Updated on 2021/08/01

写真b

 
ODA Takashi
 
*Items subject to periodic update by Rikkyo University (The rest are reprinted from information registered on researchmap.)
Affiliation*
College of Science Department of Life Science
Title*
Assistant Professor
Degree
博士(理学) ( 横浜市立大学 )
Contact information
Mail Address
Research Interests
  • archaea

  • SANS

  • IDP

  • DNA修復

  • SAXS

  • X線結晶構造解析

  • 構造生物学

  • Campus Career*
    • 4 2020 - Present 
      College of Science   Department of Life Science   Assistant Professor
     

    Research Areas

    • Life Science / Structural biochemistry

    Research History

    • 4 2020 - Present 
      RIKKYO UNIVERSITY   College of Science Department of Life Science   Assistant Professor

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    Committee Memberships

    • 4 2019 - Present 
      PF SAXS UG   -

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    Papers

    • Dynamics of proteins with different molecular structures under solution condition. International journal

      Rintaro Inoue, Takashi Oda, Hiroshi Nakagawa, Taiki Tominaga, Tomohide Saio, Yukinobu Kawakita, Masahiro Shimizu, Aya Okuda, Ken Morishima, Nobuhiro Sato, Reiko Urade, Mamoru Sato, Masaaki Sugiyama

      Scientific reports10 ( 1 ) 21678 - 21678   10 12 2020

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

      Incoherent quasielastic neutron scattering (iQENS) is a fascinating technique for investigating the internal dynamics of protein. However, low flux of neutron beam, low signal to noise ratio of QENS spectrometers and unavailability of well-established analyzing method have been obstacles for studying internal dynamics under physiological condition (in solution). The recent progress of neutron source and spectrometer provide the fine iQENS profile with high statistics and as well the progress of computational technique enable us to quantitatively reveal the internal dynamic from the obtained iQENS profile. The internal dynamics of two proteins, globular domain protein (GDP) and intrinsically disordered protein (IDP) in solution, were measured with the state-of-the art QENS spectrometer and then revealed with the newly developed analyzing method. It was clarified that the average relaxation rate of IDP was larger than that of GDP and the fraction of mobile H atoms of IDP was also much higher than that of GDP. Combined with the structural analysis and the calculation of solvent accessible surface area of amino acid residue, it was concluded that the internal dynamics were related to the highly solvent exposed amino acid residues depending upon protein's structure.

      DOI: 10.1038/s41598-020-78311-4

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    • Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy. International journal

      Noriyuki Kodera, Daisuke Noshiro, Sujit K Dora, Tetsuya Mori, Johnny Habchi, David Blocquel, Antoine Gruet, Marion Dosnon, Edoardo Salladini, Christophe Bignon, Yuko Fujioka, Takashi Oda, Nobuo N Noda, Mamoru Sato, Marina Lotti, Mineyuki Mizuguchi, Sonia Longhi, Toshio Ando

      Nature nanotechnology   23 11 2020

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

      Intrinsically disordered proteins (IDPs) are ubiquitous proteins that are disordered entirely or partly and play important roles in diverse biological phenomena. Their structure dynamically samples a multitude of conformational states, thus rendering their structural analysis very difficult. Here we explore the potential of high-speed atomic force microscopy (HS-AFM) for characterizing the structure and dynamics of IDPs. Successive HS-AFM images of an IDP molecule can not only identify constantly folded and constantly disordered regions in the molecule, but can also document disorder-to-order transitions. Moreover, the number of amino acids contained in these disordered regions can be roughly estimated, enabling a semiquantitative, realistic description of the dynamic structure of IDPs.

      DOI: 10.1038/s41565-020-00798-9

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    • Serine 298 Phosphorylation in Linker 2 of UHRF1 Regulates Ligand-Binding Property of Its Tandem Tudor Domain Peer-reviewed

      Satomi Kori, Tomohiro Jimenji, Toru Ekimoto, Miwa Sato, Fumie Kusano, Takashi Oda, Motoko Unoki, Mitsunori Ikeguchi, Kyohei Arita

      Journal of Molecular Biology14 ( 432 ) 59 - 77   5 2020

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

      DOI: 10.1016/j.jmb.2020.05.006

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    • Calcium sensing via EF-hand 4 enables thioredoxin activity in the sensor-responder protein calredoxin in the green alga <i>Chlamydomonas reinhardtii</i>. Peer-reviewed

      Charoenwattanasatien R, Zinzius K, Scholz M, Wicke S, Tanaka H, Brandenburg JS, Marchetti GM, Ikegami T, Matsumoto T, Oda T, Sato M, Hippler M, Kurisu G

      The Journal of biological chemistry   11 2019

    • Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation. Peer-reviewed

      Kori S, Ferry L, Matano S, Jimenji T, Kodera N, Tsusaka T, Matsumura R, Oda T, Sato M, Dohmae N, Ando T, Shinkai Y, Defossez PA, Arita K

      Structure (London, England : 1993)27 ( 3 ) 485 - 496.e7   3 2019

    • Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid. Peer-reviewed

      Hayashi I, Oda T, Sato M, Fuchigami S

      Journal of molecular biology430 ( 24 ) 5015 - 5028   11 2018

    • Structural analysis of the STAT1:STAT2 heterodimer revealed the mechanism of Sendai virus C protein-mediated blockade of type 1 interferon signaling Peer-reviewed

      Kosuke Oda, Takashi Oda, Yasuyuki Matoba, Mamoru Sato, Takashi Irie, Takemasa Sakaguchi

      JOURNAL OF BIOLOGICAL CHEMISTRY292 ( 48 ) 19752 - 19766   12 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

