2007 Fiscal Year Final Research Report Summary
Structure Formation of the Neck which Links the Head and the Tail of Bacteriophage
Project/Area Number |
18570147
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Research Category |
Grant-in-Aid for Scientific Research (C)
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Allocation Type | Single-year Grants |
Section | 一般 |
Research Field |
Biophysics
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Research Institution | Tokyo Institute of Technology |
Principal Investigator |
ARISAKA Fumio Tokyo Institute of Technology, GRADUATE SCHOOL OF BIOSCIENCE AND BIOTECHNOROGY, ASSOCIATE PROFESSOR (80133768)
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Co-Investigator(Kenkyū-buntansha) |
KANAMARU Shuji TOKYO INSTITUTE OF TECHNOLOGY, GRADUATE SCHOOL OF BIOSCIENCE AND BIOTECHNOROGY, ASSISTANT PROFESSOR (50376951)
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Project Period (FY) |
2006 – 2007
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Keywords | bacteriophage / molecular assembly / analytical ultracentrifugation / multiangle laser light scattering / protein interactions / neck protein / X-ray crystallography / virus |
Research Abstract |
During the assembly of phage T4, the neck is formed to block the DNA leakage and to prepare for the tail association after DNA packaging into the head is completed. The neck is composed of gp13 (gp: gene product) and gp14 each consists of 309 and 256 amino acid residues with the molecular weight of 41,226 and 32,868, respectively. In order to elucidate the structure and the subunit arrangement of the neck, genes coding for the two proteins were cloned by PCR method, an overexpression system was constructed and the genes were induced by IPTG. The two proteins were purified by ammonium sulfate fractionation, ion exchange chromatography, gen filtration as a single band in SDS-PAGE. Far-ultraviolet circular dichroism spectra of the two proteins indicated that gp13 is rich in α-helix, whereas gp13 is rich in β-sheet. On the other hand, sedimentation velocity indicated that both proteins are monomers with the sedimentation coefficient of 2.80S and 2.00S, respectively and that the frictional ratios were 1.22 and 1.73, respectively, which indicated that gp14 is more elongated than gp13. The two proteins did not interact each other under normal physiological conditions, but it was found that the two proteins formed a specific complex with the sedimentation coefficient of 16.6S. The complex had the molecular weight of 497,000 which together with the molar ratio of 2:1 based on SDS-PAGE indicated that the complex is a hetero 15-mer, (gp 13)10(gp 14)5. This complex is considered to be identical with the complex which was observed when the two proteins were co-expressed. Electron microscopic observations revealed that the complex formed a ring with the diameter of 156 Å which coincided with the electron density of the three-dimensional image of the neck reconstructed from electron micrograph.
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Research Products
(128 results)
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[Journal Article] From structure of the complex to understanding of the biology2007
Author(s)
Rossmann, M. G., Arisaka, F., Battisti, A. J., Bowman, V. D., Chipman, P. R., Fokine, A., Hafenstein, S., Kanamaru, S., Kostyuchenko, V. A., Mesyanzhinov, V. V., Shneider, M. M., Morais, M. C., Leiman, P. G., Palermo, L. M., Parrish, C. R., and Xiao, C.
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Journal Title
Acta Cryst. D63
Pages: 9-16
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing2007
Author(s)
Abe M, Ohno S, Yokogawa T, Nakanishi T, Arisaka F, Hosoya T, Hiramatsu T, Suzuki M, Ogasawara T, Sawasaki T, Nishikawa K, Kitamura M, Hori H, Endo Y.
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Journal Title
Proteins 67
Pages: 643-652
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] The neck of bacteriophage T4 is a ring-like strucure formed by a hetero-oligomer of gp13 and gp142007
Author(s)
Akhter, T., Zhao, L., Kohda, A., Mio, K., Kanamaru, S. & Arisaka, F.
