Assembly and Mechanism of Infection of Bacteriophage

2009 Fiscal Year Final Research Report

• Project/Area Number: 16087204
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: ARISAKA Fumio Tokyo Institute of Technology, 大学院・生命理工学研究科, 准教授 (80133768)
• Co-Investigator(Kenkyū-buntansha): KANAMARU Shuji 東京工業大学, 大学院・生命理工学研究科, 助教 (50376951) ; TAKEDA Shigeki 群馬大学, 大学院・工学研究科, 准教授 (80282854)
• Research Collaborator: MOH LAN Yap ; NEMOTO Mai ; TAHMINA Akhter ; SUBODH Sarkar ; ABURAI Kohei ; MONZAKI Yasunori ; OKUDA Mako ; UCHIDA Kazuya ; NAMURA Mikiyoshi ; TERAUCHI Makoto ; ITO Masako ; HORIKOSHI Yusuke ; FUJITA Daigo ; SUGAI Shinnji ; NAGAO Tatsuya ; DONNY Sunanda ; NAKAO Tomoko
• Project Period (FY): 2004 – 2009
• Keywords: 微生物 / 蛋白質 / ナノバイオ / 分子認識 / ウイルス

Research Abstract

All the subunit proteins were localized in the baseplate before and after infection by a combination of X-ray crystallography and three-dimensional image econstruction from electron-micrographs. As a result, the gross structural change of the baseplate upon infection can be interpreted by the change of the relative positions of the subunits. Also, a new method was developed, which indicated that the stringent sequential assembly of the baseplate wedge is based on the induced-fit of the subunits upon binding.

Research Products

• [Journal Article] The Baseplate Wedges of Bacteriophage T4 Spontaneously Assemble into Hubless Baseplate-like Structure In Vitro (2010)
  • Author(s): Yap M.L., Mio K., Leiman P.G., Kanamaru S., Arisaka F.
  • Journal Title: J. Mol. Biol 395 Pages: 349-360
  • Peer Reviewed
• [Journal Article] Construction of an energy transfer system in the bio-nanocup space by heteromeric assembly of gp27 and gp5 proteins isolated from bacteriophage T4. (2009)
  • Author(s): Koshiyama T., Ueno T., Kanamaru S., Arisaka F., Watanabe Y.
  • Journal Title: Org Biomol Chem. 7(12) Pages: 2649-54
  • Peer Reviewed
• [Journal Article] The motor protein prestin is a bullet-shaped molecule with inner cavities. (2008)
  • Author(s): Mio K., Kubo Y., Ogura T., Yamamoto T., Arisaka F., Sato C.
  • Journal Title: J. Biol. Chem. 283(2) Pages: 1137-45
  • Peer Reviewed
• [Journal Article] Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor (2008)
  • Author(s): Koshiyama T., Yokoi N., Ueno T., Kanamaru S., Nagano S., Shiro Y., Arisaka F., Watanabe Y.
  • Journal Title: Small 4(1) Pages: 50-4
  • Peer Reviewed
• [Journal Article] ORF334 in Vibrio phage KVP40 plays the role of gp27 in T4 phage to form a hetero-hexameric complex. (2008)
  • Author(s): Nemoto M., Mio K., Kanamaru S., Arisaka F.
  • Journal Title: J. Bacteriol. 190(10) Pages: 3606-3612
  • Peer Reviewed
• [Journal Article] From structure of the complex to understanding of the biology (2007)
  • Author(s): Rossmann M.G., Arisaka F., Battisti A.J., Bowman V.D., Chipman P.R., Fokine A., Hafenstein H., Kanamaru S., Kostyuchenko V.A., Mesyanzhinov V.V., Shneider M.M., Morais M.C., Leiman P.G., Palermo L.M., Parrish C.R., Xiao C.
  • Journal Title: Acta Cryst D63 Pages: 9-16
  • Peer Reviewed
• [Journal Article] The neck of bacteriophage T4 is a ring-like structure formed by a hetero-oligomer of gp13 and gp14 (2007)
  • Author(s): Akhter T., Zhao L., Kohda A., Mio K., Kanamaru S., Arisaka F.
  • Journal Title: Biochim Biophys Acta 1774(8) Pages: 1036-43
  • Peer Reviewed
• [Journal Article] ウイルスに見られる新しいβモチーフ (2007)
  • Author(s): 金丸周司、有坂文雄
  • Journal Title: 日本結晶学会誌 49 Pages: 161-170
  • Peer Reviewed
• [Journal Article] バクテリオファージの構造生物学野本・西山編 (2007)
  • Author(s): 金丸周司・有坂文雄
  • Journal Title: ウイルス研究の現在と展望蛋白質核酸酵素8月号増刊 52(10) Pages: 1069-1074
• [Journal Article] Construction of a Balland- Spike Protein Supramolecule (2006)
  • Author(s): Sugimoto K., Kanamaru S., Iwasaki K., Arisaka F., Yamashita I.