      Sendai virus (SeV), which causes respiratory diseases in rodents, possesses the C protein that blocks the signal transduction of interferon (IFN), thereby escaping from host innate immunity. We previously demonstrated by using protein crystallography that two molecules of Y3 (the C-terminal half of the C protein) can bind to the homodimer of the N-terminal domain of STAT1 (STAT1ND), elucidating the mechanism of inhibition of IFN- signal transduction. SeV C protein also blocks the signal transduction of IFN-/ by inhibiting the phosphorylation of STAT1 and STAT2, although the mechanism for the inhibition is unclear. Therefore, we sought to elucidate the mechanism of inhibition of the IFN signal transduction via STAT1 and STAT2. Small angle X-ray scattering analysis indicated that STAT1ND associates with the N-terminal domain of STAT2 (STAT2ND) with the help of a Gly-rich linker. We generated a linker-less recombinant protein possessing a STAT1ND:STAT2ND heterodimeric structure via an artificial disulfide bond. Analytical size-exclusion chromatography and surface plasmon resonance revealed that one molecule of Y3 can associate with a linker-less recombinant protein. We propose that one molecule of C protein associates with the STAT1:STAT2 heterodimer, inducing a conformational change to an antiparallel form, which is easily dephosphorylated. This suggests that association of C protein with the STAT1ND:STAT2ND heterodimer is an important factor to block the IFN-/ signal transduction.

      DOI: 10.1074/jbc.M117.786285

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    • Molecular level analyses of mechanical properties of PTFE sterilized by Co-60 gamma-ray irradiation for clinical use Peer-reviewed

      Masakazu Furuta, Aira Matsugaki, Takayoshi Nakano, Isao Hirata, Koichi Kato, Takashi Oda, Mamoru Sato, Masayuki Okazaki

      RADIATION PHYSICS AND CHEMISTRY139   126 - 131   10 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:PERGAMON-ELSEVIER SCIENCE LTD  

      Recently, Co-60 gamma-ray rradiation has become markedly popular for the sterilization of biomedical materials, including expanded PTFE. However, its effect on the properties of PTFE has not been thoroughly examined. In this study, changes in the properties of PTFE before and after irradiation were analyzed physicochemically and discussed crystallographically. The tensile breaking strengths of PTFE decreased markedly on irradiation at 1 kGy, and were maintained at almost one fourth of the original value (44.3 +/- 2.5 N/mm(2)) ranging from 5 to 100 kGy. XPS analysis indicated that the atomic concentrations of carbon (C) and fluorine (F) of PTFE were not different among samples irradiated at various dosages. Raman spectra of PTFE showed a slight increase of the absorption peak intensity at 735 cm(-1) in an irradiation dosage dependent manner. X-ray diffraction showed that the crystal size of PTFE (56.7 +/- 1.0 nm) became smaller after radiation at 100 kGy (48.5 +/- 0.6 nm). These results are consistent with the above results of Raman analysis. It is suggested that the observed changes in the mechanical properties of PTFE may be due to nano-scale C C bond scission by gamma ray irradiation, and not due to the formation of micro-scale cracks.

      DOI: 10.1016/j.radphyschem.2017.04.005

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    • Structural basis of autoinhibition and activation of the DNA-targeting ADP-ribosyltransferase pierisin-1 Peer-reviewed

      Takashi Oda, Hirokazu Hirabayashi, Gen Shikauchi, Ryouma Takamura, Kiyoshi Hiraga, Hiroshi Minami, Hiroshi Hashimoto, Masafumi Yamamoto, Keiji Wakabayashi, Toshiyuki Shimizu, Mamoru Sato

      JOURNAL OF BIOLOGICAL CHEMISTRY292 ( 37 ) 15445 - 15455   9 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

      ADP-ribosyltransferases transfer the ADP-ribose moiety of beta NAD(+) to an acceptor molecule, usually a protein that modulates the function of the acceptor. Pierisin-1 is an ADP-ribosyltransferase from the cabbage butterfly Pieris rapae and is composed of N-terminal catalytic and C-terminal ricin B-like domains. Curiously, it ADP-ribosylates the DNA duplex, resulting in apoptosis of various cancer cells, which has raised interest in pierisin-1 as an anti-cancer agent. However, both the structure and the mechanism of DNA ADP-ribosylation are unclear. Here, we report the crystal structures of the N-terminal catalytic domain of pierisin-1, its complex with beta NAD(+), and the catalytic domain with the linker connecting it to the ricin B-like domains. We found that the catalytic domain possesses a defined, positively charged region on the molecular surface but that its overall structure is otherwise similar to those of proteintargeting ADP-ribosyltransferases. Electrophoretic mobility shift assays and site-directed mutagenesis indicated that pierisin- 1 binds double-stranded but not single-stranded DNA and that Lys(122), Lys(123), and Lys(124), which are found in a loop, and Arg(181) and Arg(187), located in a basic cleft near the loop, are required for DNA binding. Furthermore, the structure of the catalytic domain with the linker revealed an autoinhibitory mechanism in which the linker occupies and blocks both the beta NAD(+) - and DNA-binding sites, suggesting that proteolytic cleavage to remove the linker is necessary for enzyme catalysis. Our study provides a structural basis for the DNA-acceptor specificity of pierisin-1 and reveals that a self-regulatory mechanism is required for its activity.

      DOI: 10.1074/jbc.M117.776641

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    • Structural insights into a 20.8-kDa tegumental-allergen-like (TAL) protein from Clonorchis sinensis Peer-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 REPORTS7 ( 1 ) 1764   5 2017

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

      Survival of Clonorchis sinensis, a cause of human clonorchiasis, requires tegument proteins, which are localized to the tegumental outer surface membrane. These proteins play an important role in a host response and parasite survival. Thus, these proteins are interesting molecular targets for vaccine and drug development. Here, we have determined two crystal structures of the calmodulin like domain (amino acid [aa] positions 1-81) and dynein light chain (DLC)-like domain (aa 83-177) of a 20.8-kDa tegumental-allergen-like protein from Clonorchis sinensis (CsTAL3). The calmodulin like domain has two Ca2+-binding sites (named CB1 and CB2), but Ca2+ binds to only one site, CB1. The DLC-like domain has a dimeric conformation; the interface is formed mainly by hydrogen bonds between the main chain atoms. In addition, we have determined full-length structure of CsTAL3 in solution and showed the conformational change of CsTAL3 induced by Ca2+ ion binding using small-angle X-ray scattering analysis and molecular dynamics simulations. The Ca2+-bound form has a more extended conformation than the Ca2+-free from does. These structural and biochemical analyses will advance the understanding of the biology of this liver fluke and may contribute to our understanding of the molecular mechanism of calcium-responsive and tegumental-allergen-like proteins.

