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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