleosome by X-ray crystallography. Determined structure revealed that CENP-A nucleosome contains two each of histones H2A, H2B, H4 and CENP-A and DNA is wrapped around histone octamer in a left-hand orientation. Surprisingly, only 121 bp of DNA are visible and 13 bp from both ends of DNA are flexible in the CENP-A-nucleosome. Structural comparison of the CENP-A and H3-nucleosomes revealed that the loop1 region of CENP-A is different from canonical H3 because of insertion of two extra amino acid residues. In vivo analysis revealed these amino acids are important to retain CENP-A at centromere region.

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  • タイマータンパク質EA4の計時機構解明を目指した研究

    Grant number：20657031  2008 - 2009

    日本学術振興会  科学研究費助成事業  挑戦的萌芽研究

    柴山 修哉, 朴 三用

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    Grant amount：\3500000 （ Direct Cost: \3500000 ）

    1. 初期状態EA4のX線結晶構造解析
    EA4はカイコ休眠卵の休眠打破に必要な冬期低温持続時間(5℃で約2週間)を計る機能を持つタイマータンパク質であり、室温の休眠卵中では時間読み停止機能を持つ38残基ペプチド(PIN)との複合体を形成することで時間読み開始前の初期状態に凍結されると報告されている。このような情報をもとに、カイコサナギ個体を宿主としたEA4とPINの共発現系を構築し結晶化スクリーニングを集中的に行った。しかし、複合体の構造解析にはまだ成功していない。これには理由がある。先ず、カイコ個体中ではPINが酵素分解を受け雑多な部分配列ペプチド集合体となり試料を複雑にしていること。また、試料中にPIN以外の未知のEA4結合性ペプチドが混在し、EA4・PIN複合体の形成効率を低下させていることである。本年度は、粗精製した共発現試料に対して大腸菌発現で作製したPINを大過剰に加え、25℃での限外濾過(分画分子量1万)を繰り返すことにより雑ペプチドを除去する方法を新たに取り入れた。ごく最近、この方法で精製した試料の微小結晶を得ることに成功した。現在、X線回折実験に適した大型単結晶の作製条件を検討している。また本年度は、上述の未知のEA4結合性ペプチドの全48アミノ酸配列を決定した。
    2. 計時現象の計算機シミュレーション
    EA4の時間読みは、低温刺激によりPINが解離することで始まり、10日以上の遅延相の後に一過性の鋭いATPase活性を発現することで終了する。この計時現象を説明する最も有力なモデルは、EA4分子内の銅イオンが配位子交換反応を経ながら活性中心までゆっくり移動し活性型に転移する「多段階逐次モデル」である。本年度は、このモデルの妥当性を計算機シミュレーションで検討した。その結果、実際のデータを再現するためには60以上の異なる段階を仮定する必要があることが分かった。これはかなり無理のある状態数であり、モデルの修正を検討中である。

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  • Signal discrimination analyses based on the domain structure of soluble guanylate cyclase

    Grant number：19510224  2007 - 2009

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    MAKINO Ryu, SHIRO Yoshitugu, PAKU Sanyou

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    Grant amount：\4160000 （ Direct Cost: \3200000 、 Indirect Cost：\960000 ）

    We have revealed that there were two kinds of nucleotide binding sites, a catalytic and a pseudo-nucleotide sites in soluble guanylate cyclase. When carbon monoxide combined to the enzymic heme, the binding of YC-1 to the pseudo-nucleotide binding site increased the affinity of a nucleotide for the pseudo nucleotide binding site, through interaction between two binding sites. Furthermore, we have first confirmed the formation of the oxygenated form of the enzyme, which was stable under frozen conditions. The formation of the oxygenated form was noted to be regulated by YC-1 binding, and also was suggested to be governed by the deformation of the heme iron from the heme plane, based on the EXAFS analyses.

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  • Structure and function of autotransporter proteins from pathogenic bacteria

    Grant number：19370045  2007 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    TAME Jeremy R.H., PARK Sam-yong, UNZAI Satoru

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    Grant amount：\18460000 （ Direct Cost: \14200000 、 Indirect Cost：\4260000 ）

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  • Crystal structures of penicillin binding proteins from Haemophilus influenzae

    Grant number：19570109  2007 - 2008

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    PARK Sam-yong, UNZAI Satoru

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    Grant amount：\4550000 （ Direct Cost: \3500000 、 Indirect Cost：\1050000 ）

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  • 膜結合型AAA-ATPase p47/p97複合体による細胞膜認識とその制御

    Grant number：15083206  2003 - 2008

    日本学術振興会  科学研究費助成事業  特定領域研究

    JEREMYR.H. Tame, 朴 三用, 雲財 悟

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    Grant amount：\80600000 （ Direct Cost: \80600000 ）

    (1)TRAPチューブ
    E50CのみTRAPに変異導入したものとV69Cのみに変異導入したものをチューブの最小単位となるように作製した。これはTRAP同士がどのように結合しチューブとなるかをX線結晶構造解析により解明するためである。D8H、F32D、E50C、R66H、V69C(以下HCCDH)と、D8H、F32A、E50C、R66H、V69C(以下HCCAH)というように5箇所に変異を導入し、E50とV69に導入したシステインによりS-S結合を形成することを予想し設計した。
    (2)TRAP-AT複合体
    Bacillus subtilisの細胞質の中では、TRAP活性はanti-TRAPというタンパク質に制御されており、トリプトファンの不足している状態で、TRAPとantiTRAPは複合体を作る。したがって、RNA結合が阻害される。今まではどのようにTRAPとantiTRAPが相互作用しているか明らかではなかった。そのため、我々はこの複合体の結晶化を行い、結晶構造を決定した。
    TRAP-antiTRAP複合体のX線結晶構造を決定した。結晶化とともに、TRAPは11量体から12量体になった。結晶対称軸とTRAPリング軸を合わせて、非対称単位が数個の分子しか含まない。それから、通常では大きい複合体は十分に分解能回折データを測ることができないが、今回は高い分解能のデータを測ることができた。