      DOI: 10.1038/s41598-017-02044-0

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    • Extended string-like binding of the phosphorylated HP1 alpha N-terminal tail to the lysine 9-methylated histone H3 tail Peer-reviewed

      Hideaki Shimojo, Ayumi Kawaguchi, Takashi Oda, Nobuto Hashiguchi, Satoshi Omori, Kei Moritsugu, Akinori Kidera, Kyoko Hiragami-Hamada, Jun-ichi Nakayama, Mamoru Sato, Yoshifumi Nishimura

      SCIENTIFIC REPORTS6   22527   3 2016

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

      The chromodomain of HP1 alpha binds directly to lysine 9-methylated histone H3 (H3K9me). This interaction is enhanced by phosphorylation of serine residues in the N-terminal tail of HP1 alpha by unknown mechanism. Here we show that phosphorylation modulates flexibility of HP1 alpha's N-terminal tail, which strengthens the interaction with H3. NMR analysis of HP1 alpha's chromodomain with N-terminal tail reveals that phosphorylation does not change the overall tertiary structure, but apparently reduces the tail dynamics. Small angle X-ray scattering confirms that phosphorylation contributes to extending HP1 alpha's N-terminal tail. Systematic analysis using deletion mutants and replica exchange molecular dynamics simulations indicate that the phosphorylated serines and following acidic segment behave like an extended string and dynamically bind to H3 basic residues; without phosphorylation, the most N-terminal basic segment of HP1 alpha inhibits interaction of the acidic segment with H3. Thus, the dynamic string-like behavior of HP1 alpha's N-terminal tail underlies the enhancement in H3 binding due to phosphorylation.

      DOI: 10.1038/srep22527

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    • A novel 3 ' splice site recognition by the two zinc fingers in the U2AF small subunit Peer-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 & DEVELOPMENT29 ( 15 ) 1649 - 1660   8 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT  

      The pre-mRNA splicing reaction of eukaryotic cells has to be carried out extremely accurately, as failure to recognize the splice sites correctly causes serious disease. The small subunit of the U2AF heterodimer is essential for the determination of 3 ' splice sites in pre-mRNA splicing, and several single-residue mutations of the U2AF small subunit cause severe disorders such as myelodysplastic syndromes. However, the mechanism of RNA recognition is poorly understood. Here we solved the crystal structure of the U2AF small subunit (U2AF23) from fission yeast, consisting of an RNA recognition motif (RRM) domain flanked by two conserved CCCH-type zinc fingers (ZFs). The two ZFs are positioned side by side on the beta sheet of the RRM domain. Further mutational analysis revealed that the ZFs bind cooperatively to the target RNA sequence, but the RRM domain acts simply as a scaffold to organize the ZFs and does not itself contact the RNA directly. This completely novel and unexpected mode of RNA-binding mechanism by the U2AF small subunit sheds light on splicing errors caused by mutations of this highly conserved protein.

      DOI: 10.1101/gad.267104.115

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    • Structural basis of a nucleosome containing histone H(2)A.B/H(2)A.Bbd that transiently associates with reorganized chromatin (vol 3, 3510, 2013) Peer-reviewed

      Yasuhiro Arimura, Hiroshi Kimura, Takashi Oda, Koichi Sato, Akihisa Osakabe, Hiroaki Tachiwana, Yuko Sato, Yasuha Kinugasa, Tsuyoshi Ikura, Masaaki Sugiyama, Mamoru Sato, Hitoshi Kurumizaka

      SCIENTIFIC REPORTS5   9628   7 2015

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      DOI: 10.1038/srep09628

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    • Molecular Basis for SMC Rod Formation and Its Dissolution upon DNA Binding Peer-reviewed

      Young-Min Soh, Frank Buermann, Ho-Chul Shin, Takashi Oda, Kyeong Sik Jin, Christopher P. Toseland, Cheolhee Kim, Hansol Lee, Soo Jin Kim, Min-Seok Kong, Marie-Laure Durand-Diebold, Yeon-Gil Kim, Ho Min Kim, Nam Ki Lee, Mamoru Sato, Byung-Ha Oh, Stephan Gruber

      MOLECULAR CELL57 ( 2 ) 290 - 303   1 2015

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CELL PRESS  

      SMC condensin complexes are central modulators of chromosome superstructure in all branches of life. Their SMC subunits form a long intramolecular coiled coil, which connects a constitutive "hinge'' dimerization domain with an ATP-regulated "head'' dimerization module. Here, we address the structural arrangement of the long coiled coils in SMC complexes. We unequivocally show that prokaryotic Smc-ScpAB, eukaryotic condensin, and possibly also cohesin form rod-like structures, with their coiled coils being closely juxtaposed and accurately anchored to the hinge. Upon ATP-induced binding of DNA to the hinge, however, Smc switches to a more open configuration. Our data suggest that a long-distance structural transition is transmitted from the Smc head domains to regulate Smc-ScpAB's association with DNA. These findings uncover a conserved architectural theme in SMC complexes, provide a mechanistic basis for Smc's dynamic engagement with chromosomes, and offer a molecular explanation for defects in Cornelia de Lange syndrome.

