Structure analysis of cytoplasmic dynein stalk domain

• Project/Area Number: 20770118
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: The University of Tokyo
• Principal Investigator: SHIBA Tomoo The University of Tokyo, 大学院・医学系研究科, 助教 (80401206)
• Project Period (FY): 2008 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2009: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2008: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: モーター蛋白質 / X 線結晶構造解析 / 多波長異常分散法 / セレノメチオニン / ダイニン / 微小官 / X線結晶構造解析

Research Abstract

In order to reveal the recognition mechanism of the microtubule by motor protein dynein, I have searched the crystallization condition of the mouse dynein stalk domain and could obtain single crystals. I prepared the selenomethionine-substituted protein and collected the diffraction data of the crystals using Synchrotron Radiation (2.8 A resolution). Initial phase are calculated by the multiwavelength anomalous dispersion (MAD) method, I could obtain the partial model of the protein (coiled-coil region). The model revealed that the positions of the methionine, which are calculated by using the anomalous dispersion signal of the selenium, are shifted those of the reported crystal structure.

Research Products

• [Journal Article] Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase (2010)
  • Author(s): Balogun, E.O., Inaoka, D.K., Kido, Y., Shiba, T., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, Michels, P.S., Harada, S., Kita, K.
  • Journal Title: Acta Cryst F66 Pages: 304-308
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei (2010)
  • Author(s): Kido, Y., Shiba, T., Inaoka, D.K., Sakamoto, K., Nara, T., Aoki, T., Honma, T., Tanaka, A., Inoue, M., Matsuoka, S., Moore, A., Harada, S., Kita, K.
  • Journal Title: Acta Cryst F66 Pages: 275-278
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary crystallographic analysis of cyanide-insensitive alternative oxidase from Trypanosoma brucei brucei (2010)
  • Author(s): Yasutoshi Kido
  • Journal Title: Acta Crystallographica Section F F66 Pages: 275-278
  • Peer Reviewed
• [Journal Article] Overproduction, purification, crystallization and preliminary X-ray diffraction analysis of Trypanosoma brucei gambiense glycerol kinase (2010)
  • Author(s): Emmanuel Oluwadare Balogun
  • Journal Title: Acta Crystallographica Section F F66 Pages: 304-308
  • Peer Reviewed
• [Journal Article] Functional importance of Crenarchaeaspecific extra-loop revealed by an X-ray structure of a hetero-tetrameric crenarchaeal splicing endonuclease (2009)
  • Author(s): Yoshinari1, S., Shiba, T., Inaoka, D.K., Itoh, T., Kurisu, G., Harada, S., Kita, K., Watanabe, Y.
  • Journal Title: Nucleic. Acids Res. 37 Pages: 4787-4798
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray studies of the chromophore-binding domain of cyanobacteriochrome AnPixJ from Anabaena sp. PCC 7120 (2009)
  • Author(s): Narikawa, R., Muraki, N., Shiba, T., Ikeuchi, M., Kurisu, G.
  • Journal Title: Acta Cryst F65 Pages: 159-162
  • Peer Reviewed
• [Journal Article] Functional importance of Crenarchaea-specific extra-loop revealed by an X-ray structure of a hetero-tetrameric crenarchaeal splicing endonuclease (2009)
  • Author(s): Shigeo Yoshinaril
  • Journal Title: Nucleic Acids Research 37 Pages: 4787-4798
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray studies of the chromophorebinding domain of (2009)
  • Author(s): Rei Narikawa, Norifumi Muraki, T
  • Journal Title: Acta Crystallographica Section F F65 Pages: 159-162
  • Peer Reviewed
• [Journal Article] Structures of Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexed with Substrates and Products: Atomic Resolution Insights into Mechanisms of Dihydroorotate Oxidation and Fumarate Reduction (2008)
  • Author(s): Inaoka, D.K., Sakamoto, K., Shimizu, H., Shiba, T., Kurisu, G., Nara, T., Aoki, T., Kita, K., Harada, S.
  • Journal Title: Biochemistry 47 Pages: 10881-10891
  • Peer Reviewed
• [Journal Article] Structures of Trypanosoma cruzi Dihydroorotate Dehydrogenase Complexed with Su (2008)
  • Author(s): Daniel Ken Inaoka, Kimitoshi Sak
  • Journal Title: Biochemistry 47 Pages: 10881-10891
  • Peer Reviewed
• [Presentation] Crystallographic studies of ferredoxin-NAD(P)+ reductase from Chlorobium tepidum (2008)
  • Author(s): Shiba, T., Muraki, N., Seo, D., Sakurai, T., Kurisu, G.
  • Organizer: 第21回国際結晶学会議
  • Place of Presentation: 大阪国際会議場
  • Year and Date: 2008-08-29
• [Presentation] Crystallographic studies of ferredoxinNAD(P)+ reductase from Chlorobium tepidum (2008)
  • Author(s): Tomoo Shiba , Norifumi Muraki, D
  • Organizer: The International Union of Crystallography (IUCr) 2008
  • Place of Presentation: 大阪