論文 - 苙口　友隆

Internal dynamics of multidomain protein as revealed by an optimized neutron spin echo measurement and all-atom molecular dynamics simulation

Rintaro Inoue*, Tomotaka Oroguchi*, Takashi Oda*, Bela Farago, Anne Martel, Lionel Porcar, Mamoru Sato, Masaaki Sugiyama (*equally contributed)

Physical Review Research 5 （ 4 ） 043154 2023年12月

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Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser

Amane Kobayashi, Yuki Takayama, Takeshi Hirakawa, Koji Okajima, Mao Oide, Tomotaka Oroguchi, Yayoi Inui, Masaki Yamamoto, Sachihiro Matsunaga, Masayoshi Nakasako

Scientific Reports 11 （ 1 ） 3877 2021年12月

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Domain organization in plant blue-light receptor phototropin2 of arabidopsis thaliana studied by small-angle x-ray scattering

Masayoshi Nakasako, Mao Oide, Yuki Takayama, Tomotaka Oroguchi, Koji Okajima

International journal of molecular sciences 21 （ 18 ） 6638 2020年09月

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Assessment of force field accuracy using cryogenic electron microscopy data of hyper-thermostable glutamate dehydrogenase

Tomotaka Oroguchi, Mao Oide, Taiki Wakabayashi, Masayoshi Nakasako

Journal of Physical Chemistry B 124 （ 39 ） 8479 - 8494 2020年10月

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

Mao Oide, Takayuki Kato, Tomotaka Oroguchi, Masayoshi Nakasako

FEBS Journal 287 （ 16 ） 3472 - 3493 2020年08月

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

Mao Oide, Takaaki Hikima, Tomotaka Oroguchi, Takayuki Kato, Yuhki Yamaguchi, Shizue Yoshihara, Masaki Yamamoto, Masayoshi Nakasako, Koji Okajima

FEBS Journal 287 （ 8 ） 1612 - 1625 2020年04月

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Dipole-dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic Stokes shift of lysozyme

Asahi Fukuda, Tomotaka Oroguchi, Masayoshi Nakasako

Biochimica et Biophysica Acta - General Subjects 1864 （ 2 ） 129406 2020年02月

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Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments

Toru Ekimoto, Yuichi Kokabu, Tomotaka Oroguchi, Mitsunori Ikeguchi

Biophysics and physicobiology 16   377 - 390 2019年

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

Amane Kobayashi, Yuki Takayama, Koji Okajima, Mao Oide, Takahiro Yamamoto, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Yoshiki Kohmura, Masaki Yamamoto, Takahiko Hoshi, Yasufumi Torizuka

Journal of Synchrotron Radiation 25 （ 6 ） 1803 - 1818 2018年11月

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

Mao Oide, Yuki Sekiguchi, Asahi Fukuda, Koji Okajima, Tomotaka Oroguchi, Masayoshi Nakasako

Journal of Synchrotron Radiation 25 （ 5 ） 1379 - 1388 2018年09月

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

Tomotaka Oroguchi, Takashi Yoshidome, Takahiro Yamamoto, Masayoshi Nakasako

Nano Letters 18 （ 8 ） 5192 - 5197 2018年08月

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

Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Masaki Yamamoto, Masayoshi Nakasako

Scientific Reports 8 （ 1 ） 831 2018年12月

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

Mao Oide, Koji Okajima, Hirofumi Nakagami, Takayuki Kato, Yuki Sekiguchi, Tomotaka Oroguchi, Takaaki Hikima, Masaki Yamamoto, Masayoshi Nakasako

Journal of Biological Chemistry 293 （ 3 ） 963 - 972 2018年01月

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Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acids side chains in molecular dynamics simulation

Tomotaka Oroguchi, Masayoshi Nakasako

Scientific Reports 7 （ 1 ） 15859 2017年12月

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A protocol for searching most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting relationship between convergence of retrieved phase and success of calculation

Yuki Sekiguchi, Saki Hashimoto, Amane Kobayashi, Tomotaka Oroguchi, Masayoshi Nakasako

Journal of Synchrotron Radiation 24 （ 5 ） 1024 - 1038 2017年09月

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

Hiroshi Kameda, Sayaka Usugi, Mana Kobayashi, Naoya Fukui, Seki Lee, Kunihiro Hongo, Tomohiro Mizobata, Yuki Sekiguchi, Yu Masaki, Amane Kobayashi, Tomotaka Oroguchi, Masayoshi Nakasako, Yuki Takayama, Masaki Yamamoto, Yasushi Kawata