      DOI: 10.1016/j.molcel.2014.11.023

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    • Distinct Features of the Histone Core Structure in Nucleosomes Containing the Histone H2A.B Variant Peer-reviewed

      Masaaki Sugiyama, Yasuhiro Arimura, Kazuyoshi Shirayama, Risa Fujita, Yojiro Oba, Nobuhiro Sato, Rintaro Inoue, Takashi Oda, Mamoru Sato, Richard K. Heenan, Hitoshi Kurumizaka

      BIOPHYSICAL JOURNAL106 ( 10 ) 2206 - 2213   5 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CELL PRESS  

      Nucleosomes containing a human histone variant, H2A.B, in an aqueous solution were analyzed by small-angle neutron scattering utilizing a contrast variation technique. Comparisons with the canonical H2A nucleosome structure revealed that the DNA termini of the H2A.B nucleosome are detached from the histone core surface, and flexibly expanded toward the solvent. In contrast, the histone tails are compacted in H2A.B nucleosomes compared to those in canonical H2A nucleosomes, suggesting that they bind to the surface of the histone core and/or DNA. Therefore, the histone tail dynamics may function to regulate the flexibility of the DNA termini in the nucleosomes.

      DOI: 10.1016/j.bpj.2014.04.007

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    • A Structure-Based Model of Substrate Discrimination by a Noncanonical PDZ Tandem in the Intramembrane-Cleaving Protease RseP Peer-reviewed

      Yohei Hizukuri, Takashi Oda, Sanae Tabata, Keiko Tamura-Kawakami, Rika Oi, Mamoru Sato, Junichi Takagi, Yoshinori Akiyama, Terukazu Nogi

      STRUCTURE22 ( 2 ) 326 - 336   2 2014

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:CELL PRESS  

      During the extracytoplasmic stress response in Escherichia coli, the intramembrane protease RseP cleaves the anti-sigma(E) protein RseA only after the membrane-anchored protease DegS truncates the perk plasmic part of RseA that suppresses the action of RseP. Here we analyzed the three-dimensional structure of the two tandemly arranged PSD-95/DIg/ZO-1 (PDZ) domains (PDZ tandem) present in the periplasmic region of RseP and revealed that the two putative ligand-binding grooves constitute a single pocket-like structure that would lie just above the active center sequestrated within the membrane. Complete removal of the PDZ tandem from RseP led to the intramembrane cleavage of RseA without prior truncation by DegS. Furthermore, mutations expected to destabilize the tertiary structure of the PDZ tandem also caused the deregulation of the sequential cleavage. These observations suggest that the PDZ tandem serves as a size-exclusion filter to accommodate the truncated form of RseA into the active center.

      DOI: 10.1016/j.str.2013.12.003

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    • Structural basis of a nucleosome containing histone H2A.B/H2A.Bbd that transiently associates with reorganized chromatin Peer-reviewed

      Yasuhiro Arimura, Hiroshi Kimura, Takashi Oda, Koichi Sato, Akihisa Osakabe, Hiroaki Tachiwana, Yuko Sato, Yasuha Kinugasa, Tsuyoshi Ikura, Masaaki Sugiyama, Mamoru Sato, Hitoshi Kurumizaka

      SCIENTIFIC REPORTS3   3510   12 2013

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

      Human histone H2A.B (formerly H2A.Bbd), a non-allelic H2A variant, exchanges rapidly as compared to canonical H2A, and preferentially associates with actively transcribed genes. We found that H2A. B transiently accumulated at DNA replication and repair foci in living cells. To explore the biochemical function of H2A. B, we performed nucleosome reconstitution analyses using various lengths of DNA. Two types of H2A.B nucleosomes, octasome and hexasome, were formed with 116, 124, or 130 base pairs (bp) of DNA, and only the octasome was formed with 136 or 146 bp DNA. In contrast, only hexasome formation was observed by canonical H2A with 116 or 124 bp DNA. A small-angle X-ray scattering analysis revealed that the H2A.B octasome is more extended, due to the flexible detachment of the DNA regions at the entry/exit sites from the histone surface. These results suggested that H2A. B rapidly and transiently forms nucleosomes with short DNA segments during chromatin reorganization.

      DOI: 10.1038/srep03510

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    • Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1 Peer-reviewed

      Kyohei Arita, Shin Isogai, Takashi Oda, Motoko Unoki, Kazuya Sugita, Naotaka Sekiyama, Keiko Kuwata, Ryuji Hamamoto, Hidehito Tochio, Mamoru Sato, Mariko Ariyoshi, Masahiro Shirakawa

      PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA109 ( 32 ) 12950 - 12955   8 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATL ACAD SCIENCES  

      Multiple covalent modifications on a histone tail are often recognized by linked histone reader modules. UHRF1 [ubiquitin-like, containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1], an essential factor for maintenance of DNA methylation, contains linked two-histone reader modules, a tandem Tudor domain and a PHD finger, tethered by a 17-aa linker, and has been implicated to link histone modifications and DNA methylation. Here, we present the crystal structure of the linked histone reader modules of UHRF1 in complex with the amino-terminal tail of histone H3. Our structural and biochemical data provide the basis for combinatorial readout of unmodified Arg-2 (H3-R2) and methylated Lys-9 (H3-K9) by the tandem tudor domain and the PHD finger. The structure reveals that the intermodule linker plays an essential role in the formation of a histone H3-binding hole between the reader modules by making extended contacts with the tandem tudor domain. The histone H3 tail fits into the hole by adopting a compact fold harboring a central helix, which allows both of the reader modules to simultaneously recognize the modification states at H3-R2 and H3-K9. Our data also suggest that phosphorylation of a linker residue can modulate the relative position of the reader modules, thereby altering the histone H3-binding mode. This finding implies that the linker region plays a role as a functional switch of UHRF1 involved in multiple regulatory pathways such as maintenance of DNA methylation and transcriptional repression.

