Identification of protein dynamics for enzymatic reaction using four-dimensional visualizing analysis

• Project/Area Number: 20750137
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Chemistry related to living body
• Research Institution: Osaka University
• Principal Investigator: NOJIRI Masaki Osaka University, 大学院・理学研究科, 助教 (20333346)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2010: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2008: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: X線結晶構造解析 / 酵素反応機構 / 時間分解 / 生体分子 / 酵素反応 / 酵素 / X線 / 結晶構造解析

Research Abstract

The objective for this research project is to establish the methods for visualizing the protein dynamics on enzymatic reaction mechanism. In this case, we selected a crystal for copper-containing nitrite reductase as a test case, and collected the diffraction data during high-brilliant x-ray induced reduction. As a result, we have succeeded in observation of some unambiguous structural changes at the copper binding sites in the difference fourier electron density maps.

Research Products

• [Journal Article] Cloning, expression, purification, crystallization and preliminary X-ray crystallographic study of GK0767, the copper-containing nitrite reductase from Geobacillus kaustophilus. (2011)
  • Author(s): Fukuda,Y., Tamada,T., Takami,H., Suzuki,S., Inoue,T., Nojiri,M
  • Journal Title: Acta Cryst., F (in press)
• [Journal Article] Electroreduction of nitrite to nitrogen oxide by a copper-containing nitrite reductase model complex incorporated into collagen film. (2010)
  • Author(s): Isoda,N., Yokoyama,H., Nojiri,M., Suzuki,S., Yamaguchi,K
  • Journal Title: Bioelectrochemistry 77 Pages: 82-82
• [Journal Article] Electroreduction of Nitrite to Nitrogen Oxide by a Copper-Containing Nitrite Reductase Model Complex Incorporated into Collagen Film (2010)
  • Author(s): Naoko Isoda, Hiroshi Yokoyama, Masaki Nojiri, Shinnichiro Suzuki, Kazuya Yamaguchi
  • Journal Title: Bioelectrochemistry Volume: 77 Pages: 82-88
  • Peer Reviewed
• [Journal Article] 過渡的複合体結晶構造解析による蛋白質電子伝達機構の構造生物化学 (2010)
  • Author(s): 野尻正樹、小手石泰康、鈴木晋一郎
  • Journal Title: 酵素工学ニュース(酵素工学研究会誌) Volume: 63 Pages: 29-34
• [Journal Article] Structural basis of inter-protein electron transfer for nitrite reduction in denitrification. (2009)
  • Author(s): Nojiri,M., Koteishi,H., Nakagami,T., Kobayashi,K., Inoue,T., Yamaguchi,K., Suzuki,S
  • Journal Title: Nature 462 Pages: 117-117
• [Journal Article] Cytochrome c551 is a mediator of electron transfer between copper-containing nitrite reductase and azurin in a denitrifying bacterium, Achromobacter xylosoxidans. (2009)
  • Author(s): Koteishi,H., Nojiri,M., Nakagami,T., Yamaguchi,K., Suzuki,S
  • Journal Title: Bull.Chem.Soc.Jpn. 82 Pages: 1003-1003
  • NAID: 130004152644
• [Journal Article] Expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of PPA0092, a putative nitrite reductase from Propionibacterium acnes. (2009)
  • Author(s): Nojiri,M., Shirota,F., Hira,D., Suzuki,S
  • Journal Title: Acta Cryst. F65 Pages: 123-123
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of a complex between the electron-transfer partners hexameric Cu-containing nitrite reductase and pseudoazurin. (2009)
  • Author(s): Hira,D., Nojiri,M., Suzuk,S
  • Journal Title: Acta Cryst. F65 Pages: 116-116
• [Journal Article] Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans : structural insights into its spectroscopic properties. (2009)
  • Author(s): Hira,D., Nojiri,M., Suzuki,S