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Journal Title
Biochim. Biophys. Acta 1774
Pages: 1036-1043
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Arisaka, F., Battisti, A. J., Bowman, V. D., Chipman, P. R. Fokine, A., Hafenstein, S., Kanamaru, S., Kostyuchenko, V.A., Mesyanzhinov, V. V., Shneider, M. M., Morais, M.C., Leiman, P.G., Palermo, L. M., Parrish, C.R., and Xiao, C. From structure of the complex to understanding of the biology.2007
Author(s)
M. G., Rossmann
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Journal Title
Acta Cryst D63
Pages: 9-16
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Detection of structural changes in a cofactor binding protein by using a wheat germ cell-free protein synthesis system coupled with unnatural amino acid probing2007
Author(s)
M, Abe, S, Ohno, T, Yokogawa, T, Nakanishi, F, Arisaka, T, Hosoya, T, Hiramatsu, M, Suzuki, T, Ogasawara, T, Sawasaki, K, Nishikawa, M, Kitamura, H, Hori, Y., Endo
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Journal Title
Proteins 67
Pages: 643-652
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Reversible and Irreversible Coiled Coils in the Stalk Domain of ncd Motor Protein2007
Author(s)
T, Makino, H, Morii, T, Shimizu, F, Arisaka, Y, Kato, K, Nagata, M. Tanokura
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Journal Title
Biochemistry 46
Pages: 9523-9532
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Aggregation Aspects and Techniques for Assessment, Part 2 Analytical Ultracentrifugation and Dynamic Light Scattering.2007
Author(s)
T, Arakawa, S., John, Philo, D, Ejima, K, Tsumoto, F, Arisaka
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Journal Title
BioProcess International 5(4)
Pages: 36-50
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Kawabata SI An arthropod cuticular chitin-binding protein endows injured sites with transglutaminase-dependent mesh.2007
Author(s)
Y, Matsuda, T, Koshiba, T, Osaki, H, Suyama, F, Arisaka, Y, Toh
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Journal Title
J.Biol.Chem. 282
Pages: 37316-37324
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Molecular Mechanism for Pterin-Mediated Inactivation of Tyrosine Hydroxylase: Formation of Insoluble Aggregates of Tyrosine Hydroxylase2006
Author(s)
Urano, F., Hayashi, N., Arisaka, F., Kurita, H., Murata, S., and Ichinose, H.
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Journal Title
J. Biochem. 139
Pages: 625-635
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Bionanotube Tetrapod Assembly by In Situ Synthesis of a Gold Nanocluster with(gp5-His6)3 from Bacteriophage T42006
Author(s)
Ueno, T., Koshiyama, T., Tsuruga, T., Goto, T., Kanamaru, S., Arisaka, F., and Watanabe, Y.
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Journal Title
Angew. Chem. Int. Ed. 45
Pages: 4508-4512
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] The Asymmetric IscA Homodimer with and Exposed[2Fe-2S]Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold2006
Author(s)
Morimoto, K., Yamashita, E., Kondou, Y., Lee, Soo Jae., Arisaka, F., Tsukihara, T., and Nakai, M.
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Journal Title
J. Mol. Biol. 360,
Pages: 117-132
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Thioredoxin-hl reduces and reactivates the oxidized cytosolic malate dehydeogenase dimer in higher plants2006
Author(s)
Hara, S., Motohashi, K., Arisaka, F., Romano, P. G. N., Hosoya-Matsuda, N., Kikuchi, N., Fusada, N., and Hisabori, T.
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Journal Title
J. Biol. Chem. 281(43)
Pages: 32065-32071
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Aggregation Analysis of Therapeutic Proteins, Part 1.2006
Author(s)
Arakawa, T., Philo, J. S., Ejima, D., Tsumoto, K., and Arisaka, F.