      DOI: 10.1073/pnas.1203701109

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    • Structural Analysis of the Hexasome, Lacking One Histone H2A/H2B Dimer from the Conventional Nucleosome Peer-reviewed

      Yasuhiro Arimura, Hiroaki Tachiwana, Takashi Oda, Mamoru Sato, Hitoshi Kurumizaka

      BIOCHEMISTRY51 ( 15 ) 3302 - 3309   4 2012

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER CHEMICAL SOC  

      Genomic DNA is packaged into chromatin in eukaryotes, and the nucleosome is the fundamental unit of chromatin. The canonical nucleosome is the octasome, which is composed of two H2A/H2B dimers and two H3/H4 dimers. During transcription elongation, one of the H2A/H2B dimers is removed from the octasome. The depletion of the H2A/H2B dimer is also suggested to occur during DNA replication and repair. The remaining histone components are believed to maintain a nucleosomal structure called a "hexasome", which is probably important for the regulation of gene expression, DNA replication, and repair in chromatin. However, hexasomes are currently poorly understood, due to the lack of in vivo and in vitro studies. Biochemical and structural studies of hexasomes have been hampered by the difficulty of preparing purified hexasomes. In the present study, we successfully reconstituted hexasomes, using recombinant human histones. A micrococcal nuclease treatment and in vitro reconstitution assays revealed that the hexasome tightly wraps approximately 110 base-pairs of DNA, about 40 base-pairs shorter than the length of the DNA wrapped within the canonical nucleosome. A small-angle X-ray scattering analysis revealed that the global structure of the hexasome is similar to that of the canonical nucleosome. Our studies suggest that octasomes can be converted into hexasomes by the eviction of one of the H2A/H2B dimers, and the release of about 40 base-pairs of DNA, without involving large structural changes in the nucleosome core particle.

      DOI: 10.1021/bi300129b

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    • Crystal structure of the human centromeric nucleosome containing CENP-A Peer-reviewed

      Hiroaki Tachiwana, Wataru Kagawa, Tatsuya Shiga, Akihisa Osakabe, Yuta Miya, Kengo Saito, Yoko Hayashi-Takanaka, Takashi Oda, Mamoru Sato, Sam-Yong Park, Hiroshi Kimura, Hitoshi Kurumizaka

      NATURE476 ( 7359 ) 232 - U135   8 2011

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

      In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment(1,2). 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(3-12). 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 alpha-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 alpha N 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(13). 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.

      DOI: 10.1038/nature10258

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    • Structure of the N-terminal Regulatory Domain of a Plant NADPH Oxidase and Its Functional Implications Peer-reviewed

      Takashi Oda, Hiroshi Hashimoto, Naoyuki Kuwabara, Satoko Akashi, Kokoro Hayashi, Chojiro Kojima, Hann Ling Wong, Tsutomu Kawasaki, Ko Shimamoto, Mamoru Sato, Toshiyuki Shimizu

      JOURNAL OF BIOLOGICAL CHEMISTRY285 ( 2 ) 1435 - 1445   1 2010

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

      Plant NADPH oxidases (Rboh, for respiratory burst oxidase homolog) produce reactive oxygen species that are key regulators of various cellular events including plant innate immunity. Rbohs possess a highly conserved cytoplasmic N-terminal region containing two EF-hand motifs that regulate Rboh activity. Rice (Oryza sativa) RbohB (OsRbohB) is regulated by the direct binding of a small GTPase (Rac1) to this regulatory region as well as by Ca(2+) binding to the EF-hands. Here, we present the atomic structure of the N-terminal region of OsRbohB. The structure reveals that OsRbohB forms a unique dimer stabilized by swapping the EF-hand motifs. We identified two additional EF-hand-like motifs that were not predicted from sequence data so far. These EF-hand-like motifs together with the swapped EF-hands form a structure similar to that found in calcineurin B. We observed conformational changes mediated by Ca(2+) binding to only one EF-hand. Structure-based in vitro pulldown assays and NMR titration experiments defined the OsRac1 binding interface within the coiled-coil region created by swapping the EF-hands. In addition, we demonstrate a direct intramolecular interaction between the N and C terminus, and that the complete N-terminal cytoplasmic region is required for this interaction. The structural features and intramolecular interactions characterized here might be common elements shared by Rbohs that contribute to the regulation of reactive oxygen species production.

      DOI: 10.1074/jbc.M109.058909

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    • Crystallographic characterization of the N-terminal domain of a plant NADPH oxidase Peer-reviewed

      Takashi Oda, Hiroshi Hashimoto, Naoyuki Kuwabara, Kokoro Hayashi, Chojiro Kojima, Tsutomu Kawasaki, Ko Shimamoto, Mamoru Sato, Toshiyuki Shimizu

      ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS64 ( Pt 9 ) 867 - 869   9 2008

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      Language:English   Publishing type:Research paper (scientific journal)   Publisher:INT UNION CRYSTALLOGRAPHY  

      Respiratory burst oxidase homologue (Rboh), which is found in the plasma membrane, is a generator of reactive oxygen species (ROS) in plants. Many studies have indicated that the ROS produced by Rboh play critical roles in various cellular activities, including plant defence against pathogens. Crystals of the N-terminal domain of Oryza sativa RbohB (OsRbohB) have been obtained. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 60.4, b = 72.2, c = 118.9 angstrom. An intensity data set was collected to 2.4 angstrom resolution.

      DOI: 10.1107/S1744309108026535

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    Misc.

    • 相分離生物学:相分離メガネのススメ 検出技術:天然変性タンパク質の構造生物学

      小田隆, 齋尾智英

      生物工学会誌98 ( 5 )   2020

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    • 小角散乱と計算科学で明らかにする天然変性タンパク質の動的構造と機能

      小田隆

      KEK Proceedings (Web) ( 2018-10 )   2019

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    • SANSと計算科学による天然変性タンパク質の動的構造と機能の解明

      小田隆, 関野絢子, 米山真紀, 浴本亨, 池口満徳, 苙口友隆, 杉山正明, 石野良純, 佐藤衛

      日本中性子科学会年会講演概要集18th   2018

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    • Structural insights into STAT1 dependent inhibition of STAT2 phosphorylation by Sendai virus C protein.

