Development of de novo phasing method with XFEL toward a structure determination of a drug target protein

• Project/Area Number: 15K14941
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Physical pharmacy
• Research Institution: Kyoto University
• Principal Investigator: Nakatsu Toru 京都大学, 薬学研究科(研究院), 准教授 (50293949)
• Project Period (FY): 2015-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2015: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
• Keywords: X線自由電子レーザー / X線結晶構造解析 / タンパク質 / 重原子同型置換法 / 異常分散効果 / 重原子同型置換

Outline of Final Research Achievements

We need to understand the drug target protein in order to study the drug discovery research. It is important to determine the protein structure with X-ray crystallography. However it is difficult to determine the protein structure because the size of the crystal is only 1~10 μm. The structural information is obtained from small crystals illuminated by an X-ray free electron laser.
Then we developed de novo protein structure determination method using μm-sized protein crystals at SACLA which is Japanese X-ray free electron laser fcillity.

Research Products

• [Journal Article] Redox-coupled proton transfer mechanism in nitrite reductase revealed by femtosecond crystallography. (2016)
  • Author(s): Fukuda Y, Tse KM, Nakane T, Nakatsu T, Suzuki M, Sugahara M, Inoue S, Masuda T, Yumoto F, Matsugaki N, Nango E, Tono K, Joti Y, Kameshima T, Song C, Hatsui T, Yabashi M, Nureki O, Murphy ME, Inoue T, Iwata S, Mizohata E.
  • Journal Title: PNAS Volume: 113 Issue: 11 Pages: 2828-2933
  • DOI: 10.1073/pnas.1517770113
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] An isomorphous replacement method for efficient de novo phasing for serial femtosecond crystallography. (2015)
  • Author(s): Atsushi Kodan, Tomohiro Yamaguchi, Tomohiro Murai, Keiko Gomi, Naoki Kajiyama, Eiichi Mizohata, Mamoru Suzuki, Eriko Nango, Kensuke Tono, Yasumasa Joti, Takashi Kameshima, Jaehyun Park, Changyong Song, Takaki Hatsui, Makina Yabashi, So Iwata, Hiroaki Kato, Hideo Ago, Masaki Yamamoto & Toru Nakatsu
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 14017-14017
  • DOI: 10.1038/srep14017
  • NAID: 120005651939
  • Peer Reviewed / Open Access
• [Journal Article] Native sulfur/chlorine SAD phasing for serial femtosecond crystallography. (2015)
  • Author(s): Nakane T, Song C, Suzuki M, Nango E, Kobayashi J, Masuda T, Inoue S, Mizohata E, Nakatsu T, Tanaka T, Tanaka R, Shimamura T, Tono K, Joti Y, Kameshima T, Hatsui T, Yabashi M, Nureki O, Iwata S, Sugahara M.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. Volume: 71 Issue: 12 Pages: 2519-25
  • DOI: 10.1107/s139900471501857x
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] SACLA におけるシリアルフェムト秒タンパク質結晶構造解析の現状 (2016)
  • Author(s): 中津亨
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2016-06-08
  • Invited
• [Presentation] X線自由電子レーザーを用いた新規タンパク質の立体構造決定 (2016)
  • Author(s): 山下 恵太郎, 潘 東青, 奥田 智彦, 菅原 道泰, 小段篤史, 山口 知宏, 村井 智洋, 溝端 栄一, 鈴木 守, 南後 恵理子, 登野 健介, 城地 保昌, 亀島 敬, 初井 宇記, 矢橋 牧名, 岩田 想, 加藤 博章, 吾郷 日出夫, 山本 雅貴, 中津 亨
  • Organizer: 日本薬学会136年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2016-03-27
• [Presentation] シリアル結晶学における重原子誘導体を用いた位相決定 (2015)
  • Author(s): 山下恵太郎, 潘 東青, 長谷川和也, 菅原道泰, 村井智洋, 小段篤史, 溝端栄一, 鈴木 守, 桝田哲哉, 平田邦生, 加藤博章, 吾郷日出夫, 熊坂 崇, 山本雅貴, 中津 亨
  • Organizer: 平成27年度日本結晶学会年会
  • Place of Presentation: 大阪府立大学
  • Year and Date: 2015-10-17
• [Presentation] De novo structure determination for serial femtosecond crystallography using heavy atom derivatives 重原子誘導体を利用したシリアルフェムト秒結晶学による新規構造決定 (2015)
  • Author(s): 山下 恵太郎, 潘 東青, 菅原 道泰, 吾郷 日出夫, 山本 雅貴, 中津亨
  • Organizer: 第53回生物物理学会年会
  • Place of Presentation: 金沢大学
  • Year and Date: 2015-09-13
• [Book] 光と生命の事典 (2016)
  • Author(s): 中津亨
  • Total Pages: 2
  • Publisher: 朝倉書店