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Nanobiology Laboratories Protonic NanoMachine Laboratory (Prof. Namba)
Nanobiology Laboratories
Soft Biosystem Group
Protonic NanoMachine Group
Sensory Transduction Group

Biomolecular Networks Laboratories
Research Group of Lipid Biosignals
Biomolecular Dynamics Group
Developmental Biology Group
Chromosome Replication Group

Integrated Biology Laboratories
Laboratory of Genetics
Pathology Division
KOKORO-Biology Group
Cellular Biology Group

Organismal Biosystems Laboratories
Laboratory of Developmental Immunology
Developmental Genetics Group
Human Cell Biology Group
Medicine and Pathophysiology Group

Neuroscience Laboratories
Visual Neuroscience Group
Developmental and Functional Neuroscience Group
Cognitive Neuroscience Group
Cellular and Molecular Neurobiology Group
Synaptic Plasticity Group

Biophysical Dynamics Laboratories
Physiological Laboratory
Nonequilibrium Physics Group
Functional Proteomics Group
Nano-Biophotonics Group

Biomedical Engineering Laboratories
Department of Molecular Genetics
Laboratory of Intercellular Communications
Department of Signal Transduction
Laboratory of Protein Informatics
Laboratory of Biocatalysis Science
Laboratory of Protein Synthesis and Expression
Laboratory of Supramolecular Crystallgraphy

Collaborative institutes
Laboratory of Immune Regulation Chugai Pharmaceutical CO.,LTD.
Optical Nano Device Group
OMRON Corporation

  Lab. Members

Researchers
Shigehiro Nagashima, Yumiko Saijo, Tomoko Miyata,
Nobunori Kami-ike, Akiko Okura, Yumiko Uchida, Miki Kinoshita,
Kana Moriya, Hideyuki Matsunami (OIST), Yukio Furukawa (JST),
Yong-Suk Che (JSPS)
Technical Staff
Yasuyo Abe, Hisako Kawabata
Graduate Students
D5 Ken-ichi Kazetani, Masafumi Shimada, Shuichi Nakamura
D4 Yuki Kikuchi, Takashi Fujii
D3 Masamichi Ashihara, Tatsuya Ibuki, Yusuke Morimoto
D2 Akihiro Kawamoto, Fumiaki Makino, Shinsuke Yoshimura
D1 Noritaka Hara, Akira Hida, Shinji Yoshida, Kohei Yoshitomi

  Publications

Original Papers
  1. Yonekura, K., Maki, S., Morgan, D.G., DeRosier, D. J., Vonderviszt, F., Imada, K. & Namba, K. (2000) The Bacterial Flagellar Cap as the Rotary Promoter of Flagellin Self-Assembly. Science 290, 2148-2152.


  2. Namba, K. (2001) Roles of Partly Unfolded Conformations in Macromolecular Self-Assembly. Genes to Cells 6, 1-12.


  3. Oda, T., Makino, K., Yamashita, I., Namba, K. & Maeda, Y. (2001) Distinct Structural Changes Detected by X-ray Fiber Diffraction in Stabilization of F-actin by Lowering pH and Increasing Ionic Strength. Biophys. J. 80, 841-851.

  4. Samatey, F. A., Imada, K., Vonderviszt, F., Shirakihara, Y. & Namba, K. (2001) Crystallization of the F41 Fragment of Flagellin and Data Collection from Extremely Thin Crystals. J. Struct. Biol. 132, 106-111.


  5. Saijo-Hamano, Y., Namba, K. & Oosawa, K. (2001) A New Purification Method for Overproduced Proteins Sensitive to Endogenous Proteases. J. Struct. Biol. 132, 142-146.


  6. Samatey, F. A., Imada, K., Nagashima, S., Kumasaka, T., Yamamoto, M., Vonderviszt, F., & Namba, K. (2001) Structure of the Bacterial Flagellar Protofilament and Implication for a Switch for Supercoiling. Nature 410, 331-337.


  7. Yonekura, K., Maki-Yonekura, S. & Namba, K. (2001) Structure Analysis of the Flagellar Cap-Filament Complex by Electron Cryomicroscopy and Single Particle Image Analysis. J. Struct. Biol. 133, 246-253.


  8. Minamino, T., Tame, J.R.H, Namba, K. & Macnab R.M. (2001) Proteolytic Analysis of the FliH/FliI complex, the ATPase Component of the Type III Flagellar Export Apparatus of Salmonella. J. Mol. Biol. 312, 1027-1036.

