Namba Protonic NanoMachine Project
List of Publications

Peer reviewed publications
1
Siota, Y., Yokota, M., Kakizaki, A., Mitsui, T., Wakabayashi, K., Namba, K., Wada, E., Tagawa, H., Kurita, K., Nagakura, I. & Matsukawa, T. (1977)
Small-Angle Scattering of Soft X-rays by Use of Synchrotron Radiation. Jpn J. Appl. Phys. 16, 215-216.
2
Wakabayashi, K., Kakizaki, A., Siota, Y., Namba, K., Kurita, K., Yokota, M., Tagawa, H., Inoko, Y., Mitsui, T., Wada, E., Ueki, T., Nagakura I. & Matsukawa, T. (1978)
Soft X-ray Small-Angle Scattering by Polystyrene Latexes Using Synchrotron Radiation. J. Phys. Soc. Japan 44, 1314-1322.
3
Kamiya, R., Asakura, S., Wakabayashi, K. & Namba, K. (1979)
Transition of Bacterial Flagella from Helical to Straight Forms with Different Subunit Arrangements. J. Mol. Biol. 131, 725-742.
4
Namba, K., Wakabayashi, K. & Mitsui, T. (1980)
X-ray Structure Analysis of the Thin Filament of Crab Striated Muscle in the Rigor State. J. Mol. Biol. 138, 1-26.
5
Wakabayashi, K. & Namba, K. (1981)
X-ray Equatorial Analysis of Crab Striated Muscle in the Relaxed and Rigor States. Biophys. Chem. 14, 111-122.
6
Namba, K., Caspar, D.L.D. & Stubbs, G. (1985)
Computer Graphics Representation of Levels of Organization in Tobacco Mosaic Virus Structure. Science 227, 773-776.
7
Namba, K. & Stubbs, G. (1985)
Solving the Phase Problem in Fiber Diffraction. Application to Tobacco Mosaic Virus at 3.6A Resolution. Acta Cryst. A41, 252-262.
8
Stubbs, G., Namba, K. & Makowski, L. (1986)
Application of Restrained Least-Squares Refinement to Fiber Diffraction from Macromolecular Assemblies. Biophys. J. 49, 58-60.
9
Namba, K. & Stubbs, G. (1986)
Structure of Tobacco Mosaic Virus at 3.6 Å Resolution: Implications for Assembly. Science 231, 1401-1406.
10
Namba, K. & Stubbs, G. (1987)
Isomorphous Replacement in Fiber Diffraction Using Limited Numbers of Heavy-Atom Derivatives. Acta Cryst. A43, 64-69.
11
Namba, K. & Stubbs, G. (1987)
Difference Fourier Syntheses in Fiber Diffraction. Acta Cryst. A43, 533-539.
12
Lobert, S., Heil, P.D., Namba, K. & Stubbs, G. (1987)
Preliminary X-ray Fiber Diffraction Studies of Cucumber Green Mottle Mosaic Virus, Watermelon Strain.. J. Mol. Biol. 196, 935-938.
13
Namba, K., Caspar, D.L.D. & Stubbs, G. (1988)
Enhancement and Simplification of Macromolecular Images. Biophys. J. 53, 469-475.
14
Vonderviszt, F., Kanto, S., Aizawa, S.-I. & Namba, K. (1989)
Terminal Regions of Flagellin are Disordered in Solution. J. Mol. Biol. 209, 127-133.
15
Namba, K., Pattanayek, R. & Stubbs, G. (1989)
Visualization of Protein-Nucleic Acid Interactions in a Virus: Refined Structure of Intact Tobacco Mosaic Virus at 2.9 Å Resolution by X-ray Fiber Diffraction. J. Mol. Biol. 208, 307-325.
16
Namba, K., Yamashita, I. & Vonderviszt, F. (1989)
Structure of the Core and Central Channel of Bacterial Flagella. Nature 342, 648-654.
17
Hara, M., Namba, K., Hirata, Y., Majima, T., Kawamura, S., Asada, Y. & Miyake, J. (1990)
The Photoreaction Unit in Rhodopseudomonas viridis. Plant Cell Physiol. 31, 951-960.
18
Vonderviszt, F., Uedaira, H., Kidokoro, S.-I. & Namba, K. (1990)
Structural Organization of Flagellin. J. Mol. Biol. 214, 97-104.
19
Yamashita, I., Vonderviszt, F., Noguchi, T. & Namba, K. (1991)
Preparing Well-Oriented Sols of Straight Bacterial Flagellar Filaments for X-ray Fiber Diffraction. J. Mol. Biol. 217, 293-302.
20
Vonderviszt, F., Aizawa, S.-I. & Namba, K. (1991)
Role of the Disordered Terminal Regions of Flagellin in Filament Formation and Stability. J. Mol. Biol. 221, 1461-1474.