  • Journal Title: Angew. Chem. Int. Ed. 45 Pages: 2725-2728
  • Peer Reviewed
• [Journal Article] Bionanotube Tetrapod Assembly by In Situ Synthesis of a Gold Nanocluster with (gp5-His6)3 from Bacteriophage T4. (2006)
  • Author(s): Ueno T., Koshiyama T., Tsuruga T., Goto T., Kanamaru S., Arisaka F., Watanabe Y.
  • Journal Title: Angew. Chem. Int. Ed. 45 Pages: 4508-4512
  • Peer Reviewed
• [Journal Article] Association and dissociation of the cell puncturing complex of bacteriophage T4 is controlled by both pH and temperature Biochim (2006)
  • Author(s): Sarkar S.K., Takeda Y., Kanamaru S., Arisaka F.
  • Journal Title: Biophys Acta 1764(9) Pages: 1487-1492
  • Peer Reviewed
• [Journal Article] The Asymmetric IscA Homodimer with and Exposed [2Fe-2S] Cluster Suggests the Structural Basis of the Fe-S Cluster Biosynthetic Scaffold (2006)
  • Author(s): Morimoto K., Yamashita E., Kondou Y., Lee S.J., Arisaka F., Tsukihara T., Nakai M.
  • Journal Title: J. Mol. Biol. 360 Pages: 117-132
  • Peer Reviewed
• [Journal Article] Control of Bacteriophage T4 Tail Lysozyme Activity During the Infection Process (2005)
  • Author(s): Kanamaru S., Ishiwata Y., Suzuki T., Rossmann M.G., Arisaka F.
  • Journal Title: J. Mol. Biol. 346 Pages: 1013-1020
  • Peer Reviewed
• [Journal Article] The tail structure of bacteriophage T4 and its mechanism of contraction (2005)
  • Author(s): Kostyuchenko V.A., Chipman P.R., Leiman P.G., Arisaka F., Mesyanzhinov, V.V. Rossmann M.G.
  • Journal Title: Nat Struct Mol Biol. 12 Pages: 810-813
  • Peer Reviewed
• [Journal Article] Assembly and Infection Process of Bacteriophage T4 Chaos (2005)
  • Author(s): Fumio Arisaka
  • Journal Title: 15 Pages: 047502
  • Peer Reviewed
• [Journal Article] 蛋白質核酸酵素8月号増刊 (2005)
  • Author(s): 金丸周司、有坂文雄:バクテリオファージの構造と感染機構阿久津、月原、嶋田編
  • Journal Title: 生命秩序を担う生体超分子 50(10) Pages: 1341-1348
• [Journal Article] The bacteriophage T4 DNA injection machine (2004)
  • Author(s): Rossmann M.G., Mesyanzhinov V.V., Arisaka F., Leiman P.G.
  • Journal Title: Current Opinion in Structural Biology 14 Pages: 171-180
  • Peer Reviewed
• [Journal Article] Mapping of functional sites on the primary structure of the contractile tail sheath protein of bacteriophage T4 by mutation analysis (2004)
  • Author(s): Takeda S., Suzuki M., Yamada T., Kageyama M., Arisaka F.
  • Journal Title: Biochim. Biophys. Acta 1699(1-2) Pages: 163-171
  • Peer Reviewed
• [Presentation] Baseplate Wedge Assembly of Bacteriophage T4 in vitro (2009)
  • Author(s): Yap Moh Lan・有坂文雄
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 徳島
  • Year and Date: 2009-10-29
• [Presentation] 人工3本鎖β-ヘリックス蛋白質の効率的生産と会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 日本生化学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2009-10-24
• [Presentation] In vitro Assembled Wedge of Phage T4 Spontaneously Formed Baseplate-like Structure (2009)
  • Author(s): Moh Lan Yap, Yasunori Monzaki, Kazuhiro Mio, Petr Leiman, Shuji Kanamaru, Fumio Arisaka.
