Selected Publications (Shige H. Yoshimura)

  1. *S.H. Yoshimura, S. Otsuka, M. Kumeta, M. Taga and K. Takeyasu (2013) Intermolecular disulfide bonds among nucleoporins regulate karyopherin-dependent nuclear transport. J. Cell Sci. (in press)
  2. Y. Suzuki, T.A. Goetze, D. Stroebel, D. Balasuriya, S.H. Yoshimura, R.M. Henderson, P. Paoletti, K. Takeyasu, J.M. Edwardson (2013) Visualization of structural changes accompanying activation of N-methyl-D-aspartate (NMDA) receptors using fast-scan atomic force microscopy imaging. J. Biol. Chem. 288(2):778-784.
  3. E. Prieto, T. Kobori, S.H. Yoshimura, K. TakeyasuK. Hizume (2012) Core histone charge and linker histone H1 effects on the chromatin structure of Schizosaccharomyces pombe. Biosci.Biotech. Biochem. 76(12): 2261-2266.
  4. Y. Suzuki, M. Shin, A. Yoshida, S.H. Yoshimura and K. Takeyasu (2012) Fast microscopical dissection of action scenes played by Escherichia coli RNA polymerase. FEBS Lett. 586(19):3187-3192.
  5. M. Kumeta, H. Yamaguchi, S.H. Yoshimura, and K. Takeyasu (2012) Karyopherin-independent spontaneous transport of amphiphilic proteins through the nuclear pore. J. Cell Sci. 125(Pt 21): 4979-4984.
  6. *S.H. Yoshimura, S. Khan, S. Ohno, T. Yokogawa, K. Nishikawa, T. Hosoya, H. Maruyama, Y. Nakayama and K. Takeyasu (2012) Site-specific attachment of a protein to the end of carbon nanotube without loss of protein function. Bioconj. Chem. 23(7):1488-1493.
  7. S. Sekiguchi, K. Niikura, Y. Mastuo, S.H. Yoshimura, K. Ijiro (2012) Nuclear transport facilitated by the interaction between nuclear pores and carbohydrates. RSC Advances 2: 1656-1662.
  8. H. Maruyama, S.H. Yoshimura, S. Ohno, K. Nishikawa and Y. Nakayama (2012) Covalent attachment of a specific site of a protein molecule on a carbon nanotube tip. J. Appl. Phys. 111, 074701.
  9. M. Asally, Y. Yasuda, M. Oka, S. Otsuka, S.H. Yoshimura, K. Takeyasu and Y. Yoneda (2011) Nup358, a nucleoporin, functions as a key determinant of the nuclear pore complex structure remodeling during skeletal myogenesis. FEBS J. 278(4): 610-621.
  10. H. Ohno, T. Kobayashi, R. Kabata, K. Endo, T. Iwasa, S.H. Yoshimura, K. Takeyasu, T. Inoue and H. Saito (2011) Synthetic RNA-protein complex shaped like an equilateral triangle. Nat. Nanotechol., 6(2):116-120.
  11. H. Maruyama, M. Shin, T. Oda, R. Matsumi, R.L. Ohniwa, T. Ito, K. Shirahige, T. Imanaka, H. Atomi, S.H. Yoshimura and K. Takeyasu (2011) Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis. Mol. Biol. Cell, 22(3): 386-398.
  12. *S.H. Yoshimura, S. Khan, H. Maruyama, Y. Nakayama and K. Takeyasu (2011) Fluorescence labeling of carbon nanotubes and visualization of a nanotube-protein hybrid under fluorescence microscope. Biomacromolecules 12(4):1200-1204.
  13. Y. Akai, Y. Kurokawa, N. Nakazawa, Y. Tonami-Murakami, Y. Suzuki, S.H. Yoshimura, H. Iwasaki, Y. Shiroiwa, T. Nakamura, E. Shibata and M. Yanagida (2011) Opposing role of condensin hinge against replication protein A in mitosis and interphase through promoting DNA annealing. Open Biology 1(4): 110023.