21
Akiba, T., Yoshimura, H. & Namba, K. (1991)
Monolayer Crystallization of Flagellar L-P Rings by Sequential Addition and Depletion of Lipid. Science 252, 1544-1546.
22
Vonderviszt, F., Sonoyama, M., Tasumi, M. & Namba, K. (1992)
Conformational Adaptability of the Terminal Regions of Flagellin. Biophys. J. 63, 1672-1677.
23
Kubori, T., Shimamoto, N., Yamaguchi, S., Namba, K. & Aizawa, S.-I. (1992)
Morphological Pathway of Flagellar Assembly in Salmonella typhimurium. J. Mol. Biol. 226, 433-446.
24
Mimori, Y., Yamashita, I., Murata, K., Fujiyoshi, Y., Yonekura, K., Toyoshima, C. & Namba, K. (1995)
The Structure of the R-type Straight Flagellar Filament of Salmonella at 9 Å Resolution by Electron Cryomicroscopy. J. Mol. Biol. 249, 69-87.
25
Vonderviszt, F., Zábodszky, P., Ishimura, M., Uedaira, H. & Namba, K. (1995)
Structural Organization and Assembly of Flagellar Hook Protein from Salmonella typhimurium. J. Mol. Biol. 251, 520-532.
26
Yamashita, I., Vonderviszt, F., Mimori, Y., Oosawa, K. & Keiichi, N. (1995)
Radial Mass Analysis of the Flagellar Filament of Salmonella - Implications for the Subunit Folding. J. Mol. Biol. 253, 547-558.
27
Akiba, T., Toyoshima, C., Matsunaga, T., Kawamoto, M., Kubota, T., Fukuyama, K., Namba, K. & Matsubara, H. (1996)
Three Dimensional Structure of Bovine Cytochrome bc1 Complex by Electron Cryomicroscopy and Helical Image Reconstruction. Nature Struct. Biol. 3, 553-561.
28
Mimori-Kiyosue, Y., Vonderviszt, F., Yamashita, I., Fujiyoshi, Y. & Namba, K. (1996)
Direct Interaction of Flagellin Termini Essential for Polymorphic Ability of Flagellar Filament. Proc. Natl. Acad. Sci. USA 93, 15108-15113.
29
Tamura, Y., Gekko, K., Yshioka, K., Vonderviszt, F. & Namba, K. (1997)
Adiabatic Compressibility of Flagellin and Flagellar Filament of Salmonella typhimurium. Biochim. Biophys. Acta 1335, 120-126.
30
Mimori-Kiyosue, Y., Vonderviszt, F. & Namba, K. (1997)
Locations of Terminal Segments of Flagellin in the Filament Structure and Their Roles in Polymerization and Polymorphism. J. Mol. Biol. 270, 222-237.
31
Mitsuoka, K., Murata, K., Kimura, Y., Namba, K. & Fujiyoshi, Y. (1997)
Examination of the LeafScan 45, a Line-Illuminating Micro-Densitometer, for Its Use in Electron Crystallography. Ultramicroscopy 68, 109-121.
32
Hasegawa, K., Yamashita, I. & Namba, K. (1998)
Quasi- and Non-Equivalence in the Structure of Bacterial Flagellar Filament. Biophys. J. 74, 569-575.
33
Yamashita, I., Hasegawa, K., Suzuki, H., Vonderviszt, F. Mimori-Kiyosue, Y. & Namba, K. (1998)
Structure and Switching of Bacterial Flagellar Filament Studied by X-ray Fiber Diffraction. Nature Struct. Biol. 5, 125-132.
34
Imada, K., Vonderviszt, F., Furukawa, Y., Oosawa, K. & Namba, K. (1998)
Assembly Characteristics of Flagellar Cap Protein HAP2 of Salmonella:: Decamer and Pentamer in the pH-Sensitive Equilibrium. J. Mol. Biol. 277,883-891.
35
Maki, S., Vonderviszt, F., Furukawa, Y., Imada, K. & Namba, K. (1998)
Plugging Interactions of HAP2 Pentamer into the Distal End of Flagellar Filament Revealed by Electron Microscopy. J. Mol. Biol. 277, 771-777.
36
Yamashita, I., Suzuki, H. & Namba, K. (1998)
Multiple-Step Method for Making Exceptionally Well-Oriented Liquid-Crystalline Sols of Macromolecular Assemblies. J. Mol. Biol. 278, 609-615.
37
Imada, K., Matsunami, H., Kawaguchi, H., Inagaki, K., Tanaka, H., Tanaka, N. & Namba, K. (1998)
Structure of 3-Isopropylmalate Dehydrogenase from Thiobacillus ferrooxidans with 3-Isopropylmalate. Structure 6, 971-982.
