Publications by authors named "Tomotaka Oroguchi"

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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

Sci Rep· February 2021

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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

J Phys Chem B· October 2020

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Domain Organization in Plant Blue-Light Receptor Phototropin2 of Studied by Small-Angle X-ray Scattering.
Masayoshi Nakasako, Mao Oide, Yuki Takayama, Tomotaka Oroguchi, Koji Okajima

Int J Mol Sci· September 2020

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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 J· August 2020

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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

FEBS J· April 2020

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Methods and application of coherent X-ray diffraction imaging of noncrystalline particles.
Masayoshi Nakasako, Amane Kobayashi, Yuki Takayama, Kenta Asakura, Mao Oide, Tomotaka Oroguchi

Biophys Rev· April 2020

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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

Biochim Biophys Acta Gen Subj· February 2020

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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

Biophys Physicobiol· November 2019

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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, Tomotaka Oroguchi

J Synchrotron Radiat· November 2018

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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

J Synchrotron Radiat· September 2018

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Growth of Cuprous Oxide Particles in Liquid-Phase Synthesis Investigated by X-ray Laser Diffraction.
Tomotaka Oroguchi, Takashi Yoshidome, Takahiro Yamamoto, Masayoshi Nakasako

Nano Lett· August 2018

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Blue light-excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from .
Mao Oide, Koji Okajima, Hirofumi Nakagami, Takayuki Kato, Yuki Sekiguchi, Tomotaka Oroguchi

J Biol Chem· January 2018

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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

Sci Rep· January 2018

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Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation.
Tomotaka Oroguchi, Masayoshi Nakasako

Sci Rep· November 2017

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A protocol for searching the most probable phase-retrieved maps in coherent X-ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation.
Yuki Sekiguchi, Saki Hashimoto, Amane Kobayashi, Tomotaka Oroguchi, Masayoshi Nakasako

J Synchrotron Radiat· September 2017

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Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.
Hiroshi Kameda, Sayaka Usugi, Mana Kobayashi, Naoya Fukui, Seki Lee, Tomotaka Oroguchi

J Biochem· January 2017

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Blue Light-excited Light-Oxygen-Voltage-sensing Domain 2 (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

J Biol Chem· September 2016

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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.
Amane Kobayashi, Yuki Sekiguchi, Tomotaka Oroguchi, Koji Okajima, Asahi Fukuda

J Synchrotron Radiat· July 2016

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Changes in hydration structure are necessary for collective motions of a multi-domain protein.
Tomotaka Oroguchi, Masayoshi Nakasako

Sci Rep· May 2016

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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

Rev Sci Instrum· May 2016

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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

J Synchrotron Radiat· January 2016

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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

Phys Rev E Stat Nonlin Soft Matter Phys· September 2015

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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 Sekiguchi, Amane Kobayashi, Tomotaka Oroguchi

Plant Cell Physiol· July 2015

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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

Sci Rep· January 2015

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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

Opt Express· November 2014

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