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Development of Analysis Method for Reconbinant Biomacromolecular System utlizing Neutron Scattering

Research Project

Project/Area Number 15H02042
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Quantum beam science
Research InstitutionKyoto University

Principal Investigator

Sugiyama Masaaki  京都大学, 複合原子力科学研究所, 教授 (10253395)

Co-Investigator(Kenkyū-buntansha) 加藤 晃一  名古屋市立大学, 大学院薬学研究科, 教授 (20211849)
矢木 宏和  名古屋市立大学, 大学院薬学研究科, 講師 (70565423)
井上 倫太郎  京都大学, 原子炉実験所, 准教授 (80563840)
藤井 紀子  京都大学, 原子炉実験所, 教授 (90199290)
Co-Investigator(Renkei-kenkyūsha) TAKATA SHIN-ICHI  独立行政法人日本原子力研究開発機構, J-PARCセンター, 研究員 (70435600)
Project Period (FY) 2015-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥42,900,000 (Direct Cost: ¥33,000,000、Indirect Cost: ¥9,900,000)
Fiscal Year 2017: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2016: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Fiscal Year 2015: ¥26,000,000 (Direct Cost: ¥20,000,000、Indirect Cost: ¥6,000,000)
Keywords蛋白質重水素化 / クラウディング / 中性子小角散乱 / コントラスト同調 / クリスタリン / 中性子散乱 / 重水素化 / SANS / SAXS / クラウド系 / 逆転コントラスト同調法 / j重水素化 / コントラストマッチング
Outline of Final Research Achievements

Biomacromolucle is functionalized in a polydispersed and high density system, namely a crowding system. Therefore, this study has developed a method to observe and analyze a structure and dynamics of a biomacromolucle in the crowding system. For this purpose, αB-crystallin which is eye lens protein is taken as a sample. A method to prepare 75% deuterated αB-crystallin was established and then it was confirmed that this protein is scatteringly invisible in 100% D2O solution. Based on the result, using the mixture of high concentration of 75% deuterated αB-crystallin with low concentration of not-deuterated αB-crystallin, which is one of crowding systems, it has been succeeded to observe not-deuterated αB-crystallin selectively with small-angle neutron scattering.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (31 results)

All 2018 2017 2016 2015

All Journal Article (16 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 16 results,  Open Access: 9 results,  Acknowledgement Compliant: 6 results) Presentation (14 results) (of which Int'l Joint Research: 8 results,  Invited: 9 results) Funded Workshop (1 results)

  • [Journal Article] Elucidating the Solvent Effect on the Switch of the Helicity of Poly(quinoxaline-2,3-diyl)s: A Conformational Analysis by Small-Angle Neutron Scattering2018

    • Author(s)
      Yuuya Nagata, Tsuyoshi Nishikawa, Michinori Suginome, Sota Sato, Masaaki Sugiyama, Lionel Porcar, Anne Martel, Rintaro Inoue, and Nobuhiro Sato
    • Journal Title

      J. Am. Chem. Soc.

      Volume: 140 Issue: 8 Pages: 2722-2726

    • DOI

      10.1021/jacs.7b11626

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Conversion of functionally undefined homopentameric protein PbaA into a proteasome activator by mutational modification of its C-terminal segment conformation2018

    • Author(s)
      M. Yagi-Utsumi, A. Sikdar, T. Kozai, R. Inoue, M. Sugiyama, T. Uchihashi, H. Yagi, T. Satoh, and K. Kato
    • Journal Title

      Protein Engineering, Design, and Selection

      Volume: 31 Issue: 1 Pages: 29-36

    • DOI

      10.1093/protein/gzx066

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Solution scattering approaches to dynamical ordering in biomolecular systems2018

    • Author(s)
      Bernad? Pau、Shimizu Nobutaka、Zaccai Giuseppe、Kamikubo Hironari、Sugiyama Masaaki
    • Journal Title

      Biochimica et Biophysica Acta (BBA) - General Subjects

      Volume: 1862 Issue: 2 Pages: 253-274

    • DOI

      10.1016/j.bbagen.2017.10.015

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Crystal structure of the overlapping dinucleosome composed of hexasome and octasome2017

    • Author(s)
      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
    • Journal Title

      Science

      Volume: 356 Issue: 6334 Pages: 205-208

    • DOI

      10.1126/science.aak9867

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Characterization of conformational deformation-coupled interaction between immunoglobulin G1 Fc glycoprotein and a low-affinity Fcγ receptor by deuteration-assisted small-angle neutron scattering2017

