Structure and assembly of the central hub of the baseplate of bacteriophage T4

• Project/Area Number: 23570190
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Biophysics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: ARISAKA Fumio 東京工業大学, 生命理工学研究科, 教授 (80133768)
• Co-Investigator(Kenkyū-buntansha): KANAMARU Shuji 東京大学, 大学院生命理工学研究科, 助教 (50376951)
• Project Period (FY): 2011 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2012: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2011: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: バクテリオファージ / 分子集合 / 立体構造 / 蛋白質間相互作用 / 感染機構 / 溶菌 / 溶菌阻止 / 尾繊維 / テイルリゾチーム / 分子内シャペロン / ものさし蛋白質 / T4リゾチーム / Ｔ４リゾチーム

Research Abstract

1. Tube initiator protein, gp48, which were fused with SlyD at the N-terminus was expressed in a soluble fraction and crystallized. 2. The C-terminal domain of gp37 from phage PP01 which constitutes the tail fiber together with gp38 were co-expressed and the complex with 3:1 stoichiometry was isolated and crystallized. It was shown that the C-terminal 13 kDa polypeptide was self-cleaved. 3. The complex of the soluble domain of the holin and the rapid lysis protein gp rI was crystallized and the structure has been successfully determined, which is expected to contribute to understanding the mechanisma of lysis inhibition.

Research Products

• [Journal Article] Structural basis for Sec-independent membrane protein insertion by YidC. (2014)
  • Author(s): Kumazaki, K., Chiba, S., Takemoto, M., Furukawa, A., Nishiyama, K., Sugano, Y., Mori, T., Dohmae, N., Hirata, K., Nakada-Nakura, Y., Maturana, A.D., Tanaka, Y., Mori, H., Sugita, Y., Arisaka, F., Ito K., Ishitani, R., Tsukazaki, T. and Nureki, O.
  • Journal Title: Nature Volume: 509 Issue: 7501 Pages: 516-520
  • DOI: 10.1038/nature13167
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Role of Positions e and g in the Fibrous Assembly Formation of an Amphipathic alpha-Helix-Forming Polypeptide (2014)
  • Author(s): Takei, T.
  • Journal Title: Biopolymers Volume: in press Issue: 3 Pages: 260-72
  • DOI: 10.1002/bip.22479
  • Peer Reviewed
• [Journal Article] Structure and properties of the C-terminal β-helical domain of VgrG protein from Escherichia coli O157 (2014)
  • Author(s): Uchida K, Leiman PG, Arisaka F, Kanamaru S.
  • Journal Title: J Biochem. Volume: 155 Issue: 3 Pages: 173-182
  • DOI: 10.1093/jb/mvt109
  • NAID: 40020021439
  • Peer Reviewed
• [Journal Article] Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals (2014)
  • Author(s): Iwura T, Fukuda J, Yamazaki K, Kanamaru S, Arisaka F.
  • Journal Title: J.Biochem Volume: 155(1) Pages: 63-71
  • Peer Reviewed
• [Journal Article] Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals (2014)
  • Author(s): Iwura T, Fukuda J, Yamazaki K, Kanamaru S, Arisaka F.
  • Journal Title: J Biochem Volume: 155 Issue: 1 Pages: 63-71
  • DOI: 10.1093/jb/mvt095
  • Peer Reviewed
• [Journal Article] Assembly of pyrene-modified DNA/RNA duplexes incorporating a G-rich single strand region. Bioorg (2013)
  • Author(s): Seio, K.; Tokugawa, M.; Tsunoda, H.; Ohkubo, A.; Arisaka, F.; Sekine, M
  • Journal Title: Med. Chem. Lett Volume: 23 Issue: 24 Pages: 6822-6824
  • DOI: 10.1016/j.bmcl.2013.10.012
  • Peer Reviewed
• [Journal Article] Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity (2013)
  • Author(s): Araki Y, Ku W-C, Akioka M, May AI, Hayashi Y, Arisaka F, Ishihama Y, Ohsumi Y.