  • Organizer: The 21st Biannual Phage/Virus Assembly Meeting
  • Place of Presentation: Annecy, France
  • Year and Date: 2009-09-25
• [Presentation] In vitro Assembly of the Tail Wedge of Phage T4 as observed by AUC-SV (2009)
  • Author(s): Moh Lan Yap, Yasunori Monzaki, Kazuhiro Mio, Petr Leiman, Shuji Kanamaru, Fumio Arisaka
  • Organizer: The 18th International Conference on Analytical Ultracentrifugation
  • Place of Presentation: Uppsala, Sweden
  • Year and Date: 2009-09-18
• [Presentation] In vitro Assembled Wedges of Phage T4 Spontaneously Form Baseplate -like Structure (2009)
  • Author(s): 有坂文雄
  • Organizer: the 18th Evergreen Inter -national Phage Biology meeting
  • Place of Presentation: The Evergreen State College, WA, USA
  • Year and Date: 2009-08-11
• [Presentation] t4ファージの溶菌阻止に関与するSp蛋白質の構造と機能 (2009)
  • Author(s): 根本舞・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-22
• [Presentation] The baseplate wedge assembly pathway of phage T4 in vitro (2009)
  • Author(s): Yap Moh Lan・中尾朋子・長尾達也・門崎泰憲・三尾和弘・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21
• [Presentation] 人工3本鎖β-Helix蛋白質の効率的生産と会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21
• [Presentation] 太さの調節可能な人工三本鎖β-ヘリックス蛋白質の作製 (2008)
  • Author(s): 油井孔兵、寺内充、金丸周司、有坂文雄、長 さ
  • Organizer: 第81回生化学会大会(BMB2008)
  • Place of Presentation: 神戸
  • Year and Date: 20081209-20081212
• [Presentation] Identification of interacting domains of the wedge proteins gp11, gp10, gp7, and gp8 of bacteriophage T4 by limited proteolysis (2008)
  • Author(s): Moh Lan Yap, Tomoko Nakao, Tatsuya Nagao, Syuiji Kanamaru, Fumio Arisaka
  • Organizer: 第46回日本生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 20081203-20081205
• [Presentation] Tatsuya Nagao and Fumio Arisaka Domain interaction analyses of gp7, gp10 and gp11 of bacteriophage T4 for crystallization (2008)
  • Author(s): Shuji Kanamaru, Tomoko Naka
  • Organizer: IUCr2008
  • Place of Presentation: 大阪
  • Year and Date: 20080824-20080828
• [Presentation] Structural Analysis of Baseplate Wedge Proteins of Bacteriophage, T4 (2008)
  • Author(s): Arisaka F
  • Organizer: PRICPS-AOHUPO 2008
  • Place of Presentation: Cairns, Australia
  • Year and Date: 20080622-20080626
• [Presentation] Domain interaction analyses of gp7, gp10 and gp11 of bacteriophage (2008)
  • Author(s): Shuji Kanamaru, Tomoko Nakao, Tatsuya Nagao, Fumio Arisaka
  • Organizer: T4 FASEB 2008 Summer Research Conferences
  • Place of Presentation: Saxtons River U.S. A
  • Year and Date: 20080620-20080629
• [Presentation] Interaction of gp34, the proximal half long tail fiber of T4 with the socket baseplate protein, gp9 FASEB (2008)
  • Author(s): Donny Sunanda, Shuji Kanamaru, Fumio Arisaka
  • Organizer: 2008 Summer Research Conference
  • Place of Presentation: Saxtons River U.S. A
  • Year and Date: 20080620-20080629
• [Presentation] ビブリオファージKVP40のgp5-ORF334複合体の構造と機能 (2008)
  • Author(s): 根本舞、金丸周司、有坂文雄
  • Organizer: 第8回蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 20080610-20080613
• [Presentation] T4類縁ファージS-PM2テイルリゾチームgp5の発現と性状解析 (2008)
  • Author(s): 油井孔兵、金丸周司、有坂文雄
  • Organizer: 第8回蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 20080610-20080613
• [Presentation] t4ファージ基盤構成蛋白質gp7, gp10, gp11の相互作用部位の同定 (2007)
  • Author(s): 中尾朋子、長尾達也、金丸周司、有坂文雄
  • Organizer: 第80回日本生化学会大会
  • Place of Presentation: 横浜
  • Year and Date: 20071211-20071215
• [Presentation] t4ファージ基盤終結蛋白質gp48, gp54の大量発現系の構築と性状解析 (2007)