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Journal Title
Bio Process International 4(10)
Pages: 32-42
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] F., Hayashi, N., Arisaka, F., Kurita, H., Murata, S., and Ichinose, H., Molecular Mechanism for Pterin-Mediated Inactivation of Tyrosine Hydroxylase : Formation of Insoluble Aggregates of Tyrosine Hydroxylase.2006
Author(s)
F., Urano
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Journal Title
J. Biochem 139
Pages: 625-635
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Koshiyama, T., Tsuruga, T., Goto, T., Kanamaru, S., Arisaka, F., and Watanabe, Y. : Bionanotube Tetrapod Assembly by In Situ Synthesis of a Gold Nanocluster with (gp5-His6)3 from Bacteriophage T4.2006
Author(s)
T., Ueno
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Journal Title
Angew. Chem. Int. Ed. 45
Pages: 4508-4512
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Yamashita,E., Kondou, Y., Lee, Soo Jae., Arisaka, F., Tsukihara, T., and Nakai, M. : The Asymmetric IscA Homodimer with and Exposed [2Fe-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold.2006
Author(s)
K., Morimoto
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Journal Title
J.Mol.Biol. 360
Pages: 117-132
Description
「研究成果報告書概要(欧文)」より
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[Journal Article] Motohashi, K., Arisaka,F., Romano,P.G.N., Hosoya-Matsuda, N., Kikuchi, N., Fusada, N., and Hisabori, T. : Thioredoxin-h1 reduces and reactivates the oxidized cytosolic malate dehydeogenase dimer in higher plants.2006
Author(s)
S., Hara
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Journal Title
J.Biol.Chem. 281 43)
Pages: 32065-32071
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Are six AAA+ modules sufficient to form the ring of dynein?2007
Author(s)
Naomi, Numata, Roberts, Anthony, Reiko, Ogura, Fumio, Arisaka, Takahide, Kon, Knight, Peter, Burgrss, Stan, Kazuo, Sutoh
Organizer
The 45th annual meeting " The Biophysical Society of Japan
Place of Presentation
Yokohama
Year and Date
2007-12-21
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Identification of the interaction sites of gp7, gp10, gp11, the baseplate proteins of bacteriophage T4.2007
Author(s)
Tomoko, Nakao, Tatsuya, Nagao, Shuji, Kanamaru, Fumio, Arisaka
Organizer
BMB2007 Biochem. & Mol. Biol.
Place of Presentation
Yokohama
Year and Date
2007-12-11
Description
「研究成果報告書概要(欧文)」より
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[Presentation] An arthropod cuticular chitin-binding protein endows injured sites with transglutaminase-dependent mesh2007
Author(s)
Yasuyuki, Matsuda, Takumi, Koshiba, Tskasa, Osaki, Haruka, Toyama, Fumio, Arisaka,Yoshihiro, Fuji, Syunishiro, Kawabata
Organizer
BMB2007 Biochem. & Mol. Biol.
Place of Presentation
Yokohama
Year and Date
2007-12-11
Description
「研究成果報告書概要(欧文)」より
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[Presentation] Flexible and rigid regions in the stalk domain of ncd motor protein. Fifth East Asian Biophysics Symposium and 44th Annual Meeting of the Biophysical Society of Japan, November 12-16, Naha, Okinawa(2006)2006
Author(s)
Tsukasa Makino, Hiisayuki Morii, Takashi Shimizu, Fumio Arisaka, Yusuke Kato, Koji Nagata, Masaru Tanokura
Organizer
Fifth East Asian Biophysics Symposium and 44th Annual Meeting of the Biophysical Society of Japan
Place of Presentation
Naha, Okinawa
Year and Date
2006-11-12
Description
「研究成果報告書概要(和文)」より
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[Presentation] Incorporation of unnatural amino acid by in vitro translation systemfor detection of the conformation change of confactorbinding protein2006
Author(s)
Masato Abe, Takashi Yokogawa, Satoshi Ohno, Masaaki Suzuki, Takamitsu Hosoya, Takeshi Nakanishi, FumioArisaka, Tomio Ogasawara, Tatsuya Sawasaki, Kazaya Nishikawa, Masaya Kitamura, Niroyuki Hori, Yaeta Endo
Organizer
20th IUBMB International Congress of Biochemistry and Molecular Biology and 11th FAOBMB Congress
Place of Presentation
Kyoto
Year and Date
2006-06-18
Description
「研究成果報告書概要(和文)」より
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[Presentation] Takashi Yokogawa, Satoshi Ohno, Masaaki Suzuki, Takamitsu Hosoya, Takeshi Nakanishi, FumioArisaka,Tomio Ogasawara, Tatsuya Sawasaki,Kazaya Nishikawa,Masaya Kitamura, Hiroyuki Hori, Yaeta Endo : Incorporation of unnatural amino acid by in vitro translation system for detection of the conformation change of confactorbinding protein.2006
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