  • Journal Title: J. Cell Biol Volume: 203(2) Issue: 2 Pages: 299-313
  • DOI: 10.1083/jcb.201304123
  • Peer Reviewed
• [Journal Article] Protein interactions in the assembly of the tail of bacteriophage T4 (2013)
  • Author(s): F. Arisaka and S. Kanamaru.
  • Journal Title: Biophys Rev Volume: 5 Pages: 79-84
  • Peer Reviewed
• [Journal Article] The molecular architecture of the bacteriophage T4 neck (2013)
  • Author(s): Fokine A, Zhang Z, Kanamaru S, Bowman VD, Aksyuk AA, Arisaka F, Rao VB, Rossmann MG.
  • Journal Title: J Mol Biol Volume: 425(10) Issue: 10 Pages: 1731-44
  • DOI: 10.1016/j.jmb.2013.02.012
  • Peer Reviewed
• [Journal Article] Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm (2013)
  • Author(s): K. Nozawa, R. Ishitani, T. Yoshihisa, M. Sato, F. Arisaka, S. Kanamaru, N. Dohmae, D. Mangroo, B. Senger, H. D. Becker and O. Nureki
  • Journal Title: Nucleic Acids Research Volume: 41 Issue: 6 Pages: 3901-3914
  • DOI: 10.1093/nar/gkt010
  • Peer Reviewed
• [Journal Article] Atg38 is required for autophagy-specific phosphatidylinositol 3-kinase complex integrity (2013)
  • Author(s): Araki Y, Ku WC, Akioka M, May AI, Hayashi Y, Arisaka F, Ishihama Y, Ohsumi Y.
  • Journal Title: J Cell Biol. Volume: 203 Pages: 299-313
  • Peer Reviewed
• [Journal Article] Semi-synthesis of an artificial scandium(iii) enzyme with aβ-helical bio-nanotube (2012)
  • Author(s): Inaba H, Kanamaru S, Arisaka F, Kitagawa S, Ueno T.
  • Journal Title: Dalton Trans Volume: 41(37) Pages: 11424-7
  • Peer Reviewed
• [Journal Article] Stoichiometry of Protein Interactions in Bacteriophage T4 Tail Assembly in "Stoichiometry and Research --- The Importance of Quantity in Biomedicine" Edited by Alessio Innocenti (2012)
  • Author(s): Fumio Arisaka.
  • Journal Title: INTECH, Rijeka, Croatia Pages: 243-258
  • Peer Reviewed
• [Journal Article] “Indolepyruvate ferredoxin oxidoreductase: An oxygen-sensitive iron-sulfur enzyme from the hyperthermophilic archaeon Thermococcus profundus (2012)
  • Author(s): Ozawa Y, Siddiqui, MA, Takahashi Y, Urushiyama A, Ohmori, D, Yamakura F, Arisaka F, Imai, T
  • Journal Title: J Biosci Bioeng Volume: 114 Issue: 1 Pages: 23-27
  • DOI: 10.1016/j.jbiosc.2012.02.014
  • Peer Reviewed
• [Journal Article] Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition (2012)
  • Author(s): Ishii R
  • Journal Title: EMBO Journal Volume: 31 Issue: 11 Pages: 2541-2552
  • DOI: 10.1038/emboj.2012.77
  • Peer Reviewed
• [Journal Article] Archaeal ribosomal stalk protein interacts with translation factors in a nucleotide-independent manner via its conserved C terminus, Proc.Natl (2012)
  • Author(s): Nomura N, Honda T, Baba K, Naganuma T, Tanzawa T, Arisaka F, Noda M, Uchiyama S, Tanaka I, Yao M, Uchiumi T
  • Journal Title: Acad. Sci. USA Volume: 109 Issue: 10 Pages: 3748-3753
  • DOI: 10.1073/pnas.1112934109
  • Peer Reviewed
• [Journal Article] Accumulation of β-conglycinin in soybean cotyledon through the formation of disulfide bonds between α'- and α-subunits (2012)
  • Author(s): Wadahama H, Iwasaki K, Matsusaki M, Nishizawa K, Ishimoto M
