• 3866 Citations
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1988 …2020

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Article
2020

Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo-electron microscopy

Oide, M., Kato, T., Oroguchi, T. & Nakasako, M., 2020 Jan 1, (Accepted/In press) In : FEBS Journal.

Research output: Contribution to journalArticle

Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B

Oide, M., Hikima, T., Oroguchi, T., Kato, T., Yamaguchi, Y., Yoshihara, S., Yamamoto, M., Nakasako, M. & Okajima, K., 2020 Apr 1, In : FEBS Journal. 287, 8, p. 1612-1625 14 p.

Research output: Contribution to journalArticle

2019
2018

Blue light– excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from arabidopsis

Oide, M., Okajima, K., Nakagami, H., Kato, T., Sekiguchi, Y., Oroguchi, T., Hikima, T., Yamamoto, M. & Nakasako, M., 2018 Jan 19, In : Journal of Biological Chemistry. 293, 3, p. 963-972 10 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Classification of ab initio models of proteins restored from small-angle X-ray scattering

Oide, M., Sekiguchi, Y., Fukuda, A., Okajima, K., Oroguchi, T. & Nakasako, M., 2018 Sep 1, In : Journal of Synchrotron Radiation. 25, 5, p. 1379-1388 10 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation

Kobayashi, A., Takayama, Y., Okajima, K., Oide, M., Yamamoto, T., Sekiguchi, Y., Oroguchi, T., Nakasako, M., Kohmura, Y., Yamamoto, M., Hoshi, T. & Torizuka, Y., 2018 Jan 1, (Accepted/In press) In : Journal of Synchrotron Radiation.

Research output: Contribution to journalArticle

1 Citation (Scopus)

Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser diffraction

Oroguchi, T., Yoshidome, T., Yamamoto, T. & Nakasako, M., 2018 May 28, (Accepted/In press) In : Nano Letters.

Research output: Contribution to journalArticle

5 Citations (Scopus)

Shot-by-shot characterization of focused X-ray free electron laser pulses

Kobayashi, A., Sekiguchi, Y., Oroguchi, T., Yamamoto, M. & Nakasako, M., 2018 Dec 1, In : Scientific Reports. 8, 1, 831.

Research output: Contribution to journalArticle

10 Citations (Scopus)
2017
4 Citations (Scopus)

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging

Kameda, H., Usugi, S., Kobayashi, M., Fukui, N., Lee, S., Hongo, K., Mizobata, T., Sekiguchi, Y., Masaki, Y., Kobayashi, A., Oroguchi, T., Nakasako, M., Takayama, Y., Yamamoto, M. & Kawata, Y., 2017 Jan 1, In : Journal of Biochemistry. 161, 1, p. 55-65 11 p.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Controlled Terahertz Birefringence in Stretched Poly(lactic acid) Films Investigated by Terahertz Time-Domain Spectroscopy and Wide-Angle X-ray Scattering

Iwasaki, H., Nakamura, M., Komatsubara, N., Okano, M., Nakasako, M., Sato, H. & Watanabe, S., 2017 Jul 20, In : Journal of Physical Chemistry B. 121, 28, p. 6951-6957 7 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)
5 Citations (Scopus)
2016

Blue light-excited light-oxygen-voltage-sensing domain 2 (LOV2) triggers a rearrangement of the kinase domain to induce phosphorylation activity in arabidopsis phototropin

Oide, M., Okajima, K., Kashojiya, S., Takayama, Y., Oroguchi, T., Hikima, T., Yamamoto, M. & Nakasako, M., 2016 Sep 16, In : Journal of Biological Chemistry. 291, 38, p. 19975-19984 10 p.

Research output: Contribution to journalArticle

5 Citations (Scopus)
21 Citations (Scopus)
20 Citations (Scopus)

Specimen preparation for cryogenic coherent X-ray diffraction imaging of biological cells and cellular organelles by using the X-ray free-electron laser at SACLA

Kobayashi, A., Sekiguchi, Y., Oroguchi, T., Okajima, K., Fukuda, A., Oide, M., Yamamoto, M. & Nakasako, M., 2016 Jul 1, In : Journal of Synchrotron Radiation. 23, 4, p. 975-989 15 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA

Kobayashi, A., Sekiguchi, Y., Takayama, Y., Oroguchi, T., Shirahama, K., Torizuka, Y., Manoda, M., Nakasako, M. & Yamamoto, M., 2016 May 1, In : Review of Scientific Instruments. 87, 5, 053109.

