publication
研究業績

研究業績

教員の履歴と業績

発表論文(2013〜)

  1. Kanaoka Y, *Mori T, Nagaike W, Itaya S, Nonaka Y, Kohga H, Haruyama T, Sugano Y, Miyazaki R, Ichikawa M, *Uchihashi T and *Tsukazaki. Nat. Commun.  accepted in principle

  2. Ikeda Y, Miyazaki R, Tsukazaki T, Akiyama Y and *Mori H.  Translation arrest cancellation of VemP, a secretion monitor in Vibrio, is regulated by multiple cis and trans factors, including SecY. J. Biol. Chem.  300, 107735 (2024)

  3. Ikei M, Miyazaki R, Monden K, Naito Y, Takeuchi A, Takahashi YS, Tanaka Y, Mori T, *Ichikawa M and *Tsukazaki T.  YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition. PLoS Biol.  22, e3002601 (2024)

  4. Sato Y, Hashimoto T, Kato K, Okamura A, Hasegawa K, Shinone T, Tanaka Y, Tanaka Y, Tsukazaki T, Tsukamoto T, Demura M, Yao M and Kikukawa T.  Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin. J. Biol. Chem.  299, 105393 (2023)

  5. *Kohga H, Lertpreedakorn N, Miyazaki R and *Tsukazaki T.  Critical residues of the antibiotic peptide LysM that inhibits lipid II flipping.  bioRxiv  2023.05.22.541694 (2023)

  6. *Miyazaki R and *Akiyama Y. Analyzing protein intermediate interactions in living E. coli cells using site-specific photo-crosslinking combined with chemical crosslinking. STAR Protocols 4, 102178 (2023)
  7. Takeda H, Busto JV, Lindau C, Tsutsumi A, Tomii K, Imai K, Yamamori Y, Hirokawa T, Motono C, Genesan I, Wenz L, Becker T, Kikkawa M, Pfanner N, Wiedemann N and Endo T. A multipoint guidance mechanism for β-barrel folding on the SAM complex. Nat. Struct. Mol. Biol. 30, 176-187 (2023)
  8. Miyazaki R, Ai M, Tanaka N, Suzuki T, Dhomae N, Tsukazaki T, Akiyama Y and *Mori H. Inner membrane YfgM-PpiD heterodimer acts as a functional unit that associates with the SecY/E/G translocon and promotes protein translocation. J. Biol. Chem. 298, 102572 (2022)
  9. *Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T and *Matsuura K. Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside. Sci. Adv. 8, eabq3817 (2022)
  10. Kohga H, Mori T, Tanaka Y, Yoshikaie K, Taniguchi K, Fujimoto K, Fritz L, Schneider T and *Tsukazaki T. Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms. Structure 30, 1088-1097 (2022)

  11. Tanaka Y, Iwaki S, Sasaki A and *Tsukazaki T. Crystal structures of a nicotine MATE transporter provide insight into its mechanism of substrate transport. FEBS Letters 595, 1902-1913 (2021)

    FEBS Letters
  12. Miyazaki R, Watanabe T, Yoshitani K and *Akiyama Y. Edge-strand of BepA interacts with immature LptD on the β-barrel assembly machine to direct it to on- and off-pathways. eLife 10, e70541 (2021)
  13. Kubo S, Yang SK, Black CS, Dai D, Valente-Paterno M, Gaertig J, *Ichikawa M and *Bui KH. Remodeling and activation mechanisms of outer arm dyneins revealed by cryo-EM. EMBO Rep. 22, e52911 (2021)
  14. Black C, Dai DC, Peri K, *Ichikawa M and *Bui KH. Preparation of Doublet Microtubule Fraction for Single ParticleCryo-electron Microscopy. Bio Protoc. 11, e4041 (2021)
  15. Khan N, Pelletier D, McAlear TS, Croteau N, Veyron S, Bayne AN, Black C, Ichikawa M, Khalifa AAZ, Chaaban S, Kurinov I, Brouhard G, Bechstedt S, Bui KH and *Trempe JF. Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding. Structure 29, 572-586 (2021)
  16. *Sheibani S, Basu K, Farnudi A, Ashkarran A, Ichikawa M, Presley JF, Bui KH, *Ejtehadi MR, Vali H and *Mahmoudi M. Nanoscale characterization of the biomolecular corona by cryo-electron microscopy, cryo-electron tomography, and image simulation. Nat. Commun. 12, 573 (2021)
  17. Daimon Y, Narita S, Miyazaki R, Hizukuri Y, Mori H, Tanaka Y, Tsukazaki T and *Akiyama Y. Reversible autoinhibitory regulation of Escherichia coli metallopeptidase BepA for selective β-barrel protein degradation. Proc. Natl. Acad. Sci. USA 117, 27989-27996 (2020)
  18. Tanaka Y, Yoshikaie K, Takeuchi A, Ichikawa M, Mori T, Uchino S, Sugano Y, Hakoshima T, Takagi H, Nonaka G and *Tsukazaki T. Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Sci. Adv. 6, eaba7637 (2020) [Diffraction data on zenodo.org: Native, Se-Met]

