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2009 Fiscal Year Final Research Report

In vivo Reconstruction of Functional Protein Complexes by Using Nano-particles and its Application for Artificial Cell

Research Project

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Project/Area Number 17076008
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionKyoto University

Principal Investigator

YOSHIMURA Shige h.  Kyoto University, 大学院・生命科学研究科, 准教授 (90346106)

Co-Investigator(Kenkyū-buntansha) TAKEYASU Kunio  京都大学, 大学院・生命科学研究科, 教授 (40135695)
HIZUME Kohjiv  京都大学, 大学院・生命科学研究科, 助教 (10378846)
Project Period (FY) 2005 – 2009
Keywordsナノパーティクル / 核輸送 / 量子ドット / クロマチン / 核内骨格 / 染色体タンパク質
Research Abstract

In this project, we have obtained the following results;
i) By combining in vitro nucleosome reconstitution procedure and atomic force microscopy, "30-nm-chromatin fiber" was successfully reconstituted.
ii) By utilizing fast-scanning atomic force microscopy, molecular mechanisms of various enzymatic functions and processes have been elucidated.
iii) We established the technique to microinject a fluorescent particle into a living cell and manipulate it by optical trap without damaging the cell.
iv) By attaching nuclear localization signal peptide to quantum dots, we established the method to deliver nano-particles into a living cell nucleus.
v) Structural and functional properties of nuclear scaffold proteins have been obtained by combining proteomics, bioinformatics, molecular biology and biochemistry.

  • Research Products

    (37 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (33 results) (of which Peer Reviewed: 33 results) Presentation (3 results) Remarks (1 results)

  • [Journal Article] Molecular mechanisms underlying nucleocytoplasmic shuttling of actinin-4.2010

    • Author(s)
      M. Kumeta, S.H. Yoshimura, M. Harata, K. Takeyasu
    • Journal Title

      J. Cell. Sci. 123(Pt7)

      Pages: 1020-1030

    • Peer Reviewed
  • [Journal Article] Molecular Dynamics of DNA and Nucleosomes in Solution Studied by Fast-scanning Atomic Force Microscopy.2010

    • Author(s)
      Y. Suzuki, Y. Higuchi, K. Hizume, M. Yokokawa, S.H. Yoshimura, K. Yoshikawa, K. Takeyasu
    • Journal Title

      Ultramicroscopy (in press)

    • Peer Reviewed
  • [Journal Article] Proteomic and targeted analytical identification of BXDC1 and EBNA1BP2 as dynamic scaffold proteins in the nucleolus2009

    • Author(s)
      Y. Hirano, K. Ishii, M. Kumeta, K. Furukawa, K. Takeyasu, T. Horigome
    • Journal Title

      Genes Cells 14

      Pages: 155-166

    • Peer Reviewed
  • [Journal Article] Human transcriptional coactivator PC4 stimulates DNA end joining and activates DSB repair activity2009

    • Author(s)
      K. Batta, M. Yokokawa, K. Takeyasu, T.K. Kundu
    • Journal Title

      J. Mol. Biol. 385

      Pages: 788-799

    • Peer Reviewed
  • [Journal Article] Cell cycle-dependent phosphorylation of MAN12009

    • Author(s)
      Y. Hirano, Y. Iwase, K. Ishii, M. Kumeta, T. Horigome, K. Takeyasu
    • Journal Title

      Biochemistry 48(7)

      Pages: 1636-1643

    • Peer Reviewed
  • [Journal Article] Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction and 30-nm fiber formation of the nucleosome array2009

    • Author(s)
      K. Hizume, T. Nakai, S. Araki, E. Prieto, K. Yoshikawa, K. Takeyasu
    • Journal Title

      Ultramicroscopy 109(8)

      Pages: 868-873

    • Peer Reviewed
  • [Journal Article] Single-molecule analysis of protein-DNA complexes formed during partition of newly replicated plasmid molecures in Streptococcus pyogenes.2009

    • Author(s)
      F. Pratto, Y. Suzuki, K. Takeyasu, J.C. Alonso
    • Journal Title

      J. Biol. Chem. 284(44)

      Pages: 30298-30306

    • Peer Reviewed
  • [Journal Article] Nucleosomal array reconstituted from ring and linear DNA.2009

    • Author(s)
      S. Araki, K. Hizume, T. Iwaki, Y. Suzuki, K. Takeyasu, K. Yoshikawa
    • Journal Title

      Chem. Phys. Lett. 479

      Pages: 284-289

    • Peer Reviewed
  • [Journal Article] Single-Molecule analysis of protein-DNA EcoRII protein complexes revealed with high-speed atomic force microscopy.2009

    • Author(s)
      J. Gilmore, Y. Suzuki, G. Tamulaitis, V. Siksnys, K. Takeyasu, Y.L. Lyubchenko
    • Journal Title

      Biochemistry 48(44)

      Pages: 10492-10498

    • Peer Reviewed
  • [Journal Article] Nuclear Architectures and Chromatin Dynamics Revealed by Atomic Force Microscopy in Combination with Biochemistry and Cell Biology.2008