  9. Liu, H & Namba, K. (2001) A Numerical study of Micro-Fluid Dynamics of Undulatory Locomotion. Theoret. Appl. Mechanics 50, 257-270.

  10. Tame, J. R. H., Namba, K., Dodson, E. J. & Roper, D. I. (2002) The Crystal Structure of HpcE, a Bifunctional Decarboxylase/Isomerase with a Multifunctional Fold. Biochem. 41, 2982-2989.

  11. Yonekura, K., Maki-Yonekura, S. & Namba, K. (2002) Quantitative Comparison of Zero-Loss and Conventional Electron Diffraction from Two-Dimensional and Thin Three-Dimensional Protein Crystals. Biophys. J. 82, 2784-2797.

  12. Furukawa, Y., Imada, K., Vonderviszt, F., Matsunami, H., Sano, K., Kutsukake, K. & Namba, K. (2002) Interactions between Bacterial Flagellar Axial Proteins in Their Monomeric State in Solution. J. Mol. Biol. 318, 889-900.

  13. Goda, S., Takano, K., Yamagata, Y., Maki, S., Namba, K. & Yutani, K. (2002) Elongation in a -Structure Promotes Amyloid-Like Fibril Formation of Human Lysozyme. J. Biochem. 132, 655-661.

  14. Minamino T., Gonzalez-Pedrajo, B., Oosawa, K., Namba, K. & Macnab, R. M. (2002) Structural Properties of FliH, an ATPase Regulatory Component of the Salmonella Type III Flagellar Export Apparatus. J. Mol. Biol. 322, 281-290.

  15. Hayashi, F., Suzuki, H., Iwase, R., Uzumaki, T., Miyake, A., Shen, J.-R., Imada, K., Yukio Furukawa, Y., Yonekura, K., Namba, K., & Ishiura, M. (2003) ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC. Genes to Cells 8, 287-296.

  16. Hirano, T., Minamino T., Namba, K. & Macnab, R. M. (2003) Substrate Specificity Classes and the Recognition Signal for Salmonella type III Flagellar Export. J. Bacteriol. 185, 2485-2492.

  17. Minamino, T., Gonzalez-Pedrajo, B., Kihara, M., Namba, K. & Macnab, R. M. (2003) The ATPase FliI can interact with the type III flagellar protein export apparatus in the absence of its regulator, FliH. J. Bacteriol. 185, 3983-3988.

  18. Yonekura, K., Maki-Yonekura, S. & Namba, K. (2003) Complete Atomic Model of the Bacterial Flagellar Filament by Electron Cryomicroscopy. Nature 424, 643-650.

  19. Maki-Yonekura, S., Yonekura, K. & Namba, K. (2003) Domain movements of HAP2 in the cap-filament complex formation and growth process of the bacterial flagellum. Proc. Natl. Acad. Sci. USA 100, 15528-15533.

  20. Yonekura, K., Toyoshima, C. Maki-Yonekura, S. & Namba, K. (2003) GUI programs for processing individual images in early stages of helical image reconstruction ? for high resolution structure analysis. J. Struct. Biol. 144, 184-914.

  21. Kishimoto, A., Hasegawa, K., Suzuki, H., Taguchi, H., Namba, K. & Yoshida, M. (2004) Beta-helix is a likely core structure of yeast prion Sup35 amyloid fibers. Biochem. Biophys. Res. Comm. 315, 739-745.

  22. Suzuki, H., Yonekura, K. & Namba, K. (2004) Structure of the rotor of the bacterial flagellar motor revealed by electron cryomicroscopy and single particle image analysis. J. Mol. Biol. 337, 105-113.

  23. Iwase, R., Imada, K., Hayashi, F., Uzumaki, T., Namba, K. & Ishiura, M. (2004) Crystallization and preliminary crystallographic analysis of the circadian clock protein KaiB form the thermophilic cyanobacterium Themosynechococcus elongatus BP-1. Acta Crystallogr. Acta Crystallogr. D60, 727-729.

  24. Saijo-Hamano, Y., Uchida, N., Namba, K. & Oosawa, K. (2004) In vitro characterization of FlgB, FlgC, FlgF, FlgG and FliE, flagellar basal body proteins of Salmonella. J. Mol. Biol. 339, 423-435.

  25. Minamino, T., Saijo-Hamano, Y., Furukawa, Y., Gonzalez-Pedrajo, B., Macnab, R. M. & Namba, K. (2004) Domain organization and function of Salmonella FliK, a flagellar hook-length control protein. J. Mol. Biol. 341, 491-502.