  19. Dai D, Ichikawa M*, Peri K, Rebinsky R, Bui KH*. Identification and mapping of central pair proteins by proteomic analysis. Biophys. Physicobiol. 17, 71-85 (2020) (*co-corresponding authors)

    Biophysics and Physicobiology.
  20. Khalifa AAZ†, Ichikawa M† Dai D, Kubo S, Black C, Peri K, McAlear TS, Veyron S, Yang SK, Vargas J, Bechstedt S, Trempe JF and Bui KH. The inner junction complex of the cilia is an interaction hub that involves tubulin post-translational modifications. eLife 9, e52760 (2020) († equally contributed)
  21. Sasaki M, Nishikawa H, Suzuki S, Moser M, Huber M, Sawasato K, Matsubayashi H, Kumazaki K, Tsukazaki T, Kuruma Y, Nureki O, Ueda T and Nishiyama KI. The bacterial protein YidC accelerates MPIase-dependent integration of membrane proteins. J. Biol. Chem. 294, 18898-18908 (2019)
  22. Ichikawa M, Khalifa AAZ, Kubo S, Dai D, Basu K, Maghrebi MAF, Vargas J and Bui KH. Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins. Proc. Natl. Acad. Sci. USA. 116, 19930-19938 (2019)
  23. Yang M, Chen YS, Ichikawa M, Calles-Garcia D, Basu K, Fakih R, Bui KH and Gehring K. Cryo-electron microscopy structures of ArnA, a key enzyme for polymyxin resistance, revealed unexpected oligomerizations and domain movements. J. Struct. Biol. 208, 43-50 (2019)
  24. Tanaka Y and Tsukazaki T. A snapshot of membrane protein insertion. EMBO Rep. 20, e49034 (2019)
  25. Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. The Protein Journal 38, 249-261 (2019)
  26. Inoue M, Sakuta N, Watanabe A, Zhang Y, Yoshikaie K, Tanaka Y, Ushioda R, Kato Y, Takagi J, Tsukazaki T, Nagata K and *Inaba K. Structural Basis of Sarco/Endoplasmic Reticulum Ca2+-ATPase 2b Regulation via Transmembrane Helix Interplay. Cell Rep. 27, 1221–1230 (2019)
  27. Shahrizal M, Daimon Y, Tanaka Y, Hayashi Y, Nakayama S, Iwaki S, Narita S, Kamikubo H, *Akiyama Y, and *Tsukazaki T. Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA. J. Mol. Biol. 431, 625-635 (2019)
  28. Kusakizako T, Claxton DP, Tanaka Y, Maturana AD, Kuroda T, Ishitani R, Mchaourab HS and Nureki O. Structural Basis of H(+)-Dependent Conformational Change in a Bacterial MATE Transporter. Structure 27, 293-301 (2019)
  29. Haruyama T, Sugano Y, Kodera N, Uchihashi T, Ando T, Tanaka Y, Konno H and *Tsukazaki T. Single-unit imaging of membrane protein-embedded nanodiscs. Structure 27, 152-160 (2019)
  30. Tanaka Y, Izumioka A, Abdul HA, Fujii A, Haruyama T, Furukawa A and *Tsukazaki T. 2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop. Biochem. Biophys. Res. Commun. 505, 141-145 (2018)
  31. *Tsukazaki T. Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor. FEMS Microbiology Letters 365, fny112 (2018)
  32. Furukawa A, Nakayama S, Yoshikaie K, Tanaka Y and *Tsukazaki T. Remote Coupled Drastic β-Barrel to β-Sheet Transition of the Protein Translocation Motor. Structure 26, 485–489 (2018)

