Structure and organization of nano-sized giant hemoglobin

2009 Fiscal Year Final Research Report

• Project/Area Number: 16087205
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kanazawa University
• Principal Investigator: FUKUMORI Yoshihiro Kanazawa University, 自然システム学系, 教授 (60135655)
• Co-Investigator(Renkei-kenkyūsha): NUMOTO Nobutaka 京都大学, 原子炉実験所, 助教 (20378582)
• Project Period (FY): 2004 – 2009
• Keywords: 巨大ヘモグロビン / 立体構造 / 協同性 / 有鬚動物 / 超分子複合体

Research Abstract

A marine invertebrate, Oligobrachia mashikoi, has a novel extracellular giant hemoglobin which transports oxygen and sulfide simultaneously. In the present study, we determined the crystal structures of a 400-kDa Hb oxy from and deoxy form by X-ray crystallographic analyses and proposed the new mechanism on oxygen cooperativity which is quite different from those of the well-studied mammalian Hbs.

Research Products

• [Journal Article] 巨大ヘモグロビンの構造と機能 (2008)
  • Author(s): 沼本修孝, 中川太郎, 福森義宏, 三木邦夫
  • Journal Title: 日本血液代替物学会誌「人工血液」 16 Pages: 188-197
• [Journal Article] Distribution and population of free-living cells related to endosymbiont a harbored in Oligobrachia mashikoi (a Siboglinid Polychaete) inhabiting Tsukumo Bay. (2008)
  • Author(s): Aida, M., M. Kanemori, Kubota, N., Matada, M., Sasayama, Fukumori, Y
  • Journal Title: Microbes and Environments 23 Pages: 81-88
  • Peer Reviewed
• [Journal Article] Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins. (2008)
  • Author(s): Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.
  • Journal Title: Proteins 73 Pages: 113-125
  • Peer Reviewed
• [Journal Article] Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. (2008)
  • Author(s): Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.
  • Journal Title: Biochemistry 47 Pages: 11231-11238
  • Peer Reviewed
• [Journal Article] Oxygenation Properties of Extracellular Giant Hemoglobin from Oligobrachia mashikoi (2007)
  • Author(s): Aki, Y., Nakagawa, T, Nagai, Y., Sasayama, Y, Fukumori, Y, K. Imai
  • Journal Title: Biochem. Biophys. Res. Comm. 360 Pages: 673-678
  • Peer Reviewed
• [Journal Article] Identification of endosymbionts in Oligobrachia mashikoi (Siboglinidae, Annelida) (2007)
  • Author(s): Kubota N, Kanemori M, Sasayama Y, Aida M, Fukumori Y
  • Journal Title: Microbes and Environments 22(2) Pages: 136-144
  • Peer Reviewed
• [Journal Article] Actual distribution of bacteriocytes in the trophosome of a beard worm (Oligobrachia mashikoi, Siboglinidae, Annelida): Clarification using whole-mount in situ hybridization. (2007)
  • Author(s): Deguchi, M, Kubota, N, Matsuno, A, Kanemori, M, Fukumori Y, Sasayama Y
  • Journal Title: Acta Zoologica 88 Pages: 129-135
  • Peer Reviewed
• [Journal Article] Relationship between the lifestyle of a Siboglinid (Pogonophoran) polychaete, Oligobrachia mashikoi, and the total sulfide and nitrogen levels in its habitat. (2007)
  • Author(s): Sasayama Y., Higashide Y., Sakai M., Tatada M., Fukumori Y.
  • Journal Title: Zoolog Sci. 24 Pages: 131-136
  • Peer Reviewed
• [Journal Article] 巨大ヘモグロビンの謎に迫る?X線結晶構造解析で構造と機能を解き明かせ! (2006)
  • Author(s): 沼本修孝、福森義宏、三木邦夫
  • Journal Title: 化学 61 Pages: 30-34
• [Journal Article] Purification, characterization and sequence analyses of the extracellular giant hemoglobin from Oligobrachia mashikoi. (2005)
  • Author(s): T. Nakagawa, S. Onoda, M. Kanemori, Y. Sasayama, Y. Fukumori
  • Journal Title: Zool. Sci 22 Pages: 283-291
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray crystallographic analysis of extracellular giant hemoglobin from pogonophoran Oligobrachia mashikoi. (2005)
  • Author(s): Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.
  • Journal Title: Biochim. Biophys. Acta 1750 Pages: 173-176
  • Peer Reviewed
• [Journal Article] Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi. (2005)
