High pressure protein crystal structure analysis

• Project/Area Number: 21657027
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Nagoya University
• Principal Investigator: WATANABE Nobuhisa 名古屋大学, シンクロトロン光研究センター, 教授 (70212321)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥3,410,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥210,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥800,000 (Direct Cost: ¥800,000); Fiscal Year 2009: ¥1,700,000 (Direct Cost: ¥1,700,000)
• Keywords: 生物物理 / X線 / 結晶構造 / 圧力 / ダイヤモンドアンビルセル / 好圧菌 / 蛋白質 / DAC

Research Abstract

In order to elucidate the mechanism of pressure adaptation of proteins, we have developed structural studies of proteins by a high-pressure protein crystallography method using a diamond-anvil cell. IPMDH from the deep-sea bacterium Shewanella benthica DB21MT-2 is more tolerant towards HP stress than its counterpart from the land bacterium S. oneidensis MR-1, even though these two enzymes share 85% amino-acid identity. Crystal structures of IPMDH have been determined at about 2 A resolution under pressures ranging from 0. 1 to 650 MPa. Penetration of water molecules into IPMDH is observed at high-pressure, and relationship of the structure and pressure resistance has been elucidated.

Research Products

• [Journal Article] High-pressure-induced water penetration into 3-isopropylmalate dehydrogenase (2012)
  • Author(s): Nagae, T., Kawamura, T., Chavas, LMG., Niwa, K., Hasegawa, M., Kato, C. and Watanabe, N.
  • Journal Title: Acta Cryst Volume: D68(3) Issue: 3 Pages: 300-309
  • DOI: 10.1107/s1744309112001443
  • Peer Reviewed
• [Journal Article] Structural analysis of 3-isopropylmalate dehydrogenase from the obligate piezophile Shewanella benthica DB21MT-2 and the nonpiezophile Shewanella oneidensis MR-1 (2012)
  • Author(s): Nagae, T., Kato, C. and Watanabe, N.
  • Journal Title: Acta Cryst. Volume: F68(3) Issue: 3 Pages: 265-268
  • DOI: 10.1107/s0907444912001862
  • Peer Reviewed
• [Presentation] Structure study of IPMDH from piezosensitive and piezophilic Shewanella species (2011)
  • Author(s): T. Nagae, T. Kawamura, L. Chavas, K. Niwa, M. Hasegawa, C. Kato, N. Watanabe
  • Organizer: XXII Congress of the International Union of Crystallography
  • Place of Presentation: Madrid, Spain
• [Presentation] 高圧蛋白質結晶構造解析 (2011)
  • Author(s): 永江峰幸,河村高志, Leonard Chavas,丹羽健,長谷川正,加藤千明,渡邉信久
  • Organizer: 第28回PFシンポジウム
  • Place of Presentation: つくば国際会議場
• [Presentation] Photon Factory and High-Pressure Macromolecular Crystallography (2011)
  • Author(s): Chavas L. M. G, Nagae T, Watanabe N, Hiraki M, Yamada Y, Igarashi N, Matsugaki N, Wakatsuki S
  • Organizer: 第28回PFシンポジウム
  • Place of Presentation: つくば国際会議場
• [Presentation] Shewanella属常圧菌と好圧菌由来3-イソプロピルリンゴ酸脱水素酵素の高圧蛋白質結晶構造解析 (2011)
  • Author(s): 永江峰幸,河村高志,レオナルドシャバス,丹羽健,長谷川正,加藤千明,渡邉信久
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エクスポパーク
• [Presentation] High-Pressure Macromolecular Crystallography at PF (2011)
  • Author(s): Chavas L. M. G, Nagae T, Watanabe NHiraki M, Yamada Y, Igarashi N, Matsugaki N, Wakatsuki S
  • Organizer: 日本放射光学会年会
  • Place of Presentation: つくば国際会議場
• [Presentation] Structure study of IPMDH from piezosensitive and piezophilic Shewanella species (2011)
  • Author(s): T.Nagae, T.Kawamura, L.Chavas, K.Niwa, M.Hasegawa, C.Kato, N.Watanabe
  • Organizer: XXII Congress of the International Union of Crys tallography (IUCr2011)
  • Place of Presentation: Madrid (Spain)
• [Presentation] 高圧蛋白質結晶構造解析 (2011)
  • Author(s): 永江峰幸, 河村高志, Leonard Chavas, 丹羽健, 長谷川正, 加藤千明, 渡邉信久
  • Organizer: 第28回PFシンポジウム
  • Place of Presentation: つくば国際会議場(茨城県)
• [Presentation] Photon Factory and High-Pressure Macromolecular Crystallography (2011)
  • Author(s): Chavas LMG, Nagae T, Watanabe N, Hiraki M, Yamada Y, Igarashi N, Matsugaki N, Wakatsuki S
  • Organizer: 第28回PFシンポジウム
  • Place of Presentation: つくば国際会議場(茨城県)
• [Presentation] Shewanella属常圧菌と好圧菌由来3-イソプロピルリンゴ酸脱水素酵素の高圧蛋白質結晶構造解析 (2011)
  • Author(s): 永江峰幸, 河村高志, レオナルドシャバス, 丹羽健, 長谷川正, 加藤千明, 渡邉信久
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エクスポパーク(大阪府)
• [Presentation] Shewanella属好圧性細菌由来3-isopropylmalate dehydrogenaseの高圧結晶構造解析 (2010)
  • Author(s): 永江峰幸, 河村高志, Leonard Chavas, 加藤千明, 渡邉信久
  • Organizer: 日本結晶学会年会
  • Place of Presentation: 大阪大学コンベンションセンター
  • Year and Date: 2010-12-05
• [Presentation] Shewanella属好圧性細菌由来3-isopropylmalate dehydrogenaseの結晶構造解析と圧力耐性の構造基盤 (2010)
  • Author(s): 永江峰幸, 河村高志, 山根隆, 加藤千明, 渡邉信久
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2010-06-17
• [Presentation] Shewanella属好圧性細菌由来3-isopropylmalate dehydrogenaseの高圧結晶構造解析 (2010)
  • Author(s): 永江峰幸,河村高志, Leonard Chavas,加藤千明,渡邉信久
  • Organizer: 結晶学会年会
  • Place of Presentation: 大阪大学コンベンションセンター
• [Presentation] Shewanella属好圧性細菌由来3-isopropylmalate dehydrogenaseの結晶構造解析と圧力耐性の構造基盤 (2010)
  • Author(s): 永江峰幸,河村高志,山根隆,加藤千明,渡邉信久
  • Organizer: 蛋白質科学会年会
  • Place of Presentation: 札幌コンベンションセンター
• [Presentation] Shewanella属好圧性細菌の3-イソプロピルリンゴ酸脱水素酵素の結晶構造解析 (2009)
  • Author(s): 永江峰幸,河村高志,山根隆,渡邉信久
  • Organizer: 日本結晶学会年会
  • Place of Presentation: 関西学院大学