  33. Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, *Tsukazaki T, *Narita S and *Akiyama Y. The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex. Mol. Microbiol. 106, 760-776 (2017). ダウンロード:Putative Bam-BepA model (.pdb)

    Mol. Microbiol.
  34. Tanaka Y, Iwaki S. and *Tsukazaki T. Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein. Structure 25, 1455-1460 (2017).
  35. Sugano Y, Furukawa A, Nureki O, Tanaka Y and *Tsukazaki T. SecY-SecA fusion protein retains the ability to mediate protein transport. PLOS ONE 12, e0183434 (2017)
  36. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto VY, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y and *Tsukazaki T. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF Cell Rep. 19, 895-901 (2017).
  37. Taniguchi R, Inoue A, Sayama M, Uwamizu A, Yamashita K, Hirata K, Yoshida M, Tanaka Y, Kato HE, Nakada-Nakura Y, Otani Y, Nishizawa T, Doi T, Ohwada T, Ishitani R, Aoki J and Nureki O. Structural insights into ligand recognition by the lysophosphatidic acid receptor LPA(6). Nature 548, 356-360 (2017)
  38. Nishima W, Mizukami W, Tanaka Y, Ishitani R, Nureki O and Sugita Y. Mechanismsfor Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter. Biophys J. 110, 1346-1354 (2016).
  39. Kusakizako T, Tanaka Y, Hipolito CJ, Kuroda T, Ishitani R, Suga H and *Nureki O. LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae. Acta Crystallogr. F 72, 552-557 (2015)
  40. Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, *Nureki O and *Tsukazaki T. Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State Cell Rep. 13, 1561-1568 (2015). [naistar]
  41. Shimokawa-Chiba N, Kumazaki K, Tsukazaki T, Nureki O, Ito K and Chiba S. Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. Proc. Natl. Acad. Sci. USA 112, 5063-5068 (2015). [naistar]
  42. Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, *Tsukazaki T and *Nureki O. Structural basis of Sec-independent membrane protein insertion by YidC. Nature 509, 516-520 (2014). [naistar]
  43. Kumazaki K, Kishimoto T, Furukawa A. Mori H, Tanaka Y, Dohmae N, Ishitani R, *Tsukazaki T and *Nureki O. Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci. Rep. 4, 7299 (2014). [naistar]
  44. Kumazaki K, *Tsukazaki T, Nishizawa T, Tanaka Y, Kato HE, Nakada-Nakura Y, Hirata K, Mori Y, Suga H, Dohmae N, Ishitani R and *Nureki O. Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans. Acta Crystallogr. F 70, 1056-1060 (2014). [naistar]
  45. Mio K, Tsukazaki T, Mori H, Kawata M, Moriya T, Sasaki Y, Ishitani R, Ito K, *Nureki O and *Sato C. Conformational variation of the translocon enhancing chaperone SecDF. J. Struct. Funct. Genomics,15, 107-115 (2014). [naistar]
  46. Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, *Suga H and *Nureki O. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 496, 247-251(2013). [naistar]
  47. Doki S, Kato HE, Solcan N, Iwaki M, Koyama M, Hattori M, Iwase N, Tsukazaki T, Sugita Y, Kandori H, Newstead S, *Ishitani R and *Nureki O. Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. Proc. Natl. Acad. Sci. USA 110, 11343-11348 (2013). [naistar]