  14. Y. Suzuki, J.L. Gilmore, S.H. Yoshimura, R.M. Henderson, Y.L. Lyubchenko and K. Takeyasu (2011) Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region. Biophys. J. 101(12): 2992-2998
  15. Y. Suzuki, Y. Higuchi, K. Hizume, M. Yokokawa, S.H. Yoshimura, K. Yoshikawa and K. Takeyasu (2010) Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy. Ultramicroscopy 110(6): 682-688.
  16. J. Teramoto, S.H. Yoshimura, K. Takeyasu and A. Ishihama (2010) A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Nuc. Acids. Res., 38(11): 3605-3618.
  17. M. Kumeta, S.H. Yoshimura, M. Harata and K. Takeyasu (2010) Molecular mechanisms underlying nucleocytoplasmic shuttling of actinin-4. J. Cell. Sci. 123(Pt 7):1020-1030.
  18. H. Takahashi, K. Hizume, M. Kumeta, S.H. Yoshimura and K. Takeyasu (2009) Single-molecule anatomy by atomic force microscopy and recognition imaging. Arch. Histol. Cytol. 72(4/5): 217-225.
  19. H. Sanchez, P.P. Cardenas, S.H. Yoshimura, K. Takeyasu and J.C. Alonso (2008) Dynamic structures of Bacillus subtilis RecN–DNA complexes. Nuc. Acids Res. 36(1): 110-120.
  20. Y. Hirano, H. Takahashi, M. Kumeta, K. Hizume, Y. Hirai, S. Otsuka, S.H. Yoshimura and K. Takeyasu (2008) Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology. Pflugers Arch. 456(1):139-53.
  21. J. Wen, L. Lancaster, C. Hodges, A. Zeri, S.H. Yoshimura, H.F. Noller, C. Bustamante and I. Tinoco, Jr. (2008) Following translation by single ribosomes one codon at a time. Nature 452(7187): 598-603.
  22. M. Yokokawa, K. Takeyasu and S.H. Yoshimura (2008) Scanning probe microscope revealed mechanical properties of plasma membrane and nuclear envelope in living cells. J. Microscopy 232 (Pt I): 82-90.
  23. *S.H. Yoshimura, S. Iwasaka, W. Schwarz and K. Takeyasu (2008) Fast degradation of the auxiliary subunit of the Na/K-ATPase in the plasma membrane of HeLa cells. J. Cell Sci. 121(Pt 13):2159-2168.
  24. S. Otsuka, S. Iwasaka, Y. Yoneda, K. Takeyasu and S.H. Yoshimura (2008) Individual binding pockets of importin b for FG-nucleoporins are differently regulated by RanGTP. Proc. Natl. Acad. Sci. U S A. 105(42): 16101-16106.
  25. R.L. Ohniwa, K. Morikawa, J. Kim, T. Kobori, K. Hizume, R. Matsumi, H. Atomi, T. Imanaka, T. Ohta, C. Wada, S.H. Yoshimura and K. Takeyasu. (2007) Atomic force microscopy dissects the hierarchy of genome architecture in eukaryote, prokaryote and chloroplast. Microsc. Microanal. 13(1) 3-12.
  26. D. Liu, L. Ge, F. Wang, H. Takahashi, D. Wang, Z. Guo, S.H. Yoshimura, T. Ward, X. Ding, K. Takeyasu and X. Yao (2007) Single-molecule detection of phosphorylation-induced plasticity changes during ezrin activation. FEBS Lett. 581(18): 3563-3571.
  27. N. Crampton, M. Yokokawa, D.T. Dryden, J.M. Edwardson, D.N. Rao, K. Takeyasu, S.H. Yoshimura and R.M. Henderson. (2007) Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping. Proc. Natl. Acad. Sci. U S A. 104(31): 12755- 12760.
  28. H. Maruyama, S.H. Yoshimura, S. Akita, A. Nagataki and Y. Nakayama (2007) Covalent attachment of protein to the tip of a multiwalled carbon nanotube without sidewall decoration. J. Appl. Phys. 102: 094701.
  29. T. Kobori, M. Kodama, S.H. Yoshimura and K. Takeyasu (2006) Comparative structural biology of the genome: Nano-scale imaging of single nucleus from different kingdoms reveals the chromatin built up on a 40 nm structural unit. J. Electr. Microsc. 55(1): 31-40.