    • Author(s)
      Y. Hirano, H. Takahashi, M. Kumeta, K. Hizume, Y. Hirai, S. Otsuka, S.H. Yoshimura, K. Takeyasu
    • Journal Title

      Pflugers Arch. 456

      Pages: 139-153

    • Peer Reviewed
  • [Journal Article] In situ analysis of the higher-order genome structure in a single Escherichia coli cell.2008

    • Author(s)
      E. Shindo, K. Kubo, R.L. Ohniwa, K. Takeyasu, K. Yoshikawa
    • Journal Title

      J. Biotechnol 133(2)

      Pages: 172-176

    • Peer Reviewed
  • [Journal Article] Dynamic structures of Bacillus subtilis RecN-DNA complexes.2008

    • Author(s)
      H. Sanchez, P.P. Cardenas, S.H. Yoshimura, K. Takeyasu, J.C. Alonso
    • Journal Title

      Nuc. Acids Res. 36(1)

      Pages: 110-120

    • Peer Reviewed
  • [Journal Article] Following translation by single ribosomes one codon at a time.2008

    • Author(s)
      J. Wen, L. Lancaster, C. Hodges, A. Zeri, S.H. Yoshimura, H.F. Noller, C. Bustamante, I. Tinoco
    • Journal Title

      Jr., Nature 452(7187)

      Pages: 598-603

    • Peer Reviewed
  • [Journal Article] Scanning probe microscope revealed mechanical properties of plasma membrane and nuclear envelope in living cells.2008

    • Author(s)
      M. Yokokawa, K. Takeyasu, S.H. Yoshimura
    • Journal Title

      J. Microscopy 232

      Pages: 82-90

    • Peer Reviewed
  • [Journal Article] Fast degradation of the auxiliary subunit of the Na/K-ATPase in the plasma membrane of HeLa cells.2008

    • Author(s)
      S.H. Yoshimura, S. Iwasaka, W. Schwarz, K. Takeyasu
    • Journal Title

      J. Cell Sci. 121

      Pages: 2159-2168

    • Peer Reviewed
  • [Journal Article] Individual binding pockets of importin β for FG-nucleoporins are differently regulated by RanGTP2008

    • Author(s)
      S. Otsuka, S. Iwasaka, Y. Yoneda, K. Takeyasu, S.H. Yoshimura
    • Journal Title

      Proc. Natl. Acad. Sci. U S A. 105

      Pages: 16101-16106

    • Peer Reviewed
  • [Journal Article] Atomic Force Microscopy Dissects the Hierarchy of Genome Architectures in Eukaryote, Prokaryote, and Chloroplast.2007

    • Author(s)
      R.L. Ohniwa, K. Morikawa, J. Kim, T. Kobori, K. Hizume, R. Matsumi, H. Atomi, T. Imanaka, T. Ohta, C. Wada, S.H. Yoshimura, K. Takeyasu
    • Journal Title

      Microsc. Microanal. 13(1)

      Pages: 3-12

    • Peer Reviewed
  • [Journal Article] Biochemical, molecular genetic and structural analyses of the Staphylococcal nucleoid.2007

    • Author(s)
      K. Morikawa, R.L. Ohniwa, J. Kim, S.L. Takeshita, A. Maruyama, Y. Inose, K. Takeyasu, T. Ohta
    • Journal Title

      Microscopy and Microanalysis 13

      Pages: 30-35

    • Peer Reviewed
  • [Journal Article] Single-molecule detection of phosphorylation-induced plasticity changes during ezrin activation.2007

    • Author(s)
      D. Liu, L. Ge, F. Wang, H. Takahashi, D. Wang, Z. Guo, S.H. Yoshimura, T. Ward, X. Ding, K. Takeyasu, X. Yao
    • Journal Title

      FEBS Lett. 581(18)

      Pages: 3563-3571

    • Peer Reviewed
  • [Journal Article] Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping.2007

    • Author(s)
      N. Crampton, M. Yokokawa, D.T. Dryden, J.M. Edwardson, D.N. Rao, K. Takeyasu, S.H. Yoshimura, R.M. Henderson
    • Journal Title

      Proc. Natl. Acad. Sci. USA. 104(31)

      Pages: 12755-12760

    • Peer Reviewed
  • [Journal Article] Covalent attachment of protein to the tip of a multiwalled carbon nanotube without sidewall decoration.2007

    • Author(s)
      H. Maruyama, S.H. Yoshimura, S. Akita, A. Nagataki, Y. Nakayama
    • Journal Title

      J. Appl. Phys. 102

      Pages: 094701

    • Peer Reviewed
  • [Journal Article] Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histones.2007

    • Author(s)
      T. Kobori, S. Iwamoto, K. Takeyasu, T. Ohtani
    • Journal Title

      Biopolymers 85

      Pages: 295-307

    • Peer Reviewed
  • [Journal Article] Transcription-coupled Nucleoid Architecture in Bacteria.2007