  26. Saijo-Hamano, Y., Minamino, T., Macnab, R. M. & Namba, K. (2004) Structural and functional analysis of the C-terminal cytoplasmic domain of FlhA, an integral membrane component of the type III flagellar protein export apparatus in Salmonella. J. Mol. Biol. 343, 457-466.

  27. Samatey, F. A., Matsunami, H., Imada, K., Nagashima, S., Shaikh, T. R., Thomas, D. R., Chen, J. Z., DeRosier, D. J. & Namba, K. (2004) Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism. Nature 431, 1062-1068.

  28. Samatey, F. A., Matsunami, H., Imada, K., Nagashima, S. & Namba, K. (2004) Crystallization of a core fragment of the flagellar hook protein FlgE. Acta Crystallogr. D60, 2078-2080.

  29. Dioszeghy, Z., Zavodszky, P., Namba, K. & Vonderviszt, F. (2004) FEBS Letters 568, 105-109.

  30. Yonekura, K., Maki-Yonekura, S. & Namba, K. (2005) Building the atomic model for the bacterial flagellar filament by electron cryomicroscopy and image analysis. Structure 13, 407- 412.

  31. Shaikh, T. R., Thomas, D. R., Chen, J. Z., Samatey, F. A., Matsunami H., Imada, K., Namba, K. & DeRosier, D. J. (2005) A partial atomic structure for the flagellar hook of Salmonella typhimurium. Proc. Natl. Acad. Sci. USA 102, 1023-1028.

  32. Oda, T., Namba, K., Maeda, Y. (2005) Position and orientation of phalloidin in F-actin determined by X-ray fiber diffraction analysis. Biophys. J. 88, 2727-2736.

  33. Saijo-Hamano, Y., Imada, K., Minamino, T., Kihara, M., Macnab, R. M. & Namba, K. (2005)
    Crystallization and preliminary X-ray analysis of the C-terminal cytoplasmic domain of FlhA, a membrane-protein subunit of the bacterial flagellar type III protein-export apparatus. Acta Crystallogr. F61, 599?602

  34. Iwase, R., Imada, K., Hayashi, F., Uzumaki, T., Morishita, M., Onai, K., Furukawa, Y., Namba, K. & Ishiura, M. (2005) Functionally important substructures of circadian clock protein KaiB in unique tetramer complex. J. Biol. Chem. 280, 43141-43149.

  35. Oda, T., Stegmann, H., Schroder, R. R. Namba, K. & Maeda, Y. (2007)
    Modeling of the F-actin structure. Adv. Exp. Med. Biol. 592, 385-401.

  36. Ferris, H. U., Furukawa, Y., Minamino, T., Kroetz, M. B., Kihara, M., Namba, K. & Macnab, R. M. (2006) FlhB regulates ordered export of flagellar components via autocleavage mechanism. J. Biol. Chem. 280, 41236-41242.

  37. Gonzalez, P. B., Minamino, T., Kihara, M., Namba, K. & Macnab, R. M. (2006) FliN, a Salmonella flagellar switch protein interacts with FliH, a type III export apparatus component. Mol. Microbiol. 60, 984-998.

  38. Moriya, N., Minamino, T., Hughes, K. T., Macnab, R. M. & Namba, K. (2006) The type III flagellar export specificity switch is dependent on FliK ruler and a molecular clock. J. Mol. Biol. 359, 466-477.

  39. Kitao, A., Yonekura, K., Maki-Yonekura, S., Samatey, F. A., Imada, K., Namba, K. & Go, N. (2006) Switch interactions control energy frustration and multiple flagellar filament structures. Proc. Nat'l. Acad. Sci. U.S.A. 103, 4894-4899.

  40. Minamino, T., Kazetani, K., Tahara, A., Suzuki, H., Furukawa, Y., Kihara, M. & Namba, K. (2006) Oligomerization of the bacterial flagellar ATPase FliI is controlled by its extreme N-terminal Region. J. Mol. Biol. 360, 510-519.

  41. Minamino, T., Ferris H. U., Moriya, N., Kihara, M. & Namba, K. (2006) Two parts of the T3S4 domain of the hook-length control protein FliK are essential for the substrate specificity switching of the flagellar type III export apparatus. J. Mol. Biol. 362, 1148-1158.

  42. Minamino, T., Imada, K., Tahara, A., Kihara, M., Macnab, R. M. & Namba, K. (2006) Crystallization and preliminary X-ray analysis of Salmonella FliI, the ATPase component of the type III flagellar protein-export apparatus. Acta Crystallogr. F62, 973?975.