  30. M. Yokokawa, S.H. Yoshimura, Y. Naito, T. Ando, A. Yagi, N. Sakai and K. Takeyasu (2006) Fast-scanning atomic force microscopy revealed the molecular mechanism of DNA cleavage by ApaI endonuclease. IEE Proc. Nanobiotech. 153(4):60-66.
  31. *S.H. Yoshimura, H. Takahashi, S. Otsuka and K. Takeyasu (2006) Development of glutathione-coupled cantilever for the single-molecule force measurement by scanning force microscopy. FEBS Lett. 580(16):3961-3965.
  32. M. Yokokawa, C. Wada, T. Ando, N. Sakai, A. Yagi, S.H. Yoshimura and K. Takeyasu (2006) Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL. EMBO J. 25(19): 4567-4576.
  33. Y. Hirano, R.L. Ohniwa, C. Wada, S.H. Yoshimura and K. Takeyasu (2006) Human ObgH1 and ObgH2 participate in the maintenance of mitochondria and nucleolar architectures. Genes Cells 11(11), 1295-1304.
  34. T. Nakai, K. Hizume, S.H. Yoshimura, K. Takeyasu and K. Yoshikawa, (2005) Phase transition in reconstituted chromatin. Europhys. Lett. 69(6): 1024-1030.
  35. K. Hizume, S.H. Yoshimura and K. Takeyasu (2005) Linker histone H1 per se can induce three-dimensional folding of chromatin fiber. Biochemistry 44(39):12978-12989.
  36. *S.H. Yoshimura, H. Maruyama, R. Ohki, F. Ishikawa and K. Takeyasu (2004) Molecular mechanism of DNA end-loop formation by TRF2 Genes Cells 9(3): 205-218.
  37. J. Kim, S.H. Yoshimura, K. Hizume, R.L. Ohniwa, A. Ishihama and K. Takeyasu (2004) Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nuc. Acids Res. 32(6): 1982-1992.
  38. K. Hizume, S.H. Yoshimura, H. Wada and K. Takeyasu (2004) Atomic force microscopy demonstrates a critical role of DNA superhelicity in the nucleosome dynamics. Cell Biochem. Biophys. 40(3): 249-261.
  39. K. Takeyasu, J. Kim, R.L. Ohniwa, T. Kobori, Y. Inose, K. Morikawa, T. Ohta, A. Ishihama and S.H. Yoshimura (2004) Genome architecture studied by nanoscale imaging: analyses among bacterial phyla and their implication to eukaryotic genome folding. Cytogenet. Genome Res. 107(1-2): 38-48.
  40. K. Hizume, S.H. Yoshimura, H. Wada and K. Takeyasu (2003) Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology. Arch. Histol. Cytol., 65(5): 405-413.
  41. *S.H. Yoshimura and K. Takeyasu (2003) Differential degradation of the Na/K-ATPase subunits in the plasma membrane. Annal. New York Acad. Sci., 986: 378-381.
  42. K. Takeyasu, T. Kawase and S.H. Yoshimura (2003) Inter-molecular interaction between the Na+/K+-ATPase a-subunit and the glycogen phosphorylase. Annal. New York Acad. Sci., 986: 522-524.
  43. K. Ito, I. Toyoda, M. Higashiyama, D. Uemura, M.H. Sato, S.H. Yoshimura, T. Ishii and K. Takeyasu.(2003) Channel induction by palytoxin in yeast cells expressing Na+,K+-ATPase or its chimera with sarco/endoplasmic reticulum Ca2+-ATPase. FEBS Lett. 543 (1-3): 108-112.
  44. *S.H. Yoshimura, J. Kim and K. Takeyasu (2003) On-substrate lysis treatment combined with the scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes. J. Electr. Microsc. 52(4): 415-423.
  45. *S.H. Yoshimura, K. Hizume, A. Murakami, T. Sutani, K. Takeyasu and M. Yanagida (2002) Condensin Architecture and Interaction with DNA: Regulatory Non-SMC Subunits Bind to the head of SMC heterodimer. Curr. Biol., 12 (6): 508-512.