    • Author(s)
      R.L. Ohniwa, K. Morikawa, J. Kim, S.L. Takeshita, T. Ohta, C. Wada, K. Takeyasu
    • Journal Title

      Gene to Cells 12

      Pages: 1141-1152

    • Peer Reviewed
  • [Journal Article] Topoisomerase II, a scaffold component, promotes chromatin- compaction in vitro in a linker-histone H1-dependent manner.2007

    • Author(s)
      K. Hizume, S. Araki, K. Yoshikawa, K. Takeyasu
    • Journal Title

      Nucleic Acids Res. 35(8)

      Pages: 2787-2799

    • Peer Reviewed
  • [Journal Article] 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.2006

    • Author(s)
      T. Kobori, M. Kodama, K. Hizume, S.H. Yoshimura, T Ohtani, K. Takeyasu
    • Journal Title

      J. Electr. Microsc. 55(1)

      Pages: 31-40

    • Peer Reviewed
  • [Journal Article] Fast-scanning atomic force microscopy revealed the molecular mechanism of DNA cleavage by ApaI endonuclease.2006

    • Author(s)
      M. Yokokawa, S.H. Yoshimura, Y. Naito, T. Ando, A. Yagi, N. Sakai, K. Takeyasu
    • Journal Title

      IEE Proc. Nanobiotechnol 153(4)

      Pages: 60-66

    • Peer Reviewed
  • [Journal Article] Development of glutathione-coupled cantilever for the single-molecule force measurement by scanning force microscopy.2006

    • Author(s)
      S.H. Yoshimura, H. Takahashi, S. Otsuka, K. Takeyasu
    • Journal Title

      FEBS Lett. 580(16)

      Pages: 3961-3965

    • Peer Reviewed
  • [Journal Article] Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL.2006

    • Author(s)
      M. Yokokawa, C. Wada, T. Ando, N. Sakai, A. Yagi, S.H. Yoshimura, K. Takeyasu
    • Journal Title

      EMBO J. 25(19)

      Pages: 4567-4576

    • Peer Reviewed
  • [Journal Article] Human ObgH1 and ObgH2 participate in the maintenance of mitochondria and nucleolar architectures.2006

    • Author(s)
      Y. Hirano, R.L. Ohniwa, C. Wada, S.H. Yoshimura, K. Takeyasu
    • Journal Title

      Genes Cells 11(11)

      Pages: 1295-1304

    • Peer Reviewed
  • [Journal Article] Transcriptional co-activator PC4, a chromatin-associated protein, induces chromatin condensation.2006

    • Author(s)
      C. Das, K. Hizume, K. Batta, B.R.P. Kumar, S.S. Gadad, S. Ganguly, S. Lorain, A. Verreault, P.. P. Sadhale, K. Takeyasu, T.K. Kundu
    • Journal Title

      Mol. Cell. Biol. 26

      Pages: 8303-8315

    • Peer Reviewed
  • [Journal Article] Dynamic state of DNA topology is essential for genome condensation in bacteria.2006

    • Author(s)
      R.L. Ohniwa, K. Morikawa, J. Kim, T. Ohta, A. Ishihama, C. Wada, K. Takeyasu,
    • Journal Title

      EMBO J. 25

      Pages: 5591-5602

    • Peer Reviewed
  • [Journal Article] Linker histone H1 per se can induce three-dimensional folding of chromatin fiber.2005

    • Author(s)
      K. Hizume, S.H. Yoshimura, K. Takeyasu
    • Journal Title

      Biochemistry 44(39)

      Pages: 12978-12989

    • Peer Reviewed
  • [Journal Article] Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation.2005

    • Author(s)
      Y. Yoshikawa, K. Hizume, Y. Oda, K. Takeyasu, S. Araki, K. Yoshikawa
    • Journal Title

      Biophys. J. 90(3)

      Pages: 993-999

    • Peer Reviewed
  • [Presentation] Hydrophobic interaction between importin β and nucleoporins facilitates fast and selective transport through the nuclear pore complex2009

    • Author(s)
      S.H. Yoshimura
    • Organizer
      the EMBO conference series on Nuclear Structure and Dynamics
    • Place of Presentation
      L'Isle sur la Sorgue(France)
    • Year and Date
      2009-10-02
  • [Presentation] Advances in Single-molecular Research for Biology & Nanoscience2008

    • Author(s)
      S.H. Yoshimura, K. Takeyasu
    • Organizer
      Xth Annual Linz Winter Workshop
    • Place of Presentation
      Linz (Austria)
    • Year and Date
      2008-02-17
  • [Presentation] Single-molecule structural and functional analyses of protein transport through the nuclear pore complex.2006

    • Author(s)
      S.H. Yoshimura
    • Organizer
      The VIIIth symposium on SPM and organic materials
    • Place of Presentation
      Dresden (Germany)
    • Year and Date
      2006-09-28
  • [Remarks]

    • URL

      http://www/lif.kyoto-u.ac.jp/labs/chrom/index.html

URL: 

Published: 2011-06-18   Modified: 2016-04-21  

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