  • Journal Title: Acta Cryst. D65 Pages: 85-85
• [Journal Article] The first example of photochemical reduction of nitrite into nitrogen monoxide by a dinuclear Ru(II)-Cu(II) complex and photoinduced intramolecular electron transfer reaction between Ru(II) and Cu(II) moieties. (2009)
  • Author(s): Isoda,N., Torii,Y., Okada,T., Misoo,M., Yokoyama,H., Ikeda,N., Nojiri,M., Suzuki,S., Yamaguchi,K
  • Journal Title: Dalton Trans. 46 Pages: 10175-10175
• [Journal Article] Electrocatalytic nitrite reduction to nitrogen oxide by a synthetic analogue of the active site of Cu-containing nitrite reductase incorporated in nafion film. (2009)
  • Author(s): Migita,Y., Yokoyama,H., Minami,A., Mori,T., Nojiri,M., Suzuki,S., Yamaguchi,K
  • Journal Title: Electroanalysis 21 Pages: 2441-2441
• [Journal Article] Structural basis of inter-protein electron transfer for nitrite reduction in denitrification (2009)
  • Author(s): Nojiri, et. Al
  • Journal Title: Nature 462 Pages: 117-120
  • Peer Reviewed
• [Journal Article] Cytochrome c_551 is a mediator of electron transfer between copper-containing nitrite reductase and azurin in a denitrifying bacterium, Achromobacter xylosoxidans (2009)
  • Author(s): Koteishi, et al.
  • Journal Title: Bull. Chem. Soc. Jpn. 82 Pages: 1003-1005
  • Peer Reviewed
• [Journal Article] Atomic resolution structure of pseudoazurin from the methylotrophic denitrifying bacterium Hyphomicrobium denitrificans (2009)
  • Author(s): Hira, et.al.
  • Journal Title: Acta Crystallographica Section D 65 Pages: 85-92
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of a complex between the electron-transfer partners hexameric Cu-containing nitrite reductase and pseudoazurin (2009)
  • Author(s): Hira, et.al.
  • Journal Title: Acta Crystallographica Section F 65 Pages: 116-119
  • Peer Reviewed
• [Journal Article] Expression, purification, crystallization and preliminary X-ray diffraction analysis of the soluble domain of PPA0092, a putative nitrite reductase from Propionibacterium acnes (2009)
  • Author(s): Nojiri, et.al.
  • Journal Title: Acta Crystallographica Section F 65 Pages: 123-127
  • Peer Reviewed
• [Journal Article] Pulse radiolysis of hexameric nitrite reductase containing the type 1 Cu sites in a monomer. (2008)
  • Author(s): Suzuki,S., Maetani,T., Nojiri,M., Yamaguchi,K., Kobayashi,K., Tagawa,S
  • Journal Title: Bull.Chem.Soc.Jpn. 81 Pages: 1525-1525
• [Presentation] Role of the N-terminal cupredoxin domain of a hexameric nitrite reductase (2010)
  • Author(s): Ikebuchi, S., Koteishi, H., Yamaguchi, K., Suzuki, S., Nojiri, M.
  • Organizer: The International Chemical Congress of Pacific Basin Societies
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2010-12-15
• [Presentation] 脱窒反応における蛋白質電子伝達機構の構造生物化学的研究 (2010)
  • Author(s): 野尻正樹
  • Organizer: 第64回講演会(酵素工学研究会),(招待講演)
  • Place of Presentation: 東京大学
  • Year and Date: 2010-11-19
• [Presentation] 脱窒反応における蛋白質電子伝達機構の構造生物化学的研究 (2010)
  • Author(s): 野尻正樹
  • Organizer: 第64回 酵素工学研究会 講演会
  • Place of Presentation: 東京大学(招待講演)
  • Year and Date: 2010-11-19
• [Presentation] 六量体銅型亜硝酸還元酵素におけるタイプ1銅含有N末ドメインの役割 (2010)
  • Author(s): 池淵紗織、城田フェリシア、小手石泰康、山口和也、鈴木晋一郎、野尻正樹
  • Organizer: 第4回 バイオ関連化学シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2010-09-24
• [Presentation] 新奇c型ヘム含有銅型亜硝酸還元酵素とチトクロムcの分子間電子伝達反応 (2010)
  • Author(s): 石川遼介、津田愛子、小手石泰康、山口和也、鈴木晋一郎、野尻正樹
  • Organizer: 第4回 バイオ関連化学シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2010-09-24
• [Presentation] 銅型亜硝酸還元酵素と電子供与タンパク質間の電子移動反応における過渡的複合体の構造解析 (2010)
