Development of Analysis Method for Reconbinant Biomacromolecular System utlizing Neutron Scattering

• Project/Area Number: 15H02042
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Quantum beam science
• Research Institution: Kyoto 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: ¥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.

Research Products

• [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 Scattering (2018)
  • 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
  • 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 conformation (2018)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Solution scattering approaches to dynamical ordering in biomolecular systems (2018)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Crystal structure of the overlapping dinucleosome composed of hexasome and octasome (2017)
  • 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
  • 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 scattering (2017)
  • 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
  • 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 update (2017)
  • 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
  • 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 spectroscopy (2017)
  • 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
  • Peer Reviewed
• [Journal Article] Gliadins from wheat grain: an overview, from primary structure to nanostructures of aggregates (2017)
  • 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
  • Peer Reviewed
• [Journal Article] Structural characterization of the circadian clock protein complex composed of KaiB and KaiC by inverse contrast matching small-angle neutron scattering (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] New insight into the dynamical system of αB-crystallin oligomers (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4 (2016)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Solution structure of variant H2A.Z.1 nucleosome investigated by small-angle X-ray and neutron scatterings (2015)
  • 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
  • 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 scattering (2015)
  • 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
  • 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 range (2015)
  • 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
  • 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 molecule (2015)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Simultaneous Characterisation of Precipitates and Matrix in a Steel Using Small-Angle Neutron Scattering and Bragg-Edge Transmission Analysis (2015)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Integrative approach to protein structure and dynamics (2018)
  • 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
  • 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
• [Presentation] Neutron Scattering for Bio-molecular Systems (2017)
  • Author(s): Masaaki Sugiyama
  • Organizer: Grand Challenges in Small-angle Scattering
  • Place of Presentation: Okazaki, Japan
  • Year and Date: 2017-03-19
  • 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
• [Presentation] Study on intra- and inter-protein dynamics by neutron solution scattering (2017)
  • Author(s): Masaaki Sugiyama
  • Organizer: The 17th KIAS Conference on Protein Structure and Function
  • 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
  • Invited
• [Presentation] Investigation on domain motion of protein by neutron scattering (2017)
  • Author(s): Masaaki Sugiyama
  • Organizer: Frontier Bioorganization Forum :Dynamical ordering and integrated functions of biomolecular system
  • 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
• [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
• [Presentation] Subunit Kinetics in α-Crystallins (2016)
  • Author(s): Masaaki Sugiyama
  • Organizer: The 9th Korea-Japan Seminars on Biomolecular Sciences
  • Place of Presentation: Gyeongju, Korea
  • Year and Date: 2016-11-14
  • Int'l Joint Research / Invited
• [Presentation] Dynamic Quaternary Structure of Alpha-Crystallin (2016)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Subunit Kinetics in α-Crystallins (2015)
  • Author(s): Masaaki Sugiyama
  • Organizer: International Conference on the Lens 2015
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2015-12-06
  • Int'l Joint Research / Invited
• [Presentation] KINETICS OF SUBUNITS IN α-CRYSTALLIN AS STUDIED BY SMALL-ANGLE NEUTRON SCATTERING (2015)
  • 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
  • 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
  • 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