  • Author(s): 伊藤麻紗子、金丸周司、有坂文雄
  • Organizer: 第30回日本分子生物学会年会、第80回日本生化学会大会
  • Place of Presentation: 横浜
  • Year and Date: 20071211-20071215
• [Presentation] バクテリオファージt4尾部の膜貫通機構 (2007)
  • Author(s): 二島渉、金丸周司、有坂文雄、北尾彰朗
  • 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
  • Year and Date: 20070524-20070526
• [Presentation] Consruction and purification of N terminal of the proximal long tail fiber, gp34, of Bacteriophage T4 (2007)
  • Author(s): Donny Sunanda、金丸周司、有坂文雄
  • 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
  • Year and Date: 20070524-20070526
• [Presentation] t4ファージ基盤構成蛋白質群のドメイン構造と相互作用部位の同定 (2007)
  • Author(s): 中尾朋子、長尾達也、金丸周司、有坂文雄
  • 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
  • Year and Date: 20070524-20070526
• [Presentation] Artificial three-stranded β-helix protein as a nanotube (2006)
  • Author(s): Makoto Terauchi, Shuji Kanamaru, Fumio Arisaka
  • Organizer: Fifth East Asian Biophysics Symposium and 44th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Naha, Okinawa
  • Year and Date: 20061112-20061116
• [Presentation] Interactions between Vibrio phage KVP40 gp5 and gene product of ORF334 (2006)
  • Author(s): Mai Nemoto, Shuji Kanamaru, Fumio Arisaka
  • Organizer: T4 gp27 homologue, Fifth East Asian Biophysics Symposium and 44th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Naha, Okinawa
  • Year and Date: 20061112-20061116
• [Presentation] Flexible and rigid regions in the stalk domain of ncd motor protein (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: 20061112-20061116
• [Presentation] バクテリオファージ研究の最近の動向 (2006)
  • Author(s): 有坂文雄
  • Organizer: 大阪大学蛋白質研究所セミナー
  • Place of Presentation: 大阪
  • Year and Date: 20060915-20060916
• [Presentation] t4ファージの構造生物学 (2006)
  • Author(s): 金丸周司
  • Organizer: 大阪大学蛋白質研究所セミナー
  • Place of Presentation: 大阪
  • Year and Date: 20060915-20060916
• [Presentation] Shuji Kanamaru, Fumio Arisaka Structure and Function of the Tail-lysozyme of T4-related Bacteriophages (2006)
  • Author(s): Mai Nemoto
  • Organizer: The HFSP 17th Anniversary-Sixth Awardees Annual Meeting
  • Place of Presentation: Paris
  • Year and Date: 20060702-20060705
• [Presentation] Suji Kanamaru, Fumio Arisaka, The gene product of ORF334 of Vibrio phage KVP40 is the homologue of T4 gp27 which binds to the tail lysozyme, gp5 (2006)
  • Author(s): Mai Nemoto
  • Organizer: 2006 FASEB Summer Research Conferences, Virus Assembly
  • Place of Presentation: Vermont Academy, Saxtons River, Vermont, U.S.A.
  • Year and Date: 20060617-20060623
• [Presentation] Purification, characterization and solution interactions of the neck proteins, gp13 and gp14, from Bacteriophage T4 (2006)
  • Author(s): Tahmina Akhter, Shuji Kanamaru, Fumio Arisaka
  • Organizer: 2006 FASEB Summer Research Conferences, Virus Assembly
  • Place of Presentation: Vermont Academy, Saxtons River, Vermont
  • Year and Date: 20060617-20060623
• [Presentation] ビブリオファージKVP40におけるT4gp27ホモログの同定とテイルルゾチームgp5との結合 (2006)
  • Author(s): 根本舞、金丸周司、有坂文雄
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: 京都
  • Year and Date: 20060424-20060426
• [Presentation] T4ファージ尾鞘蛋白質の重合化に関する変異体の解析 (2006)
  • Author(s): 須貝伸治、金丸周司、有坂文雄
  • Organizer: 日本蛋白質科学会年会
  • Place of Presentation: 京都
  • Year and Date: 20060424-20060426
• [Presentation] Protein interactions among neck proteins, gp13/gp14, and the connector protein, gp15, of bacteriophage T4 (2005)
  • Author(s): Akhter Tahmina、金丸周司、有坂文雄