      Oda, K, Oda, T, Matoba, Y, Irie, T, Sato, M, Sakaguchi, T

      IUMS2017, XVII International Congress of Virology   2017

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    • DNA架橋損傷修復に関わる天然変性タンパク質Hefの構造研究

      小田隆, 関野絢子, 中筋航, 石黒あかり, 石野良純, 佐藤衛

      日本蛋白質科学会年会プログラム・要旨集16th   2016

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    • 新規ヌクレアーゼタンパク質HANとICL修復に関わる天然変性タンパク質Hefの相互作用解析

      中筋航, 小田隆, 小林裕也, 石野良純, 佐藤衛

      日本蛋白質科学会年会プログラム・要旨集16th   2016

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    • Recent Activity of KUMASANS

      Y. Oba, M. Hino, T. Oda, M. Ohnuma, N. Sato, R. Inoue, M. Sugiyama

      The 8th Meeting on Collective Action for Nomadic Small Angle Scatterers   4 2015

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    • Upgrade of Compact Small-Angle Neutron Scattering Instrument KUR-SANS Toward Next-Generation Materials Science

      Y. Oba, M. Hino, T. Oda, M. Ohnuma, N. Sato, M. Sugiyama

      The International Union of Materials Research Societies – International Conference in Asia 2014   8 2014

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    • Elucidation Of The Nonspecific DNA-Binding Mechanism Of The POU Homeodomain Using NMR

      Tsuyoshi Konuma, Erisa Harada, Takashi Oda, Mamoru Sato, Kenji Sugase

      PROTEIN SCIENCE23   111 - 112   7 2014

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      Language:English   Publishing type:Research paper, summary (international conference)   Publisher:WILEY-BLACKWELL  

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    • DNA架橋損傷修復に関わる天然変性タンパク質Hefの構造研究

      小田隆, 小林裕也, 舘岡太郎, 宮城泰城, 石黒あかり, 有田恭平, 禾晃和, 石野良純, 杉山正明, 佐藤衛

      日本蛋白質科学会年会プログラム・要旨集14th   2014

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    • Integrated Structural Biology in Combination with SAXS Analysis for Biological Macromolecules

      ODA Takashi, HASHIMOTO Hiroshi

      Nihon Kessho Gakkaishi56 ( 4 ) 247 - 252   2014

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      Language:Japanese   Publisher:The Crystallographic Society of Japan  

      Small angle X-ray scattering (SAXS) analysis is a facile and useful method to determine structures of biological macromolecules in solution. Although SAXS analysis generally provides significant information of molecular shape at low resolution, in combination with other biophysical techniques such as X-ray crystallography, SAXS analysis exhibits tremendous power for structural studies of biological macromolecules. In this review, we described our recent studies of SAXS analysis for biological macromolecules (BioSAXS) and future perspective for integrated structural biology using BioSAXS.

      DOI: 10.5940/jcrsj.56.247

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    • 細菌表層ストレス応答制御に関わる膜内切断プロテアーゼRsePのタンデムPDZドメインによる切断基質選別機構の解析

      HIZUKURI YOHEI, ODA TAKASHI, TABATA SANAE, KAWAKAMI(TAMURA) KEIKO, OI RIKA, SATO MAMORU, TAKAGI JUN'ICHI, NOGI TERUKAZU, AKIYAMA YOSHINORI

      日本生化学会大会(Web)87th   4T10P-14(4P-133) (WEB ONLY)   2014

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      Language:Japanese  

      J-GLOBAL

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    • Upgrade of Small-Angle Neutron Scattering Instrument KUR-SANS for Metallic Materials

      Y. Oba, M. Hino, T. Oda, M. Ohnuma, N. Sato, M. Sugiyama

      The International Union of Materials Research Societies – International Conference in Asia 2013, Bangalore, India   12 2013

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    • 大腸菌膜内切断プロテアーゼRsePの基質認識におけるPDZドメインの役割

      HIZUKURI YOHEI, NOGI TERUKAZU, ODA TAKASHI, TABATA SANAE, KAWAKAMI(TAMURA) KEIKO, SATO MAMORU, TAKAGI JUN'ICHI, AKIYAMA YOSHINORI

      日本生化学会大会(Web)86th   2S05P-1 (WEB ONLY)   2013

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      Language:Japanese  

      J-GLOBAL

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    • 立体構造解析に基づく大腸菌膜内切断プロテアーゼRsePのタンデムPDZドメインによる切断基質選別機構モデル

      HIZUKURI YOHEI, ODA TAKASHI, TABATA SANAE, KAWAKAMI(TAMURA) KEIKO, SATO MAMORU, TAKAGI JUN'ICHI, NOGI TERUKAZU, AKIYAMA YOSHINORI

      日本分子生物学会年会プログラム・要旨集(Web)36th   1P-0067 (WEB ONLY)   2013

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      Language:Japanese  

      J-GLOBAL

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    • 膜内切断プロテアーゼRsePの基質取り込み制御におけるPDZタンデムの役割

      NOGI TERUKAZU, HIZUKURI YOHEI, TABATA SANAE, KAWAKAMI(TAMURA) KEIKO, ODA TAKASHI, SATO MAMORU, TAKAGI JUN'ICHI, AKIYAMA YOSHINORI

      日本蛋白質科学会年会プログラム・要旨集12th   93   31 5 2012

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      J-GLOBAL

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    • 大腸菌表層ストレス応答に関与する膜内切断プロテアーゼRseP のPDZ ドメイ ンによる新たな機能制御メカニズム Peer-reviewed

