Selected Publications (Shige H. Yoshimura)
- *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)
- 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.
- 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.
- 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.
- 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.
- *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.
- 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.
- 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.
- 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.
- 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.
- 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.
- *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.
- 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.
- 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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- *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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- *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.
- 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.
- 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.
- T. Nakai, K. Hizume, S.H. Yoshimura, K. Takeyasu and K. Yoshikawa, (2005) Phase transition in reconstituted chromatin. Europhys. Lett. 69(6): 1024-1030.
- 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.
- *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.
- 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.
- 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.
- 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.
- 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.
- *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.
- 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.
- 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.
- *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.
- *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.
- 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.
- 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.
- 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.
- *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.
- 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.
- *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.
- 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.
- 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.
- 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.
- *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.
- *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.
- 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.
- 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. hiroshima-u.ac.jp/ccab/).