  • Journal Title: Plant Physiol Volume: 158 Issue: 3 Pages: 1395-1405
  • DOI: 10.1104/pp.111.189621
  • Peer Reviewed
• [Journal Article] Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus (2012)
  • Author(s): Akita F, Higashiura A, Shimizu T, Pu Y, Suzuki M, Uehara-Ichiki T, Sasaya T, Kanamaru S, Arisaka F, Tsukihara T, Nakagawa A, Omura T
  • Journal Title: J Virol Volume: 86(2) Issue: 2 Pages: 746-756
  • DOI: 10.1128/jvi.00826-11
  • Peer Reviewed
• [Journal Article] Semi-synthesis of an artificial scandium (III) enzyme with a β-helical bio-nanotube (2012)
  • Author(s): H. Inaba, S. Kanamaru, F. Arisaka, S. Kitagawa and T. Ueno
  • Journal Title: Dalton Transactions Volume: 41 Issue: 37 Pages: 11424-11427
  • DOI: 10.1039/c2dt31030a
  • Peer Reviewed
• [Journal Article] Archaeal ribosomal stalk protein interacts wi... (2012)
  • Author(s): Nomura N, Arisaka F, et al.
  • Journal Title: Proc Natl Acad Sci U S A. Volume: 109 Pages: 3748-3753
  • Peer Reviewed
• [Journal Article] Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing (2011)
  • Author(s): Nishima W, Kanamaru S, Arisaka F, Kitao A
  • Journal Title: J Am Chem Soc Volume: 133(34) Issue: 34 Pages: 13571-13576
  • DOI: 10.1021/ja204451g
  • Peer Reviewed
• [Journal Article] Genomic and proteomic characterization of the large Myoviridae bacteriophage TMA of the extreme thermophile Thermus thermophilus (2011)
  • Author(s): Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A.
  • Journal Title: Bacteriophage Volume: 1(3) Pages: 152-164
  • Peer Reviewed
• [Journal Article] Biochemical analysis and kinetic modeling of the thermal inactivation of MBP-fused heparinase I : Implications for a comprehensive thermostabilization strategy (2011)
  • Author(s): Chen S, Ye F, Chen Y, Chen Y, Zhao H, Yatsunami R, Nakamura S, Arisaka F, Xing XH.
  • Journal Title: Biotechnol Bioeng Volume: 108(8) Issue: 8 Pages: 1841-51
  • DOI: 10.1002/bit.23144
  • Peer Reviewed
• [Journal Article] Dimer-tetramer association equilibraia of human adult hemoglobin and its Mutants as observed by analytical ultracentrifugation Methods (2011)
  • Author(s): Fumio Arisaka, Yukifumi Nagai, Masako Nagai.
  • Journal Title: Methods. [Epub ahead of print] Volume: 54(1) Issue: 1 Pages: 175-80
  • DOI: 10.1016/j.ymeth.2011.01.003
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-stranded β-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO(2) (2011)
  • Author(s): Yokoi N, Miura Y, Huang CY, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T
  • Journal Title: Chem Commun (Camb) Volume: 47(7) Issue: 7 Pages: 2074-2076
  • DOI: 10.1039/c0cc03015e
  • Peer Reviewed
• [Journal Article] Genomic and proteomic characterization of the... (2011)
  • Author(s): Tamakoshi M, Arisaka F, et al.
  • Journal Title: Bacteriophage. Epub Volume: 1(3):1 Issue: 3 Pages: 52-164
  • DOI: 10.4161/bact.1.3.16712
  • Peer Reviewed
• [Journal Article] Redox and metal-regulated oligomeric state for... (2011)
  • Author(s): Sawada N, Nagahara N, Arisaka F, et al.