  46. T. Uemura, S.H. Yoshimura, K. Takeyasu and M.H. Sato (2002) Vacuolar membrane dynamics revealed by GFP-AtVam3 fusion protein. Genes Cells, 7(7): 743-753.
  47. T. Sakaue, K. Yoshikawa, S.H. Yoshimura and K. Takeyasu (2001) Histone core slips along DNA and prefers positioning at the chain end. Phys. Rev. Lett., 87(7): 078105.
  48. K. Takeyasu, H. Okamura, J.C. Yasuhara, Y. Ogita and S.H. Yoshimura (2001) P-type ATPase diversity and evolution: the origins of ouabain sensitivity and subunit assembly. Cell. Mol. Biol. 47(2): 325-333.
  49. *S.H. Yoshimura, C. Yoshida, K. Igarashi and K. Takeyasu (2000) AFM proposes a ‘Kiss and Pull’ mechanism for enhancer function. J. Electron Microscopy, 49(3): 407-413.
  50. K.I. Hohmura, Y. Itokazu, S.H. Yoshimura, G. Mizuguchi, Y. Masamura, K. Takeyasu, Y. Shiomi, T. Tsurimoto, H. Nishijima, S. Akita and Y. Nakayama (2000) AFM with carbon nanotube resolve the subunit organization of protein complexes. J. Electron Microscopy, 49(3): 414-421.
  51. *S.H. Yoshimura, R.L. Ohniwa, M.H. Sato, F. Matsunaga, G. Kobayashi, H. Uga, C. Wada and K. Takeyasu (2000) DNA phase transition promoted by replication initiator. Biochemistry, 39(31): 9139-9145.
  52. Y. Nakayama, H. Nishijima, S. Akita, K.I. Hohmura, S.H. Yoshimura and K.Takeyasu (2000) Microprocess for fabricating carbon-nanotube probes of a scanning probe microscope. J. Vac. Sci. Technol. B, 18(2), 661-664.
  53. H. Nishijima, S. Kamo, S. Akita, Y. Nakayama, K.I. Hohmura, S.H. Yoshimura and K. Takeyasu (1999) Carbon-nanotube tips for scanning probe microscopy: Preparation of a controlled process and observation of deoxyribonucleic acid. Applied Physics Lett., 74 (26):4061-4063.
  54. M.H. Sato, K. Ura, K.I. Hohmura, F. Tokumasu, S.H. Yoshimura, F. Hanaoka and K. Takeyasu (1999) Atomic force microscopy sees nucleosome positioning and histone H1-induced compaction in reconstituted chromatin. FEBS Lett., 452(3): 267-271.
  55. *S.H. Yoshimura, L.A. Vasilets, T. Ishii, K. Takeyasu and W. Schwarz (1998) A Modification of the Cytoplasmic Carboxyl Terminus of the Ouabain-resistant Na+/K+-ATPase Leads to Complete Loss of Electrogenicity. FEBS Lett., 425(1): 71-74.
  56. *S.H. Yoshimura, T. Ishii, J.C. Yasuhara, M.H. Sato and K. Takeyasu (1997) Ion-sensitive Domains of the SERCA- and the Na+/K+-ATPases Identified by Chimeric Recombination. Annal. New York Acad. Sci., 384: 588-591.
  57. J. Zhao, L.A. Vasilets, S.H. Yoshimura, Q. Gu, T. Ishii, K. Takeyasu and W. Schwarz (1997) The Ca2+/calmodulin binding domain of the Ca2+-ATPase linked to the Na+,K+-ATPase alters transport stoichiometry. FEBS Lett., 408(3): 271-275.
  58. K. Takeyasu, F. Tokumasu, S.H. Yoshimura, K. Maruyama and M.H. Sato (1997) Molecular Assembly of Biological Macromolecules Studied by Atomic Force Microscopy: Quantitative analyses of membrane structures and DNA-protein interactions. Trends in Analytical BioSciences, Vol.1, (electric publication at http://neo.pharm.


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