  • Organizer: 生物物理学会第43回年会
  • Place of Presentation: 札幌
  • Year and Date: 20051123-20051125
• [Presentation] Lysozyme or not? Characterization of gp5 from Vibrio phage KVp40 (2005)
  • Author(s): 根本舞、金丸周司、有坂文雄
  • Organizer: 第78回日本生化学会大会
  • Place of Presentation: 神戸
  • Year and Date: 20051019-20051022
• [Presentation] ナノ材料としての人工3本鎖βへリックスポリペプチドの作成と性状解析 (2005)
  • Author(s): 金丸周司、龍頭聡、有坂文雄
  • Organizer: 第5回日本蛋白質科学会年会
  • Place of Presentation: 福岡
  • Year and Date: 20050630-20050702
• [Presentation] T4DNAパッケージング蛋白質gp16およびgp17の相互作用の解析 (2005)
  • Author(s): 藤田大悟、金丸周司、Venigalla B. Rao、有坂文雄
  • Organizer: 第5回日本蛋白質科学会年会
  • Place of Presentation: 福岡
  • Year and Date: 20050630-20050702
• [Presentation] Assembly and Infection Process of Bacteriophage T4 (2005)
  • Author(s): 有坂文雄
  • Organizer: Self-organization-Initiative Nano-Engineering (SINE)
  • Place of Presentation: 和光
  • Year and Date: 20050117-20050118
• [Presentation] Structural landscape of assembly and infection processes of bacteriophage (2005)
  • Author(s): 金丸周司
  • Organizer: TIT-Bioxtal Symposium "Structural Biology of Genetic Flow and Control"
  • Place of Presentation: 横浜
  • Year and Date: 2005-01-19
• [Presentation] t4ファージ基盤蛋白質gp10とgp11の蛋白質間相互作用 (2004)
  • Author(s): 中尾朋子、Ali Said、金丸周司、有坂文雄
  • Organizer: 日本生物物理学会第42回年会
  • Place of Presentation: 京都
  • Year and Date: 20041213-20041215
• [Presentation] Protein-protein interactions between gp13, a neck protein, and the connector, gp15, of bacteriophage T4 (2004)
  • Author(s): Akhter Tahmina、趙麗、金丸周司、有坂文雄
  • Organizer: 日本生物物理学会第42回年会
  • Place of Presentation: 京都
  • Year and Date: 20041213-20041215
• [Presentation] Application of cell-free translation system for analysis of cofactor binding protein FMN-binding protein (2004)
  • Author(s): 有坂文雄
  • Organizer: 第77回日本生化学会大会
  • Place of Presentation: 横浜
  • Year and Date: 20041013-20041016
• [Presentation] Characterization of gp5 from cyanophage S-pm2 (2004)
  • Author(s): 根本舞、金丸周司、有坂文雄
  • Organizer: 第77回日本生化学会大会
  • Place of Presentation: 横浜
  • Year and Date: 20041013-20041016
• [Presentation] Similarity and Variation in the Tail Lysozyme of T4-Related Phages (2004)
  • Author(s): M. Nemoto, S., kanamaru, F. Arisaka
  • Organizer: The New Phage Biology
  • Place of Presentation: FLORIDA
  • Year and Date: 20040801-20040805
• [Presentation] The atomic structure and function of the tail lysozyme of bacteriopahge T4 (2004)
  • Author(s): Kanamaru, S., Ishiwata, Y., Leiman, P.G., Kostyuchenko, V.A., Mesyanzhinov, V.V., Rossmann, M.G., Arisaka, F.
  • Organizer: The HFSP 15th Anniversary -Fourth Awardees Annual Meeting
  • Place of Presentation: Hakone
  • Year and Date: 20040515-20040518
• [Book] やさしい原理からはいるタンパク質科学実験2タンパク質をみる-構造と挙動 (2009)
  • Author(s): 有坂文雄
  • Total Pages: 67-96
  • Publisher: 化学同人
• [Book] タンパク質科学 (2005)
  • Author(s): 有坂文雄
  • Total Pages: 153-167
  • Publisher: 化学同人
• [Book] 細胞に穴を開ける分子機械(第18回「大学と科学」公開シンポジウム講演収録集「タンパク質のかたちから生命のなぞを解く」-生物マシーナリー -構造生物学の最前線-(共著), 144-156) (2004)
  • Author(s): 有坂文雄
  • Total Pages: 231
• [Book] バイオサイエンスのための蛋白質科学入門 (2004)
  • Author(s): 有坂文雄
  • Publisher: 裳華房
• [Book] 図解バイオ活用技術のすべて(東京工業大学大学院生命理工学研究科編)(超遠心分析) (2004)
  • Author(s): 有坂文雄
  • Total Pages: 176-179
  • Publisher: 工業調査会
• [Book] タンパク質工学の基礎(松沢 洋編, 応用姓名科学シリーズ6, 1章～3章, (共著)) (2004)
  • Author(s): 有坂文雄
  • Total Pages: 1-40
  • Publisher: 東京化学同人
• [Remarks] ファージ研究会ウイルス構造研究会
  • URL: http://www.farisaka.bio.titech.ac.jp/