  • Journal Title: Amino Acids Volume: 41 Issue: 1 Pages: 173-180
  • DOI: 10.1007/s00726-010-0570-y
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-stranded β-helix... (2011)
  • Author(s): Yokoi N, Miura Y, Kanamaru S, Arisaka F,et al.
  • Journal Title: Chem Commun (Camb). Volume: 47 Pages: 2074-2076
  • Peer Reviewed
• [Presentation] T4ファージホーリン・アンチホーリンの構造と機能 (2013)
  • Author(s): 金丸周司,伊藤悠太,有坂文雄
  • Organizer: 第13回日本蛋白質科学会年会
  • Place of Presentation: とりぎん文化会館（鳥取）
• [Presentation] The crystal structure and the stability of C-terminal fragment of gp34, proximal half of long tail fiber of bacteriophage T4 (2013)
  • Author(s): G.Meritxell, M.Namura, S.Alvira-de Celis, C.Garcia-Doval, A.K.Singh, M.J.van Raaij, F.Arisaka, S.Kanamaru
  • Organizer: XXIII Biennial Conference on Phage/Virus Assembly of Phage/Virus Assembly
  • Place of Presentation: UCLA Lake Arrowhead Conference Center & Mountain Resort（米国）
• [Presentation] T4ファージ基盤終結蛋白質gp48のSlyD融合蛋白質発現系の構築 (2013)
  • Author(s): 金丸周司,伊藤悠太,有坂文雄
  • Organizer: 第86回日本生化学会大会
  • Place of Presentation: パシフィコ横浜(神奈川）
• [Presentation] Intermolecular interactions and conformation of antibody dimers present in IgG1 biopharmaceuticals (2013)
  • Author(s): 井浦 貴文,福田 潤,山﨑 勝由,金丸 周司,有坂 文雄
  • Organizer: 第51回日本生物物理学会年会
  • Place of Presentation: 京都国際会館（京都）
• [Presentation] 病原性大腸菌O-157のタイプ6分泌系のVgrG1蛋白質のC末端断片のX線結晶構造 (2013)
  • Author(s): 内田 一也,金丸 周司,Petr Leiman,有坂 文雄
  • Organizer: 第51回日本生物物理学会年会
  • Place of Presentation: 京都国際会館（京都）
• [Presentation] T4ファージgp34C末端側半分の結晶構造から得られたファージ尾繊維に共通の構造 (2013)
  • Author(s): 金丸 周司,名村 実公賢,有坂 文雄
  • Organizer: 第51回日本生物物理学会年会
  • Place of Presentation: 京都国際会館（京都）
• [Presentation] *Ｔ４ファージｇｐ５-Ｌｙｓ－Ｓｐ複合体のＸ線結晶構造解析によるＳｐａｃｋｌｅ蛋白質のｇｐ５リゾチーム阻害メカニズムの解明 (2012)
  • Author(s): 内田 一也、金丸周司、根本舞、酒井直規、Petr Leiman、有坂文雄
  • Organizer: 第１２回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場、名古屋市（日本）
• [Presentation] Ｔ４ファージ尾繊維蛋白質ｇｐ３４の３量体コア構造の解明 (2012)
  • Author(s): 金丸 周司、名村実公賢、有坂文雄
  • Organizer: 第１２回日本蛋白質科学会年会
  • Place of Presentation: 名古屋国際会議場、名古屋市（日本）
• [Presentation] The trimeric core structure of the proximal end of the long tail fiber, gp34, of bacteriophage T4 (2012)
  • Author(s): Shuji Kanamaru, Mikiyoshi Namura, Fumio Arisaka
  • Organizer: Viruses of Microbes 2012（Belgium)
  • Place of Presentation: The Royal Military Academy（Belgium)
• [Presentation] Specific inhibition mechanism of gp5 lysozyme by spackle protein from (2012)
  • Author(s): Kazuya Uchida, Shuji Kanamaru, Mai Nemoto, Naoki Sakai, Petr Leiman, Fumio Arisaka
  • Organizer: Viruses of Microbes 2012（Belgium)
  • Place of Presentation: The Royal Military Academy（Belgium)
• [Presentation] 病原性大腸菌のタイプ６分泌系のＶｇｒＧ蛋白質のＸ線結晶構造解析に向けた大領発現系の構築と性状解析 (2012)