  • Author(s): 小手石泰康、石本和大、山口和也、鈴木晋一郎、野尻正樹
  • Organizer: 第4回 バイオ関連化学シンポジウム
  • Place of Presentation: 大阪大学
  • Year and Date: 2010-09-24
• [Presentation] Structural analysis of the transient complexes between nitrite reductase and its redox-partner protein during inter-protein electron transfer reaction (2010)
  • Author(s): Koteishi, H., Ishimoto, K., Suzuki, S., Nojiri, M
  • Organizer: Gordon Research Conferences-Electron Transfer Processes and Energy Conversion
  • Place of Presentation: Salve Regina University, USA
  • Year and Date: 2010-08-08
• [Presentation] 亜硝酸還元酵素と電子供与蛋白質の分子間電子移動反応における分子認識と反応制御機構の構造基盤 (2010)
  • Author(s): 野尻正樹
  • Organizer: 第10回日本蛋白質科学会年会,(招待講演)
  • Place of Presentation: 札幌コンベンションセンター
  • Year and Date: 2010-06-16
• [Presentation] 亜硝酸還元酵素と電子供与蛋白質の分子間電子伝達反応における分子認識と反応制御機構の構造基盤 (2010)
  • Author(s): 野尻正樹
  • Organizer: 第10回 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(招待講演)
  • Year and Date: 2010-06-16
• [Presentation] 部位特異的変異による銅含有亜硝酸還元酵素とシトクロムcの会合様式と電子移動への影響 (2010)
  • Author(s): 小手石泰康、石本和大、鈴木晋一郎、野尻正樹
  • Organizer: 第10回 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: 2010-06-16
• [Presentation] 六量体銅型亜硝酸還元酵素におけるタイプ1銅含有N末ドメインの役割 (2010)
  • Author(s): 池淵紗織、城田フェリシア、小手石泰康、鈴木晋一郎、野尻正樹
  • Organizer: 第10回 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: 2010-06-16
• [Presentation] 銅型亜硝酸還元酵素へのX線照射効果における結晶学的研究 (2009)
  • Author(s): 野尻正樹、稲川香、小手石泰康、鈴木晋一郎
  • Organizer: 日本結晶学会2009年度年会
  • Place of Presentation: 関西学院大学
  • Year and Date: 2009-12-05
• [Presentation] 電子伝達パートナー蛋白質同士の過渡的複合体と融合蛋白質の構造的特性化.特定領域研究「生体超分子構造」 (2009)
  • Author(s): 野尻正樹、小手石泰康、津田愛子、鈴木晋一郎
  • Organizer: 第6回公開シンポジウム
  • Place of Presentation: 千里ライフサイエンスセンター(大阪府)
  • Year and Date: 2009-12-01
• [Presentation] insights into the Electron Transfer Reaction of a Copper-containing Nitrite Reductase. (2009)
  • Author(s): Nojiri, M., Structural, Mechanistic
  • Organizer: The 2nd International Symposium on Bioinorganic Chemistry of the New Era(招待講演)
  • Place of Presentation: Hida-Takayama Convention Bureau, Japan.
  • Year and Date: 2009-07-31
• [Presentation] 銅型亜硝酸還元酵素における分子間電子伝達機構の構造基盤 (2009)
  • Author(s): 野尻正樹
  • Organizer: 第36回生体分子科学討論会
  • Place of Presentation: 北海道大学
  • Year and Date: 2009-06-19
• [Presentation] 亜硝酸還元酵素と電子供与蛋白質の分子間電子移動反応機構:複合体結晶構造を基にした分子認識と反応制御機構の構造基盤 (2009)
  • Author(s): 野尻正樹、平大輔、小手石泰康、池渕紗織、津田愛子、鈴木晋一郎
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-20
• [Presentation] Structural and mechanistic insights into the electron transfer reaction of a copper-containing nitrite reductase (2009)
  • Author(s): Nojiri, et al.
  • Organizer: 2^<nd> international symposium on bioinorganic chemistry of the new era
  • Place of Presentation: Takayama, Japan
• [Presentation] Inter- and intra-molecular complex structures of Cu-containing nitrite reductase with cytochrome c. (2008)
  • Author(s): Nojiri, M., Koteishi, H., Tsuda, A., Yamaguchi, K., Suzuki, S.
  • Organizer: XXI IUCr Congress
  • Place of Presentation: Grad Cube Osaka, Japan
  • Year and Date: 2008-08-23
• [Presentation] 銅型亜硝酸還元酵素とチトクロムc間の電子伝達反応における両分子間と分子内複合体の結晶構造 (2008)
  • Author(s): 野尻正樹、小手石泰康、津田愛子、山口和也、鈴木晋一郎
  • Organizer: 第8回日本蛋白質科学会年会
  • Place of Presentation: タワーホール船堀(東京)
  • Year and Date: 2008-06-10
• [Presentation] Crystal structures of inter and intramolecular complexes of Cu-containing nitrite reductase with cytochrome c (2008)
  • Author(s): Nojiri, et.al.
  • Organizer: XXI congress and general assembly of the international union of crystallography
  • Place of Presentation: Osaka, Japan