Research output: Contribution to journalArticle

15 Citations (Scopus)
2015
8 Citations (Scopus)

Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser

Takayama, Y., Inui, Y., Sekiguchi, Y., Kobayashi, A., Oroguchi, T., Yamamoto, M., Matsunaga, S. & Nakasako, M., 2015, In : Plant and Cell Physiology. 56, 7, p. 1272-1286 15 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

Cryogenic coherent x-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA

Oroguchi, T., Sekiguchi, Y., Kobayashi, A., Masaki, Y., Fukuda, A., Hashimoto, S., Nakasako, M., Ichikawa, Y., Kurumizaka, H., Shimizu, M., Inui, Y., Matsunaga, S., Kato, T., Namba, K., Yamaguchi, K., Kuwata, K., Kameda, H., Fukui, N., Kawata, Y., Kameshima, T. & 3 others, Takayama, Y., Yonekura, K. & Yamamoto, M., 2015 Jul 29, In : Journal of Physics B: Atomic, Molecular and Optical Physics. 48, 18

Research output: Contribution to journalArticle

7 Citations (Scopus)

Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects

Takayama, Y., Maki-Yonekura, S., Oroguchi, T., Nakasako, M. & Yonekura, K., 2015 Jan 28, In : Scientific Reports. 5, 8074.

Research output: Contribution to journalArticle

15 Citations (Scopus)

Structure of a thermophilic F<inf>1</inf>-ATPase inhibited by an ε-subunit: Deeper insight into the ε-inhibition mechanism

Shirakihara, Y., Shiratori, A., Tanikawa, H., Nakasako, M., Yoshida, M. & Suzuki, T., 2015 Aug 1, In : FEBS Journal. 282, 15, p. 2895-2913 19 p.

Research output: Contribution to journalArticle

47 Citations (Scopus)
2014

Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging

Kobayashi, A., Sekiguchi, Y., Takayama, Y., Oroguchi, T. & Nakasako, M., 2014 Nov 17, In : Optics Express. 22, 23, p. 27892-27909 18 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Data processing software suite SITENNO for coherent X-ray diffraction imaging using the X-ray free-electron laser SACLA

Sekiguchi, Y., Oroguchi, T., Takayama, Y. & Nakasako, M., 2014 May, In : Journal of Synchrotron Radiation. 21, 3, p. 600-612 13 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)

IDATEN and G-SITENNO: GUI-assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA

Sekiguchi, Y., Yamamoto, M., Oroguchi, T., Takayama, Y., Suzuki, S. & Nakasako, M., 2014 Nov 1, In : Journal of Synchrotron Radiation. 21, 6, p. 1378-1383 6 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Light-induced conformational changes of LOV1 (light oxygen voltage-sensing domain 1) and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin

Okajima, K., Aihara, Y., Takayama, Y., Nakajima, M., Kashojiya, S., Hikima, T., Oroguchi, T., Kobayashi, A., Sekiguchi, Y., Yamamoto, M., Suzuki, T., Nagatani, A., Nakasako, M. & Tokutomi, S., 2014 Jan 3, In : Journal of Biological Chemistry. 289, 1, p. 413-422 10 p.

Research output: Contribution to journalArticle

27 Citations (Scopus)

Single-shot three-dimensional structure determination of nanocrystals with femtosecond X-ray free-electron laser pulses

Xu, R., Jiang, H., Song, C., Rodriguez, J. A., Huang, Z., Chen, C. C., Nam, D., Park, J., Gallagher-Jones, M., Kim, S., Kim, S., Suzuki, A., Takayama, Y., Oroguchi, T., Takahashi, Y., Fan, J., Zou, Y., Hatsui, T., Inubushi, Y., Kameshima, T. & 9 others, Yonekura, K., Tono, K., Togashi, T., Sato, T., Yamamoto, M., Nakasako, M., Yabashi, M., Ishikawa, T. & Miao, J., 2014 Jun 5, In : Nature communications. 5, 4061.

Research output: Contribution to journalArticle

65 Citations (Scopus)
2013

Application of empirical hydration distribution functions around polar atoms for assessing hydration structures of proteins

Matsuoka, D. & Nakasako, M., 2013 Jan 1, In : Chemical Physics. 419, p. 59-64 6 p.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Coherent diffraction imaging analysis of shape-controlled nanoparticles with focused hard X-ray free-electron laser pulses

Takahashi, Y., Suzuki, A., Zettsu, N., Oroguchi, T., Takayama, Y., Sekiguchi, Y., Kobayashi, A., Yamamoto, M. & Nakasako, M., 2013 Dec 11, In : Nano Letters. 13, 12, p. 6028-6032 5 p.

Research output: Contribution to journalArticle

45 Citations (Scopus)

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging

Nakasako, M., Takayama, Y., Oroguchi, T., Sekiguchi, Y., Kobayashi, A., Shirahama, K., Yamamoto, M., Hikima, T., Yonekura, K., Maki-Yonekura, S., Kohmura, Y., Inubushi, Y., Takahashi, Y., Suzuki, A., Matsunaga, S., Inui, Y., Tono, K., Kameshima, T., Joti, Y. & Hoshi, T., 2013 Sep 1, In : Review of Scientific Instruments. 84, 9, 093705.

Research output: Contribution to journalArticle

33 Citations (Scopus)
30 Citations (Scopus)
2011
9 Citations (Scopus)
26 Citations (Scopus)

Light-induced movement of the LOV2 domain in an Asp720Asn mutant LOV2-kinase fragment of arabidopsis phototropin 2

Takayama, Y., Nakasako, M., Okajima, K., Iwata, A., Kashojiya, S., Matsui, Y. & Tokutomi, S., 2011 Feb 22, In : Biochemistry. 50, 7, p. 1174-1183 10 p.