修士論文一覧

  1. 2024.3 髙橋 諄 修士「細菌のタンパク質膜透過モーターSecDFの基質認識と制御機構の解析」
  2. 2024.3 髙橋 祐太郎 修士「キシローストランスポーターによる基質認識と輸送の構造基盤」<矢野賞>
  3. 2024.3 西 建瑠 修士「細菌外膜品質管理プロテアーゼBepAの相互作用解析」
  4. 2024.3 門田 啓吾 修士「チオ硫酸トランスポーターYeeEと協同して働くYeeD複合体の機能解析」
  5. 2022.3 山本 琴美 修士「キシローストランスポーターのX線結晶構造解析」
  6. 2022.3 内藤 雄介 修士「チオ硫酸イオントランスポーターYeeEの協働因子の構造機能解析」
  7. 2022.3 佐々木 旭 修士「植物MATEトランスポーターのX線結晶構造解析」
  8. 2022.3 板家 成良 修士「高速AFMによるタンパク質膜透過装置Sec複合体の動的構造解析」
  9. 2021.3 竹内 梓 修士「細菌由来のチオ硫酸イオントランスポーターYeeEの構造機能解析」<最優秀学生賞>
  10. 2021.3 柴尾 明鋭 修士　「亜鉛メタロプロテアーゼBepAの基質認識機構および活性化機構の解明のための結晶化条件検討」
  11. 2020.3 黄 嘉栄 修士　「特殊タンパク質の膜透過に関わるタンパク質複合体の精製」
  12. 2019.3 内野 清香 修士 「硫黄イオントランスポーターの結晶構造解析」
  13. 2019.3 中山 嘉子 修士 「構造解析にむけたトランスロコン関連タンパク質の発現と精製」
  14. 2019.3 長谷英 理菜 修士 「脂質Ⅱフリッパーゼに対する抗菌ペプチドの影響」
  15. 2019.3 河瀬 拓斗 修士 「タンパク質膜透過駆動モーターSecDFとパートナーとの相互作用の探索」
  16. 2019.3 泉岡 祥也 修士 「膜タンパク質の膜組み込みに関わるYidCの構造機能相関」
  17. 2018.3 藤本 圭 修士 「細胞壁生合成経路に関わるフリッパーゼの構造機能解析」
  18. 2018.3 中山 慎太郎 修士 「新生蛋白質輸送に関わるシャペロンの立体構造解析」
  19. 2017.9 Aisyah Binti Abdul Hamid 修士 「Crystal structure of Escherichia coli YidC at 2.8 A resolution」
  20. 2017.3 岩木 薫大 修士 「植物MATEファミリーの基質認識機構および輸送機構の解明」
  21. 2017.3 谷口 勝英 修士 「共生細菌由来MATE様多剤排出トランスポーターの結晶」
  22. 2017.3 櫻田 洋人 修士 「外膜タンパク質形成分解に関わるプロテアーゼのTPRドメインの結晶構造基盤」
  23. 2016.3 岡村 英幸 修士 「ペプチドタグを利用した膜タンパク質安定性の蛍光による評価」
  24. 2016.3 藤井 景 修士 「タンパク質の膜組込みに関わる膜タンパク質の基質認識機構解明に向けた構造解析」
  25. 2015.3 菅野 泰功 修士 「1ユニット再構成系を用いた蛋白質分泌過程の動的理解」<最優秀学生賞>
  26. 2015.3 古川 新 修士 「YidC・Sec膜タンパク質複合体によるタンパク質の膜組込み・膜透過機構の解明」<矢野賞>

博士論文一覧

  1. 2024.3 伊計 舞 博士「チオ硫酸取り込みを担うYeeE-YeeD複合体の構造機能解析」
  2. 2021.3 Bin Mohammad Umar Mohammad Shahrizal 博士「Crystal structure of β-Barrel Assembly-Enhancing Protease
    (BepA) for biogenesis of outer membrane proteins」
  3. 2020.3 岩木 薫大 博士「植物MATEファミリーの構造基盤」
  4. 2018.3 菅野 泰功 博士 「タンパク質膜透過チャネルSecトランスロコンの静的動的構造基盤」<最優秀学生賞>
  5. 2018.3 古川 新 博士 「膜タンパク質YidCとSecDFの結晶構造から解明されたタンパク質輸送の原理」<井上研究奨励賞>

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