38
Oda, T., Makino, K., Yamashita, I., Namba, K. & Maeda, Y. (1998)
Effect of the Length and Effective Diameter of F-actin on the Filament Orientation in Liquid Crystalline Sols Measured by X-ray Fiber Diffraction. Biophys. J. 75, 2672-2681.
39
Mimori-Kiyosue, Y., Yamashita, I., Yamaguchi, S. & & Namba, K. (1998)
Role of the Outermost Subdomain of Salmonella Flagellin in the Filament Structure Revealed by Electron Cryomicroscopy. J. Mol. Biol. 284, 521-530.
40
Vonderviszt, F., Imada, K., Furukawa, Y., Uedaira, H., Taniguchi, H. & Namba, K. (1998)
Mechanism of Self-Association and Filament Capping by Flagellar HAP2. J. Mol. Biol. 284, 1399-1416.
41
Suzuki, H., Yonekura, K., Murata, K., Hirai, T., Oosawa, K. & Namba, K. (1998)
Structural Feature in the Central Channel of Bacterial Flagellar FliF Ring Complex is Implicated in Type III Protein Export. J. Struct. Biol. 124, 104-114.
42
Namba, K., Hasegawa, K., Yamashita, I., Kiyosue, Y., Suzuki, H., & Vonderviszt, F. (1999)
The mechanism of assembly and polymorphic switching of the bacterial flagellar filament. CCP13 News Lett. 7, 13-16. Salmonella typhimurium. FEBS Lett. 445, 126-130.
43
Uedaira, H., Morii, H., Ishimura, M., Taniguchi, H., Namba, K. & Vonderviszt, F. (1999)
Domain Organization of Flagellar Hook Protein from Salmonella typhimurium. FEBS Lett. 445, 126-130.
44
Honda, S., Uedaira, H., Vonderviszt, F., Kidokoro, S.-I. & Namba, K. (1999)
Folding Energetics of Multidomain Structure Protein, Flagellin. J. Mol. Biol. 293, 719-732.
45
Yutani, K., Takayama, G., Goda, S., Yamagata, Y., Maki, S., Namba, K., Tsunasawa, S. & Ogasahara, K. (2000)
The Process of Amyloid-like Fibril Formation by Methionine Aminopeptidase from a Hyperthermophile, Pyrococcus furiosus. Biochemistry 39, 2769-2777.
46
Goda, S., Takano, K., Yamagata, Y., Nagata, R., Akutsu, H., Maki, S., Namba, K. & Yutani, K. (2000)
Amyloid Protofilament Formation of Hen Egg Lysozyme in Highly Concentrated Ethanol Solution. Protein Science 9, 369-375.
47
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.
48
Ryuu, H., Yamaguchi, T., & Namba, K. (2001)
A computational modeling of micro-fluid dynamics of undulatory locomotion. Theoretical and Applied Mechanics. 50.
49
Namba, K. (2001)
Roles of Partly Unfolded Conformations in Macromolecular Self-Assembly. Genes to Cells 6, 1-12.
50
Oda, T., Makino, K., Yamashita, I., Namba, K. & Maéda, 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.
51
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.
52
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.
53
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.
54
Yonekura, K., Maki, 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.
55
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, 1029-1037.

Reviews and Proceedings
1
Namba, K., Wakabayashi, K. & Mitsui, T. (1978)
X-ray Structure Analysis of the Thin Filament of Crab Striated Muscle in the Rigor State. In Diffraction Studies of Biomembrane and Muscle, and Synchrotron Radiation, Proceeding of the Fourth International Symposium, Division of Biophysics (Mitsui, T., ed.), pp. 177-216. The Taniguchi Foundation.
2
Namba, K., Wakabayashi, K. & Mitsui, T. (1979)
The Structure of Thin Filament of Crab Striated Muscle in the Rigor State. In Cross-Bridge Mechanism in Muscle Contraction (Sugi, H. and Pollack, G.H., eds.), pp. 445-456. University of Tokyo Press, Tokyo.
3
Namba, K., Wakabayashi, K. & Mitsui, T. (1979)
Difference Cylindrically Symmetrical Patterson Function and Its Application to Analysis of Muscle Structures. J. Cryst. Soc. Japan. 21, 261-269.
4
Wakabayashi, K. & Namba, K. (1980)
X-ray Diffraction Studies of Myosin Head Configuration of Crab Striated Muscle in the Relaxed and Rigor States. In Protein Dynamics and Energy Transduction, Proceeding of the Sixth International Symposium, Division of Biophysics (Ishiwata, S., ed.), pp. 478-522. The Taniguchi Foundation.
5
Wakabayashi, K., Namba, K. & Mitsui, T. (1984)
Configurations of Myosin Heads in the Crab Striated Muscle as Studied by X-ray Diffraction. In Contractile Mechanism in Muscle (Sugi, H. and Pollack, G.H., eds.), pp. 237-250. University of Tokyo Press, Tokyo.