    • Author(s)
      Yogo Rina、Yanaka Saeko、Yagi Hirokazu、Martel Anne、Porcar Linoel、Ueki Yutaro、Inoue Rintaro、Sato Nobuhiro、Sugiyama Masaaki、Kato Koichi
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 12 Pages: 1-4

    • DOI

      10.1016/j.bbrep.2017.08.004

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update2017

    • Author(s)
      Trewhella Jill、Sugiyama Masaaki, etal.,
    • Journal Title

      Acta Crystallographica Section D Structural Biology

      Volume: 73 Issue: 9 Pages: 710-728

    • DOI

      10.1107/s2059798317011597

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of heteromolecular binding sites in transcription factors Sp1 and TAF4 using high-resolution nuclear magnetic resonance spectroscopy2017

    • Author(s)
      Hibino Emi、Inoue Rintaro、Sugiyama Masaaki、Kuwahara Jun、Matsuzaki Katsumi、Hoshino Masaru
    • Journal Title

      Protein Science

      Volume: 26 Issue: 11 Pages: 2280-2290

    • DOI

      10.1002/pro.3287

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Gliadins from wheat grain: an overview, from primary structure to nanostructures of aggregates2017

    • Author(s)
      Urade Reiko、Sato Nobuhiro、Sugiyama Masaaki
    • Journal Title

      Biophysical Reviews

      Volume: 10 Issue: 2 Pages: 435-443

    • DOI

      10.1007/s12551-017-0367-2

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural characterization of the circadian clock protein complex composed of KaiB and KaiC by inverse contrast matching small-angle neutron scattering2016

    • Author(s)
      M. Sugiyama, H. Yagi, K. Ishii, L. Porcar, A. Martel, K. Oyama, M. Noda, Y. Yunoki, R. Murakami, R. Inoue, N. Sato, Y. Oba, K. Terauchi, S. Uchiyama, K. Kato
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 35567-35567

    • DOI

      10.1038/srep35567

    • NAID

      120006223630

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] New insight into the dynamical system of αB-crystallin oligomers2016

    • Author(s)
      R. Inoue, T. Takata, N. Fujii, K. Ishii, S. Uchiyama, N. Sato, Y. Oba, K. Wood, K. Kato, N. Fujii, and M. Sugiyama
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 29208-29208

    • DOI

      10.1038/srep29208

    • NAID

      120006323745

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF42016

    • Author(s)
      E. Hibino, R. Inoue, M. Sugiyama, J. Kuwahara, K. Matsuzaki, and M. Hoshino
    • Journal Title

      Protein Science

      Volume: 25 Issue: 11 Pages: 2006-2017

    • DOI

      10.1002/pro.3013

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Solution structure of variant H2A.Z.1 nucleosome investigated by small-angle X-ray and neutron scatterings2015

    • Author(s)
      M. Sugiyama, N. Horikoshi, Y. Suzuki, H. Taguchi, T. Kujirai, R. Inoue, Y. Oba, N. Sato, A. Martel, L. Porcar, and H. Kurumizaka
    • Journal Title

      Biochemistry and Biophysics Reports

      Volume: 4 Pages: 28-32

    • DOI

      10.1016/j.bbrep.2015.08.019

    • NAID

      120005893550

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering2015

    • Author(s)
      61.E. Chatani, R. Inoue, H. Imamura, M. Sugiyama, M. Kato, M. Yamamoto, K. Nishida and T. Kanaya
    • Journal Title

      Scientific Report

      Volume: 5 Issue: 1 Pages: 15485-15498

    • DOI

      10.1038/srep15485

    • NAID

      120005672389

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A small-angle X-ray scattering study of gliadins in distilled water over a wide concentration range2015

    • Author(s)
      N. Sato, A. Matsumiya, Y. Higashino, S. Funaki, Y. Kitao, Y. Oba, R. Inoue, F. Arisaka, M. Sugiyama, and R. Urade, Molecular assembly of wheat gliadins into nanostructures
    • Journal Title

      Journal of Agricultural and Food Chemistry

      Volume: 63 Issue: 39 Pages: 8715-8721

    • DOI

      10.1021/acs.jafc.5b02902

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Preparation, characterization and magnetic behavior of a spin-labelled physical hydrogel containing a chiral cyclic nitroxide radical unit fixed inside the gelator molecule2015

    • Author(s)
      Y. Takemoto, T. Yamamoto, N. Ikuma, Y. Uchida, K. Suzuki, S. Shimono, H. Takahashi, N. Sato, Y. Oba, R. Inoue, M. Sugiyama, H. Tsue, T. Kato, J. Yamauchi, and R. Tamura
    • Journal Title