      檜作洋平, 禾 晃和, 田畑早苗, 川上-田村恵子, 小田 隆, 佐藤 衛, 高木淳一, 秋山芳展

      第6 回細菌学若手コロッセウム、八王子、2 012 年8月8日-10日   2012

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    • 大腸菌RIPプロテアーゼRsePのタンデムPDZドメインによる新たな機能制御メカニズム

      HIZUKURI YOHEI, NOGI TERUKAZU, TABATA SANAE, KAWAKAMI(TAMURA) KEIKO, ODA TAKASHI, SATO MAMORU, TAKAGI JUN'ICHI, AKIYAMA YOSHINORI

      日本生化学会大会(Web)85th   3T28-08 (WEB ONLY)   2012

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    • OsRac1-mediated ROS production in rice innate immunity

      Shimamoto Ko, Wong Hann Ling, Kawano Yoji, Ishikawa Yosuke, Oda Takashi, Shimizu Toshiyuki, Kawasaki Tsutomu

      Plant and Cell Physiology Supplement2010 ( 0 ) S0020 - S0020   2010

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      Publisher:The Japanese Society of Plant Physiologists  

      We have been studying molecular mechanisms regulating innate immunity in rice. In the previous studies we found that a small GTPase OsRac1 belonging to the Rac(Rop) GTPase family plays a major role in rice innate immunity. By studying a number of proteins directly and indirectly interacting with OsRac1 we have identified a network of proteins which function as a core protein complex which regulates rice innate immunity. We designate the model for this protein network as defensome model and studying various aspects of the model. OsRac1 interacts with Rboh (NADPH oxidase) and an adapter protein RACK1 (RWD) and these three proteins are major regulators of ROS production during innate immune responses in rice. We present results on regulation of ROS production by these proteins in rice.

      DOI: 10.14841/jspp.2010.0.S0020.0

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    Presentations

    • DNA修復にかかわるHefの天然変性領域の揺らいだ構造と機能

      小田 隆

      第4回LLPS研究会・ASUKA若手交流会2019  9 12 2019 

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      Language:Japanese   Presentation type:Poster presentation  

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    • The dynamic structure and function of intrinsically disordered region of Hef that is associated with a DNA repair Invited International conference

      Takashi Oda

      3rd Asia-Oceania Conference on Neutron Scattering / AOCNS 2019  18 11 2019 

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      Language:English   Presentation type:Oral presentation (invited, special)  

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    • The structure and function of intrinsically disordered region of Hef that is associated with a DNA repair

      Takashi Oda

      25 9 2019 

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    • Protein deuteration and analysis Invited International conference

      小田 隆

      J-PARC Workshop2018 / Deuterium Labeling Study for Neutron Science  15 1 2019 

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    • 溶液散乱と計算科学で明らかにする天然変性タンパク質の構造と機能 Invited

      小田 隆

      PF研究会「多様な物質・生命科学研究に広がる小角散乱 - 多(他)分野の小角散乱を学ぼう!」  21 12 2018 

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    • A study of dynamic structure and function of intrinsically disordered proteins by SANS and computing

      Takashi Oda

      The 18th Annual Meeting of the Japanese Society for Neutron Science  4 12 2018 

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    • X線小角散乱による天然変性タンパク質の構造研究 Invited

      小田 隆

      第2回生物資源セミナー 立命館大学  1 7 2017 

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    • Structural basis of a sliding mechanism of DNA clamp regulated by the intrinsically disordered protein

      Takashi Oda

      THe 17th Annual Meeting of the Protein Science Society of Japan  20 6 2017 

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    • Structural basis of a sliding mechanism of DNA clamp regulated by the intrinsically disordered region of Hef International conference

      Takashi Oda, Ayako Sekino, Akari Ishiguro, Taiki Miyagi, Wataru Nakasuji, Yuya Kobayashi, Taro Tateoka, Masaaki Sugiyama, Yoshizumi Ishino, Mamoru Sato

      第78回岡崎コンファレンス「Grand Challenges in Small-angle Scattering」  3 2017 

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    • Structural study on interaction between PCNA and intrinsically disordered protein Hef in DNA interstrand crosslink repair

      小田 隆

      第 42 回内藤コンファレンス In the Vanguard of Structural Biology: Revolutionizing Life Sciences 生命科学に革命をもたらす最先端構造生物学  4 10 2016 

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    • DNA 架橋損傷修復に関わる天然変性タンパク質 Hefの構造研究

      小田 隆, 関野 絢子, 中筋 航, 石黒 あかり, 石野 良純, 佐藤 衛

      第16回日本蛋白質科学会年会  9 6 2016 

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    • Structural analysis of tri-nucleosome containing centromere specific histone variant

      Takashi Oda, Hiroaki Tachiwana, Yusuke Takagi, Yasuhiro Arimura, Shoji Takada, Hitoshi Kurumizaka, Mamoru Sato

      International Symposium on Chromatin Structure, Dynamics, and Function  23 8 2015 

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    • DNA架橋損傷修復に関わる天然変性タンパク質Hefの構造研究

      小田隆, 小林裕也, 舘岡太郎, 宮城泰城, 石黒あかり, 有田恭平, 禾晃和, 石野良純, 杉山正明, 佐藤衛

      第14回日本蛋白質科学会年  25 6 2014 

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    • X線小角散乱によるタンパク質の揺らいだ構造の解析 Invited

      小田 隆

      第2回タンパク質X線溶液散乱講習会  3 6 2014 

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    • 揺らいだ構造を持つタンパク質のX線小角散乱解析

      小田 隆

      蛋白研セミナー「結晶構造を併用したハイブリッド構造研究の最前線」  7 2 2014 

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    Professional Memberships

    •  
      PROTEIN SCIENCE SOCIETY OF JAPAN

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      THE BIOPHYSICAL SOCIETY OF JAPAN

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      THE JAPANESE SOCIETY FOR NEUTRON SCIENCE