Journal of Biochemistry 161 （ 1 ） 55 - 65 2017年01月

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Blue-light-excited LOV2 triggers a rearrangement of the kinase domain to induce phosphorylation activity in Arabidopsis phototropin1

Mao Oide, Koji Okajima, Sachiko Kashojiya, Yuki Takayama, Tomotaka Oroguchi, Takaaki Hikima, Masaki Yamamoto, Masayoshi Nakasako

Journal of Biological Chemistry 291 （ 38 ） 19975 - 19984 2016年09月

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

Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Koji Okajima, Asahi Fukuda, Mao Oide, Masaki Yamamoto, Masayoshi Nakasako

Journal of Synchrotron Radiation 23 （ 4 ） 975 - 989 2016年07月

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Changes in hydration structure are necessary for collective motions of a multi-domain protein

Tomotaka Oroguchi, Masayoshi Nakasako

Scientific Reports 6   26302 2016年03月

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

Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, Keiya Shirahama, Yasufumi Torizuka, Masahiro Manoda, Masayoshi Nakasako, Masaki Yamamoto

Review of Scientific Instruments 87 （ 5 ） 053109 2016年03月

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Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate analysis

Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako

Journal of Synchrotron Radiation 23   312 - 323 2015年

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Classification of projection images of proteins with structural polymorphism by manifold; A simulation study for X-ray free-electron laser diffraction imaging

Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

Physical Review E 92 （ 3 ） 032710 2015年09月

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

Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi, Yu Masaki, Asahi Fukuda, Saki Hashimoto, Masayoshi Nakasako, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu, Yayoi Inui, Sachihiro Matsunaga, Takayuki Kato, Keiichi Namba, Keiichi Yamaguchi, Kazuo Kuwata, Hiroshi Kameda, Naoya Fukui, Yasushi Kawata, Takashi KameshimaYuki Takayama, Koji Yonekura, Masaki Yamamoto

Journal of Physics B: Atomic Molecular and Optical Physics 48 （ 18 ） 184003 2015年07月

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

Yuki Takayama, Yayoi Inui Yuki Sekiguchi1, Amane Kobayashi, Tomotaka Oroguchi, Masaki Yamamoto, Sachihiro Matsunaga, Masayoshi Nakasako

Plant Cell Physiology 56 （ 7 ） 1272 - 1287 2015年07月

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

Yuki Takayama, Saori Maki-Yonekura, Tomotaka Oroguchi, Masayoshi Nakasako, Koji Yonekura

Scientific Reports 5   8074 2015年01月

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

Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, Masayoshi Nakasako

Optics Express 22 （ 23 ） 27892 - 27909 2014年11月

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

Yuki Sekiguchi, Masaki Yamamoto, Tomotaka Oroguchi, Yuki Takayama, Shigeyuki Suzuki, Masayoshi Nakasako

Journal of Synchrotron Radiation 21 （ 6 ） 1378 - 1383 2014年11月

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

Rui Xu, Huaidong Jiang, Changyong Song, Jose A. Rodriguez, Zhifeng Huang, Chien-Chun Chen, Daewoong Nam, Jaehyun Park, Marcus Gallagher-Jones, Sangsoo Kim, Sunam Kim, Akihiro Suzuki, Yuki Takayama, Tomotaka Oroguchi, Yukio Takahashi, Jiadong Fan, Yunfei Zou, Takaki Hatsui, Yuichi Inubushi, Takashi Kameshima, Koji Yonekura, Kensuke Tono, Tadashi Togashi,Takahiro Sato, Masaki Yamamoto, Masayoshi Nakasako, Makina Yabashi, Tetsuya Ishikawa, Jianwei Miao

Nature Communications 5   4061 2014年06月

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

Yuki Sekiguchi, Tomotaka Oroguchi, Yuki Takayama, Masayoshi Nakasako

Journal of Synchrotron Radiation 21 （ 3 ） 600 - 612 2014年03月

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Light-induced conformational changes of LOV (Light Oxygen Voltage-sensing domain) 1 and LOV2 relative to the kinase domain and regulation of kinase activity in Chlamydomonas phototropin

Koji Okajima, Yusuke Aihara, Yuki Takayama, Mihoko Nakajima, Sachiko Kashojiya, Takaaki Hikima, Tomotaka OroguchiAmane Kobayashi, Yuki Sekiguchi, Masaki Yamamoto, Tomomi Suzuki, Akira Nagatani, Masayoshi Nakasako, Satoru Tokutomi

Journal of Biological Chemistry 289 （ 1 ） 413 - 422 2014年01月

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Coherent Diffraction Imaging Analysis of Shape-Controlled Nanoparticles with Focused Hard X-ray Free-Electron Laser Pulses