  • Author(s): Numoto, N., Nakagawa, T., Kita, A., Sasayama, Y., Fukumori, Y., Miki, K.
  • Journal Title: Proc. Natl. Acad. Sci. USA 102 Pages: 14521-14526
  • Peer Reviewed
• [Presentation] サツマハオリムシV2巨大ヘモグロビン(分子量40万)の結晶構造 (2009)
  • Author(s): 沼本修孝, 中川太郎, 福森義宏, 三木邦夫
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: アスティ徳島(徳島)
  • Year and Date: 2009-10-31
• [Presentation] サツマハオリムシV2ヘモグロビンのX線結晶構造解析 (2009)
  • Author(s): 沼本修孝, 中川太郎, 福森義宏, 三木邦夫
  • Organizer: 第82回日本生化学会大会
  • Place of Presentation: 神戸ポートアイランド(兵庫)
  • Year and Date: 2009-10-22
• [Presentation] 巨大ヘモグロビン(400 kDa)のリガンド結合に伴う協同的な構造変化 (2009)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • 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(熊本)
  • Year and Date: 2009-05-22
• [Presentation] 環形動物巨大ヘモグロビン(分子量360万)の5. 6 A分解能X線結晶構造解析 (2008)
  • Author(s): 沼本修孝, 中川太郎, 福森義宏, 三木邦夫
  • Organizer: 第31回秘本分子生物学会年会・第81回日本生化学会大会合同大会
  • Place of Presentation: 神戸ポートアイランド(兵庫)
  • Year and Date: 2008-12-12
• [Presentation] サツマハオリムシ巨大ヘモグロビン(分子量360万)の5. 6 A分解能結晶構造 (2008)
  • Author(s): 沼本修孝, 中川太郎, 福森義宏, 三木邦夫
  • Organizer: 第46回日本生物物理学会年会
  • Place of Presentation: 福岡国際会議場(福岡)
  • Year and Date: 2008-12-03
• [Presentation] Ligand-induced structural changes of giant hemoglobin, XXI Congress and General Assembly of the International Union of Crystallography (2008)
  • Author(s): Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yuichi Sasayama, Yoshihiro Fukumori, Kunio Miki
  • Organizer: invited lecture for Microsymposia "Large macromolecular complexes"
  • Place of Presentation: Osaka International Convention Center (Japan)
  • Year and Date: 2008-08-24
• [Presentation] 無脊椎動物巨大ヘモグロビンの高分解能結晶構造 (2008)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • Organizer: 第21回日本放射光学会年会・放射光科学合同シンポジウム
  • Place of Presentation: 立命館大学(滋賀)
  • Year and Date: 2008-01-14
• [Presentation] マシコヒゲムシ巨大ヘモグロビンの金属結合型結晶構造 (2007)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台国際センター(仙台)
  • Year and Date: 2007-05-24
• [Presentation] Crystal Structure of Extracellular Giant Hemoglobin of Pogonophoran Oligobrachia mashikoi (2006)
  • Author(s): Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yuichi Sasayama, Yoshihiro Fukumori, Kunio Miki
  • Organizer: The 7th Conference of the Asian Crystallographic Association (AsCA' 06/CrSJ)
  • Place of Presentation: Epochal Tsukuba, (Japan)
  • Year and Date: 2006-11-22
• [Presentation] マシコヒゲムシ巨大ヘモグロビンの一部酸素結合型結晶構造 (2006)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • Organizer: 第6回日本蛋白質科学会年会
  • Place of Presentation: 国立京都国際会館(京都)
  • Year and Date: 2006-04-26
• [Presentation] 巨大へモグロビンの分子会合機構 (2005)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • Organizer: 第43回日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター(北海道)
  • Year and Date: 2005-11-25
• [Presentation] Structure of a giant hemoglobin of the gutless beard worm Oligobrachia mashikoi (2005)
  • Author(s): Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yuichi Sasayama, Yoshihiro Fukumori, Kunio Miki
  • Organizer: XX Congress of the International Union of Crystallography
  • Place of Presentation: Fortezza da Basso (Italy)
  • Year and Date: 2005-08-28
• [Presentation] マシコヒゲムシ巨大ヘモグロビンの結晶構造 (2005)
  • Author(s): 沼本修孝, 中川太郎, 喜田昭子, 笹山雄一, 福森義宏, 三木邦夫
  • Organizer: 第5回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場(福岡)
  • Year and Date: 2005-06-30
• [Presentation] Crystallographic Study of Multi Hemoglobin System from Oligobrachia mashikoi (2004)
  • Author(s): Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yoshihiro Fukumori, Kunio Miki
  • Organizer: The 1st Pacific-Rim International Conference on Protein Science
  • Place of Presentation: Pacifico Yokohama (Japan)
  • Year and Date: 20040417-20040418
• [Remarks]
  • URL: http://pronet.s.kanazawa-u.ac.jp/