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  • NO標的酵素(可溶性グアニル酸シクラーゼー)のX線結晶構造解析

    Grant number：13780493  2001 - 2002

    日本学術振興会  科学研究費助成事業  若手研究(B)

    朴 三用

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    Grant amount：\2200000 （ Direct Cost: \2200000 ）

    哺乳類の生体内において一酸化窒素(NO)は、一酸化窒素合成酵素(NOS)により、L-アルギニンと酸素分子より合成される。このNO分子は、血管拡張、筋弛緩、細胞の殺菌、記憶など、様々な生理的機能に関わる細胞間の情報伝達物質として働いている。生体内で合成されたNOは、細胞膜や組織中を自由に拡散して標的タンパク質と直接相互作用する。現在、知られているNOの標的タンパク質であるグアニル酸シクラーゼは、NOが結合するとGTPからセカンドメーッセンジャーであるcGMPを合成し、血管を拡張させる。しかしこのタンパク質にNOが結合したという情報が、どのように同じ分子内にあるcGMP合成部位に伝達されるのか?全く理解されていないことが現状である。そこで、本研究では、アニル酸シクラーゼの分子内情報伝達機構をX線結晶構造解析手法による解明することを目的とする。
    酵素のX線結晶構造解析に向けて、大量に試料を調整を行って、単結晶作成条件の検索(現有クリスタルスクリーン等を用いる)を行った。その結果、硫安溶液とPEG4000の沈澱剤で結晶が得られた。酵素の結晶は5-6Åくらいの分解能を示した。また、構造解析に向いた良好な結晶化の条件ではないが、様々の結晶化条件の検索が必要であると考えられる。現在、クリスタルスクリーン以外の約800種類bufferを作製して、構造解析に向いた単結晶の条件を検索して行く。

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  • Structural Analysis of Ethylene (Plant Hormone) Sensor Protein

    Grant number：12680666  2000 - 2002

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    SHIRO Yoshitsugu, NAKAMURA Hiro, PAK Sam yong

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    Grant amount：\3500000 （ Direct Cost: \3500000 ）

    Ethylene is a plant hormone, which is significantly involved in life cycle of plants. Ethylene exhibits its physiological activities by virtue of binding to its sensor protein, ETR1. ETR1 belongs to the two-component regulatory system in cells, and mainly consists of two functional domain, sensor domain and histidine kinase domain. Most recently, it has been found that the ETR1 sensor domain contains Cu(I). In the present project,we have been trying to obtain the direct evidence that Cu(I) is the ethylene binding site of ETR1. We constructed expression system of the recombinant protein of the ETR1 sensor domain (trans-membrane protein) in E. coli, established it purification procedure, and measured the Cu K-edge XAFS spectra. The spectra is significantly different in the presence and absence of ethylene, showing that ethylene bind to the Cu(I) sitel of ETR1 and causes its coordination structural changes.

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  • 一酸化窒素(NO)還元機構解明

    Grant number：11780434  1999 - 2000

    日本学術振興会  科学研究費助成事業  奨励研究(A)

    朴 三用

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    Grant amount：\600000 （ Direct Cost: \600000 ）

    チトクロムP450norは、P450のスーパーファミリーにも関わらず、従来の機能である酸素一分子添加酵素として機能せず、一酸化窒素(NO)還元する機能を持っている(2NO+NADH+H^+→N_2O+H_2O+NAD^+)。前年度には、NO還元メカニズムを解明するため、機能に重要なアミノ酸である286SerをValとThrに置換した変異型P450norを調製して、活性測定及びX線の結晶構造解析を行って、NO還元メカニズムに関わる水素イオンのネットワックを特定することが出来た。今年は、それと共に、P450のI-helixに共通に保存されている243Thrに着目し、それの変異型を調整し、活性測定及びX線の結晶構造解析を行った。243Thrの変異型には、Asn,Ala,Valの3種類を調整し、NO還元活性測定を行った結果それぞれ、2%,3%,0%を示しており、NO還元に直接的に関わっていると考えられる。これらの変異型を高分解(ぞれぞれ1.4A分解能)のでX線構造解析を行った結果、NO分子からI-helixでの水素イオンのネットワックが切断せれており、NO還元に関わる電子供与体であるNADHの結合部位であると思われるところからのネットワックである。以上の結果から、NO還元メカニズムはに関わる電子は、I-helixの243Thrから、水素イオンの供給は286Serからくると推測でき、このネットワックより、NO分子を還元していると特定することが出来た。

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  • 病気関連のタンパク質のX線結晶構造解析

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    Grant type：Competitive

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  • Crystal Structure about of Disease Protein

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    Grant type：Competitive

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  • Crystal Structure of EYA protein

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    Grant type：Competitive

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  • Crystal Structure of TIME protein

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    Grant type：Competitive

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  • Crystal Structure of Fish Hemoglobins

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    Grant type：Competitive

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  • 時間を認識するタンパク質のX線結晶構造解析

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    Grant type：Competitive

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  • 魚ヘモグロビンのX線結晶構造解析

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    Grant type：Competitive

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  • EYAタンパク質のX線結晶構造解析

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    Grant type：Competitive

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