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    Research Projects

    • 新規標的因子が関わるパラミクソウイルスC蛋白質の機能とその分子基盤, 病原性解明

      日本学術振興会  科学研究費助成事業 基盤研究(C) 

      小田 康祐, 小田 隆

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      4 2020 - 3 2023

      Grant number:20K06507

      Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

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    • 配列が著しく異なる2つの天然変性タンパク質に共通する構造と機能の解明

      日本学術振興会  科学研究費助成事業 基盤研究(C) 

      小田 隆

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      4 2020 - 3 2023

      Grant number:20K06527

      Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

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    • セグメント重水素化中性子散乱法による天然変性タンパク質の動的構造解析

      日本学術振興会  科学研究費助成事業 基盤研究(B) 

      佐藤 衛, 小田 隆

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      4 2018 - 3 2021

      Grant number:18H02391

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

      本研究ではセグメント重水素化と逆転コントラスト同調法を用いた中性子小角散乱法により天然変性領域をもつマルチドメインタンパク質の動的構造を解析し天然変性タンパク質の高度な分子認識・機能発現機構の解明を目指す。
      当該年度は、(1)セグメント重水素化のためのプロテインライゲーション条件の検討、(2)X線溶液散乱法による中性子溶液散乱実験に向けた予備的解析、(3)マルチドメインタンパク質の動的構造を再現する構造アンサンブルの作成を行った。目的とするマルチドメインタンパク質はN末端とC末端にそれぞれ折れ畳まれた機能ドメインを持ち、その間に大な天然変性領域が存在する。(1)ではまず天然変性領域とC末端ドメインのプロテインライゲーションによる連結が可能であることを確認した。同様の反応でN末端ドメインを連結すれば全長タンパク質を調製できるため、セグメント重水素化タンパク質調製の道筋を示すことができた。(2)ではセグメント重水素化した全長タンパク質を用いた中性子散乱実験に先立って、X線溶液散乱法で重水素化していない全長タンパク質を用いて溶液中での動態を確認した。その結果、全長タンパク質は低濃度であれば中性子溶液散乱実験に使用可能な均一な溶液状態(単分散状態)であることがわかった。 また、(2)では実測のX線溶液散乱データが得られているため、中性子溶液散乱実験に先立ち、(3)で得られた構造アンサンブルから理論的なX線溶液散乱パターンを計算し、実測のX線溶液散乱パターンと比較した。その結果、溶液中で天然変性領域がとりうる多様な構造を再現するためには構造アンサンブルの数が不十分であることが示され、次年度への課題として構造アンサンブルの作成法の検討も予定している。

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    • 天然変性タンパク質Hefの揺らいだ構造と機能の解明

      公益財団法人横浜学術教育振興財団  研究助成 

      小田 隆

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      4 2017 - 3 2018

      Authorship:Principal investigator  Grant type:Competitive

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    • X線小角散乱を用いた再構成クロマチンの動的構造解析

      日本学術振興会  科学研究費助成事業 新学術領域研究(研究領域提案型) 

      小田 隆

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      4 2014 - 3 2016

      Grant number:26116519

      Authorship:Principal investigator  Grant type:Competitive

      Grant amount:\10400000 ( Direct Cost: \8000000 、 Indirect Cost:\2400000 )

      早稲田大学胡桃坂博士、京都大学高田博士らとの共同研究により、ヒストンH3のセントロメア特異的なバリアントであるCENP-Aを含む再構成クロマチンについてX線小角散乱解析と分子動力学計算を合わせた解析を行い、その構造的特徴を明らかにした。これまでの胡桃坂および我々の研究からCENP-Aモノヌクレオソームでは通常のH3モノヌクレオソームと異なりヒストン8量体に巻きついたDNAの両端がはがれて揺らいだ状態にあることが示されている(Tachiwana et al, 2011, Nature)。このようなCENP-Aモノヌクレオソームに特徴的な構造が高次のクロマチン構造へ与える影響と、セントロメアの形成・維持・機能における役割を明らかにするために、通常のH3からなるヌクレオソームまたはCENP-Aからなるヌクレオソームを含む高次の再構成クロマチンを調製し解析を行った。前年度までに行ったX線小角散乱実験の結果、CENP-Aを含む再構成クロマチンではH3のみからなる再構成クロマチンと高次構造が明らかに異なることが観測されていたが、より詳細な解析を行うために分子動力学計算を行った。計算結果の妥当性を検証するために、分子動力学計算結果から計算されるX線小角散乱パターンと実測のX線小角散乱パターンを比較したところ、両者はよく一致し、分子動力学計算の結果は妥当であることを検証できた。さらに分子動力学計算の結果からCENP-Aを含む再構成クロマチンは特徴的な構造を取りやすいことが示され、このことがクロマチン繊維上でCENP-Aがセントロメア形成のための目印として機能することが推測された。

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    • Dynamics of Nucleosome Assembly in Solution Revealed by X-ray and Neutron Scattering

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

      Sato Mamoru, ODA Takashi, KURUMIZAKA Hitoshi

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      4 2013 - 3 2016

      Grant number:25291037

      Grant amount:\17810000 ( Direct Cost: \13700000 、 Indirect Cost:\4110000 )

      Solution X-ray and neutron scattering analyses have showed that both ends of double stranded DNA in H2A.B nucleosome are peeled off from the histone octamer and is exposed to the solvent. This facilitates the chromatin takes a looser conformation than H2A nucleosome. Also, solution X-ray scattering analysis indicates that conformation of higher-order nucleosome complex, H3-(CENP-A)-H3 tri-nucleosome is more opened than that of H3-H3-H3 tri-nucleosome. Furthermore, MD-SAXS analysis (solution X-ray scattering analysis combined with molecular dynamics calculation) using a coarse grained model as a tri-nucleosome has analyzed the dynamical structure of the chromatin in centromere and non-centromere regions at atomic resolution and elucidated the functional significance of the chromatin containing CENP-A nucleosome in the centromere.

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