Publication

Publication

Publication List of Teaching Staff

Publications (2013-)

  1. 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)

  2. 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)

  3. 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)

  4. *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)

  5. *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)
  6. 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)
  7. 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)
  8. *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)
  9. 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)

  10. 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)

  11. 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)
  12. 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)
  13. 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)
  14. 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)
  15. *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)
  16. 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)
  17. 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]

  18. 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)

  19. 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)
  20. 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)
  21. 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)
  22. 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)
  23. Tanaka Y and Tsukazaki T. A snapshot of membrane protein insertion. EMBO Rep. 20, e49034 (2019)
  24. Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. The Protein Journal 38, 249-261 (2019)
  25. 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)
  26. 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)
  27. 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)
  28. 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)
  29. 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)
  30. *Tsukazaki T. Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor. FEMS Microbiology Letters 365, fny112 (2018)
  31. 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)

  32. 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). Download:Putative Bam-BepA model (.pdb)

  33. Tanaka Y, Iwaki S. and *Tsukazaki T. Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein. Structure 25, 1455-1460 (2017).
  34. 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)
  35. 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).
  36. 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)
  37. 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).
  38. 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)
  39. 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]
  40. 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]
  41. 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]
  42. 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]
  43. 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]
  44. 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]
  45. 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]
  46. 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]

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