Research output: Contribution to journalArticle

18 Citations (Scopus)

New monoclinic form of bovine pancreatic ribonuclease A from a salt solution and comparison of intermolecular interactions in ribonucleases A

Takusagawa, H., Yamamura, S., Endo, S., Sugawara, Y., Inagaki, T. & Nakasako, M., 2011 Mar 15, In : Journal of Crystal Growth. 319, 1, p. 49-56 8 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2010
9 Citations (Scopus)

Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface

Serve, O., Kamiya, Y., Maeno, A., Nakano, M., Murakami, C., Sasakawa, H., Yamaguchi, Y., Harada, T., Kurimoto, E., Yagi-Utsumi, M., Iguchi, T., Inaba, K., Kikuchi, J., Asami, O., Kajino, T., Oka, T., Nakasako, M. & Kato, K., 2010 Feb, In : Journal of Molecular Biology. 396, 2, p. 361-374 14 p.

Research output: Contribution to journalArticle

48 Citations (Scopus)

Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus

Nakasako, M., Maeno, A., Kurimoto, E., Harada, T., Yamaguchi, Y., Oka, T., Takayama, Y., Iwata, A. & Kato, K., 2010 Aug 17, In : Biochemistry. 49, 32, p. 6953-6962 10 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)
21 Citations (Scopus)
2009

Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis

Matsuoka, D. & Nakasako, M., 2009 Aug 13, In : Journal of Physical Chemistry B. 113, 32, p. 11274-11292 19 p.

Research output: Contribution to journalArticle

30 Citations (Scopus)
2008

Crystallization and preliminary X-ray diffraction anaylsis of the LOV1 domains of phototropin 1 and 2 from Arabidopsis thaliana

Nakasako, M., Hirata, M., Shimizu, N., Hosokawa, S., Matsuoka, D., Oka, T., Yamamoto, M. & Tokutomi, S., 2008 Jul 16, In : Acta Crystallographica Section F: Structural Biology and Crystallization Communications. 64, 7, p. 617-621 5 p.

Research output: Contribution to journalArticle

1 Citation (Scopus)
2 Citations (Scopus)

Structural Basis of the LOV1 Dimerization of Arabidopsis Phototropins 1 and 2

Nakasako, M., Zikihara, K., Matsuoka, D., Katsura, H. & Tokutomi, S., 2008 Sep 5, In : Journal of Molecular Biology. 381, 3, p. 718-733 16 p.

Research output: Contribution to journalArticle

83 Citations (Scopus)
2007

Crystal structures of blasticidin S deaminase (BSD): Implications for dynamic properties of catalytic zinc

Kumasaka, T., Yamamoto, M., Furuichi, M., Nakasako, M., Teh, A. H., Kimura, M., Yamaguchi, I. & Ueki, T., 2007 Dec 21, In : Journal of Biological Chemistry. 282, 51, p. 37103-37111 9 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)
2006

A fluorescent antibiotic resistance marker for rapid production of transgenic rice plants

Ochiai-Fukuda, T., Takahashi-Ando, N., Ohsato, S., Igawa, T., Kadokura, K., Hamamoto, H., Nakasako, M., Kudo, T., Shibata, T., Yamaguchi, I. & Kimura, M., 2006 Apr 20, In : Journal of Biotechnology. 122, 4, p. 521-527 7 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Resistance buster compounds for MBI-D insensitive rice blast fungus - Inquiry on effective compounds among derivatives of MBI-D fungicides

Kurahashi, Y., Kagabu, S., Yamada, N., Mitsugi, Y., Shimizu, M., Nakasako, M. & Yamaguchi, I., 2006 Jun 5, In : Journal of Pesticide Science. 31, 2, p. 85-94 10 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)
2005

Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten

Nakasako, M., Oka, T., Mashumo, M., Takahashi, H., Shimada, I., Yamaguchi, Y., Kato, K. & Arata, Y., 2005 Aug 19, In : Journal of Molecular Biology. 351, 3, p. 627-640 14 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Hydrogen-bond patterns in the hydration structure of a protein

Yokomizo, T., Nakasako, M., Yamazaki, T., Shindo, H. & Higo, J., 2005 Jan 11, In : Chemical Physics Letters. 401, 4-6, p. 332-336 5 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)

Light-induced global structural changes in phytochrome A regulating photomorphogenesis in plants

Nakasako, M., Iwata, T., Inoue, K. & Tokutomi, S., 2005 Jan 1, In : FEBS Journal. 272, 2, p. 603-612 10 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Patterns and networks of hydrogen-bonds in the hydration structure of human lysozyme

Yokomizo, T., Higo, J. & Nakasako, M., 2005 Jul 10, In : Chemical Physics Letters. 410, 1-3, p. 31-35 5 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)