  43. Imada, K., Minamino, T., Tahara, A. & Namba, K. (2007) Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits. Proc. Nat'l. Acad. Sci. U.S.A. 104, 485-490.

  44. Shinohara, A., Sakuma, M., Yakushi, T., Kojima, S., Namba, K., Homma, M. & Imada, K. (2007) Crystallization and preliminary X-ray analysis of MotY, a stator component of the Vibrio Alginolyticus polar flagellar. Acta Crystallogr. F63. 89-92.

  45. Furuta, T., Samatey, F. A., Matsunami, H., Imada, K., Namba, K. & Kitao, A. (2007) Gap compression/extension mechanism of bacterial Xagellar hook as the molecular universal joint. J. Struct. Biol. 157, 481-490.


  46. Arkhipov, A., Freddolino, P. L., Imada, K., Namba, K. & Shulten, K. (2006) Coarse-Grained Molecular Dynamics Simulations of a Rotating. Biophys.J. 91, 4589?4597.


  47. Oda, T., Stegmann, H., Schroder, R. R. Namba, K. & Maeda, Y. (2007) Modeling of the F-actin structure. Adv. Exp. Med. Biol. 592, 385?401.


  48. Inoue, M., Kamachi, Y., Matsunami, H., Imada, K., Uchikawa, M. & Kondoh H. (2007) PAX6 and SOX2-dependent regulation of the Sox2 enhancer N-3 involved in embryonic visual system development. Genes to Cells. 12, 1049-1061.


  49. Imada, K., Tamura, T., Takenaka, R., Kobayashi, I., Namba, K. & Inagaki, K. (2007) Structure and quantum chemical analysis of NAD+-dependent isocitrate dehydrogenase: Hydride transfer and co-factor specificity, Proteins: Structure, Function, and Bioinformatics, 70, 63-71.


  50. Minamino, T. and Namba, K. (2008) Distinct roles of the ATPase and proton motive force in bacterial flagellar protein export. Nature, 451, 485-488.


Reviews, Proceedings and Books
  1. Oda, T., Makino, K., Yamashita, I., Namba, K. & Maeda, Y. (2000) The Helical Parameters of F-actin Precisely Determined from X-ray Fiber Diffraction of Well-Oriented Sols. In Results and Problems in Cell Differentiation, 32 (dos Remedios, C., ed.) Molecular Interaction of Actin, pp.43-58. Springer-Verlag Berlin Heidelberg.


  2. Yonekura, K., Maki, S. & Namba, K. (2002) Growth Mechanism of the Bacterial Flagellar Filament. Res. Microbiol. 153, 191-197.


  3. Namba, K. (2002) Structural Insight into the Mechanism of Supercoiling of the Bacterial Flagellar Filament. In New Approaches to Structural Mechanics, Shells and Biological Structures (Drew, H.R. & Pellegrino, S. eds.) Solid Mechanics and Its Application 104, 485-497. Kluwer Academic Publishers, London.

  4. Namba, K. (2003) Dynamic aspects of the bacterial flagellum. In Conformational Proteomics of Macromolecular Architecture. Approaching the Structure of Large Molecular Assemblies and Their Mechanisms of Action (Cheng, R. H. & Hammar, L., eds.) pp. 333-344. World Scientific Publishing Co., Singapore.


  5. Minamino, T. & Namba, K. (2004) Self-assembly and type III protein export of the bacterial flagellum. J. Mol. Microbiol. Biotechnol. 7, 5-17.


  6. Yonekura, K.; Namba, K. (2004) Mobile Structures: Cilia and Flagella. The Encyclopedia of Molecular Cell Biology and Molecular Medicine (WILEY-VCH Verlag, GmbH & Co. KGaA) 3-22.


  7. Kishimoto, A.; Hasegawa, K.; Namba, K. (2005) Beta-Helix is a likely core structure of yeast prion Sup35 amyloid fibers. Spring8 Research Frontiers, 28-29.


  8. Minamino, T.; Anthony P. Pugsley. (2005) Measure for measure in the control type III secretion hook and needle. Molecular Microbiology, 56, 303-308.

  9. Beatson, S. A., Minamino, T. & Pallen, M. J. (2006) Variation in bacterial flagellins: from sequence to structure. Trends in Microbiol. 14, 151-155.

  10. Ferris, H. U.; Minamino, T. (2006) Flipping the switch: bringing order to flagellar assembly. TRENDS. Microbiol. 14, 519-526.



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