Yukio Takahashi, Akihiro Suzuki, Nobuyuki Zettsu, Tomotaka Oroguchi, Yuki Takayama, Yuki Sekiguchi, Amane Kobayashi, Masaki Yamamoto, Masayoshi Nakasako

Nano Letters 13 （ 12 ） 6028 - 6032 2013年12月

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

Masayoshi Nakasako, Yuki Takayama, Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi, Keiya Shirahama, Masaki Yamamoto, Takaaki Hikima, Koji Yonekura, Saori Maki-Yonekura, Yoshiki Kohmura, Yuichi Inubushi, Yukio Takahashi , Akihiro Suzuki, Sachihiro Matsunaga, Yayoi Inui, Kensuke Tono, Takashi Kameshima, Yasumasa Joti, Takahiko Hoshi

Review of Scientific Instruments 84 （ 9 ） 093705 2013年09月

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Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free electron laser diffraction imaging

Tomotaka Oroguchi, Masayoshi Nakasako

Physical Review E 87 （ 2 ） 022712 2013年02月

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MD-SAXS method with nonspherical boundaries

Tomotaka Oroguchi, Mitsunori Ikeguchi

Chemical Physics Letter 541   117 - 121 2012年07月

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Towards the structural characterization of intrinsically disordered proteins by SAXS and MD simulation

Tomotaka Oroguchi, Mitsunori Ikeguchi, Mamoru Sato

Journal of Physics: Conference Series 272 （ 1 ） 012005 2011年

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Fission yeast Swi5-Sfr1 protein complex, an activator of Rad51 recombinase, forms an extremely elongated dogleg-shaped structure

Yoichi Kokabu, Yasuto Murayama, Naoyuki Kuwabara, Tomotaka Oroguchi, Hiroshi Hashimoto, Yasuhiro Tsutsui, Naohito Nozaki, Satoko Akashi, Satoru Unzai, Toshiyuki Shimizu, Hitoshi Iwasaki, Matmoru Sato, Mitsunori Ikeguchi

Journal of Biological Chemistry 286 （ 50 ） 43569 - 43576 2011年12月

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Mechanism of the conformational change of the F1-ATPase beta subunit revealed by free energy simulations

Yoko Ito, Tomotaka Oroguchi, Mitsunori Ikeguchi

Journal of American Chemical Society 133 （ 10 ） 3372 - 3380 2011年03月

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Effects of ionic strength on SAXS data for proteins revealed by molecular dynamics simulations

Tomotaka Oroguchi, Mitsunori Ikeguchi

Journal of Chemical Physics 134 （ 2 ） 025102 2011年01月

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Structural and functional analysis of the intrinsic inhibitor subunit epsilon of F1-ATPase from photosynthetic organisms

Hiromasa Yagi, Hiroki Konno, Tomoe Murakami-Fuse, Atsuko Isu, Tomotaka Oroguchi, Hideo Akutsu, Mitsunori Ikeguchi, Toru Hisabori

Biochemical Journal 425 （ 1 ） 85 - 94 2010年01月

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Intrinsic dynamics of restriction endonuclease EcoO109I studied by molecular dynamics and X-ray scattering data analysis

Tomotaka Oroguchi, Hiroshi Hashimoto, Toshiyuki Shimizu, Mamoru Sato, Mitsunori Ikeguchi

Biophysical Journal 96 （ 7 ） 2808 - 2822 2009年04月

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Unfolding pathways of goat alpha-lactalbumin as revealed in multiple alignment of molecular dynamics trajectories

Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera

Journal of Molecular Biology 371 （ 5 ） 1354 - 1364 2007年08月

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The equilibrium unfolding intermediate observed at pH 4 and its relationship with the kinetic folding intermediates in green fluorescent protein

Sawako Enoki, Kosuke Maki, Tomonao Inobe, Kazunobu Takahashi, Kiyoto Kamagata, Tomotaka Oroguchi, Hiroyasu Nakatani, Katsuaki Tomoyori, Kuwajima Kunihiro

Journal of Molecular Biology 361 （ 5 ） 969 - 982 2006年09月

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Atomically detailed description of the unfolding of goat alpha-lactalbumin by combined use of experiments and simulations

Tomotaka Oroguchi, Mitsunori Ikeguchi, Kimiko Saeki, Kiyoto Kamagata, Yoriko Sawano, Masaru Tanokura, Akinori Kidera, Kunihiro Kuwajima

Journal of Molecular Biology 354 （ 1 ） 164 - 172 2005年11月

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