6
Namba, K. (1986)
A New Model for Self-Assembly of Tobacco Mosaic Virus Based on Its Molecular Structure. Biophysics 26, 147-156.
7
Namba, K. (1988)
Structure and Function of Macromolecular Assembly: Self Assembly Mechanism Revealed in the Molecular Structure of Tobacco Mosaic Virus. J. Cryst. Soc. Japan 30, 330-335.
8
Namba, K., Yamashita, I. & Vonderviszt, F. (1990)
Structure of Bacterial Flagellar Filament and Conformational Change of Flagellin upon Polymerization. Biophysics 30, 197-199.
9
Caspar, D.L.D & Namba, K. (1990)
Switching in the Self-Assembly of Tobacco Mosaic Virus. In Switching and Movements of Protein Molecules and their assemblies. (Oosawa, F., Special ed.) Adv. Biophys. 26, 157-185.
10
Hotani, H., Kudo, S., Aizawa, S.-I., Yamashita, I. & Namba, K. (1990)
Dynamic Structure of Bacterial Motility System: A Biomotor and Flagella. In U.S.-Japan Workshop on Smart/Intelligent Materials and Systems. (Ahmad, I., Crowson, A., Rogers, C.A. and Aisawa, M., eds.) pp. 119-123.
11
Namba, K. (1993)
A Biological Molecular Machine: Bacterial Flagellar Motor and Filament. Wear 168, 189-193.
12
Mimori, Y., Yamashita, I., Miyazawa, A., Fujiyoshi, Y. & Namba, K. (1994)
Structural Study of Bacterial Flagellar Filaments from Various Mutant Strains by Electron Cryomicroscopy. Electron Microscopy 1994-3A, 521-522.
13
Akiba, T., Toyoshima, C., Matsunaga, T., Kawamoto, M., Kubota, T., Fukuyama, K., Namba, K. & Matsubara, H. (1997)
Three-Dimensional Structure of Bovine Cytochrome bc1 Complex by Electron Cryomicroscopy and Helical Image Reconstruction. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 1-9. The Taniguchi Foundation.
14
Imada, K., Matsunami, H., Kawaguchi, H., Inagaki, K., Tanaka, H., Tanaka, N. & Namba, K. (1997)
Structure of 3-Isopropylmalate Dehydrogenase with 3-Isopropylmalate at 2.5 Å Resolution: Unusual Recognition Mechanism of the Isopropyl Moiety by a Glutamic-Acid Side Chain. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 121-130. The Taniguchi Foundation.
15
Yamashita, I., Suzuki, H., Hasegawa, K. & Namba, K. (1997)
X-ray Fiber Diffraction Analysis of Flagellar Filament Structure. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 175-184. The Taniguchi Foundation.
16
Mimori-Kiyosue, Y., Vonderviszt, F., Yamashita, I., Suzuki, H., Hasegawa, K., Fujiyoshi, Y. & Namba, K. (1997)
Molecular Design of Bacterial Flagellar Filament for Assembly and Polymorphism. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 185-196. The Taniguchi Foundation.
17
Maéda, Y. Maeda, K., Takeda, S., Saijo, Y., Kobayashi, T., Miegel, A., Yamamoto, K., Sano, K., Scherer, A., Makino, K., Oda, T., Yamashita, I., Namba, K., Taniguchi, H., Yao, M. & Wakatsuki, S. (1997)
Towards Elucidation of the Structure of Muscle Thin Filament; Progress in Oriented Filament Sol Preparation, in Crystallographic Studies of Troponin. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 222-234. The Taniguchi Foundation.
18
Oda, T., Makino, K., Yamashita, I., Namba, K. & Maéda, Y. (1997)
Fiber Diffraction of Well-Oriented Actin Filament Sols. In Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics (Namba, K., ed.) pp. 275-282. The Taniguchi Foundation.
19
Namba, K. & Vonderviszt, F. (1997)
Molecular Architecture of Bacterial Flagellum. Quart. Rev. Biophys. 30, 1-65.
20
Namba, K., Hasegawa, K., Yamashita, I., Mimori-Kiyosue, Y., Suzuki, H. & Vonderviszt, F. (1998)
The mechanisms of self-assembly and polymorphic switching of the bacterial flagellar filament. Fibre Diffraction Review, CCP13 Newsletter 7, 13-16.
21
Oda, T., Makino, K., Yamashita, I., Namba, K. & Maéda, 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.

Book
1
Namba, K. (1997)
Structure and Function of Macromolecular Assembly. Proceeding of the 22nd International Symposium, Division of Biophysics, The Taniguchi Foundation. (ed.)

Namba Protonic NanoMachine Project, ERATO
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