  • Author(s): 内田 一也.伊藤 豪、伊藤 悠太、新司 雄也、西條 要
  • Organizer: 第4回ファージ研究会
  • Place of Presentation: 群馬大学刀城会館、前橋市（日本）
• [Presentation] *Solubilization Approaches of artificial three-stranded beta-helix by fusing SlyD protein (2012)
  • Author(s): Kaname Nishijo, Shuji Kanamaru, Fumio Arisaka
  • Organizer: 第50回日本生物物理学会年会
  • Place of Presentation: 名古屋大学東山キャンパス、名古屋市（日本）
• [Presentation] *Conformational stability, reversibility and heat-induced aggregation of glycoprotein A (2012)
  • Author(s): Takafumi Iwura, Fumio Arisaka
  • Organizer: 第50回日本生物物理学会年会
  • Place of Presentation: 名古屋大学 東山キャンパス、名古屋市（日本）
• [Presentation] バクテリオファージT4近位尾繊維gp34C末端フラグメントの結晶構造解析 (2012)
  • Author(s): 金丸周司、名村実公賢、有坂文雄
  • Organizer: 第85回日本生化学会大会
  • Place of Presentation: 福岡国際会議場、福岡市（日本）
• [Presentation] X-ray Crystallographic Structure and Sedimentation Velocity....... (2012)
  • Author(s): 有坂 文雄
  • Organizer: 20th International Analytical Ultracentrifugation Conference
  • Place of Presentation: La Quinta Inn & Suites Medical Center & The Uni
• [Presentation] Mechanism of the strict sequential assembly pathway of the .... (2011)
  • Author(s): 有坂 文雄
  • Organizer: The 3rd Asia Pacific Protein Association (APPA)(招待講演)
  • Place of Presentation: Shanghai University, Shanghai, China
• [Presentation] Protein interactions as analyzed by sedimentation velocity (2011)
  • Author(s): 有坂 文雄
  • Organizer: 第11回蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク
• [Presentation] Protein-protein interaction analysis by composi... (2011)
  • Author(s): 金丸 周司
  • Organizer: 第11回蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク
• [Presentation] T4ファージgp7C 末端フラグメントの基盤ウェッジ形成における役割 (2011)
  • Author(s): 金丸 周司,伊藤 豪
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学・姫路書写キャンパス
• [Presentation] T4ファージのアンチホーリンによるホーリンの凝集抑制と溶菌阻止メカニズム (2011)
  • Author(s): 有坂文雄、金丸周司、伊藤 悠太
  • Organizer: 第84回日本生化学会大会
  • Place of Presentation: 国立京都国際会館
• [Presentation] Crystal structure reveals how spackle protein... (2011)
  • Author(s): 金丸 周司
  • Organizer: XXIInd Biennial Conference on Phage/Virus Assembly
  • Place of Presentation: The Marine Sciences Institute.
• [Presentation] T4ファージSpsckle蛋白質によるｇｐ5テイルリゾチームの溶菌阻害メカニズム (2011)
  • Author(s): 金丸 周司
  • Organizer: 第10回 微生物研究会
  • Place of Presentation: 千葉大学松戸キャンパス
• [Book] Edited by Alessio Innocenti. (2012)
  • Author(s): Fumio Arisaka
  • Publisher: Stoichiometry of Protein Interactions in Bacteriophage T4 Tail Assembly in "Stoichiometry and Research --- The Importance of Quantity in Biomedicine"
• [Book] Stoichiometry and Research - The Importance of Quantity in Biomedicine (2012)
  • Author(s): Fumio Arisaka
  • Publisher: InTech