      Soft Matter

      Volume: 11 Issue: 27 Pages: 5563-5570

    • DOI

      10.1039/c5sm01216c

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Simultaneous Characterisation of Precipitates and Matrix in a Steel Using Small-Angle Neutron Scattering and Bragg-Edge Transmission Analysis2015

    • Author(s)
      Y. Oba, S. Morooka, H. Sato, N. Sato, K. Ohishi, J. Suzuki, M. Sugiyama
    • Journal Title

      ISIJ International

      Volume: 55 Issue: 12 Pages: 2618-2623

    • DOI

      10.2355/isijinternational.ISIJINT-2015-315

    • NAID

      130005114990

    • ISSN
      0915-1559, 1347-5460
    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Integrative approach to protein structure and dynamics2018

    • Author(s)
      M.Sugiyama, R.Inoue, M.Morishima, Y.Sakamaki, N.Fujii, K.Ishii, S.Uchiyama
    • Organizer
      The 8th The 8th Taiwan-Japan Joint Meeting on Neutron and X-ray Scattering
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 中性子散乱による蛋白質のドメイン運動の研究2018

    • Author(s)
      杉山正明, 井上倫太郎, 小田 隆, 佐藤 衛, 苙口友隆
    • Organizer
      2017年度 量子ビームサイエンスフェスタ
    • Related Report
      2017 Annual Research Report
  • [Presentation] Neutron Scattering for Bio-molecular Systems2017

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      Grand Challenges in Small-angle Scattering
    • Place of Presentation
      Okazaki, Japan
    • Year and Date
      2017-03-19
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 統合構造生物学における中性子溶液散乱法2017

    • Author(s)
      杉山正明
    • Organizer
      第17回日本中性子科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Study on intra- and inter-protein dynamics by neutron solution scattering2017

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      The 17th KIAS Conference on Protein Structure and Function
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 溶液中性子散乱2017

    • Author(s)
      杉山正明
    • Organizer
      中性子生物構造研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Investigation on domain motion of protein by neutron scattering2017

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      Frontier Bioorganization Forum :Dynamical ordering and integrated functions of biomolecular system
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] α―クリスタリンのサブユニット動態の観察2016

    • Author(s)
      井上倫太郎、杉山正明
    • Organizer
      第16回日本中性子科学会年会
    • Place of Presentation
      名古屋大学 豊田講堂
    • Year and Date
      2016-12-01
    • Related Report
      2016 Annual Research Report
  • [Presentation] 小麦タンパク質グリアジン凝集構造の小角散乱解析2016

    • Author(s)
      佐藤信治、杉山正明
    • Organizer
      第16回日本中性子科学会年会
    • Place of Presentation
      名古屋大学 豊田講堂
    • Year and Date
      2016-12-01
    • Related Report
      2016 Annual Research Report
  • [Presentation] Subunit Kinetics in α-Crystallins2016

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      The 9th Korea-Japan Seminars on Biomolecular Sciences
    • Place of Presentation
      Gyeongju, Korea
    • Year and Date
      2016-11-14
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamic Quaternary Structure of Alpha-Crystallin2016

    • Author(s)
      Rintaro Inoue
    • Organizer
      The 7th Japan-Taiwan Joint Meeting on Neutron and X-ray Scattering
    • Place of Presentation
      Kumatori, Osaka, Reseach Reactor Institute , Kyoto University
    • Year and Date
      2016-03-10
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Subunit Kinetics in α-Crystallins2015

    • Author(s)
      Masaaki Sugiyama
    • Organizer
      International Conference on the Lens 2015
    • Place of Presentation
      Hawaii, USA
    • Year and Date
      2015-12-06
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] KINETICS OF SUBUNITS IN α-CRYSTALLIN AS STUDIED BY SMALL-ANGLE NEUTRON SCATTERING2015

    • Author(s)
      R. Inoue, T. Takata, N. Fujii, N. Sato, Y. Oba, S. Takata, N. Fujii and M. Sugiyama
    • Organizer
      16th Conference on Small Angle Scattering
    • Place of Presentation
      Berlin, Germany
    • Year and Date
      2015-09-14
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 中性子小角散乱だから見える溶液中のタンパク質の構造2015

    • Author(s)
      杉山正明
    • Organizer
      第15回日本蛋白質科学会年会
    • Place of Presentation
      徳島, あわぎんホール(徳島市)
    • Year and Date
      2015-06-24
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Funded Workshop] 第7回日台中性子・X線散乱会議2016

    • Place of Presentation
      京都大学原子炉実験所
    • Year and Date
      2016-03-10
    • Related Report
      2015 Annual Research Report

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Published: 2015-04-16   Modified: 2019-03-29  

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