Oroguchi Tomotaka 苙口友隆

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Tomotaka Oroguchi 苙口友隆

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Researcher Number	90589821
Other IDs
Affiliation (Current)	2025: 慶應義塾大学, 理工学部(矢上), 講師
Affiliation (based on the past Project Information) *help	2017 – 2023: 慶應義塾大学, 理工学部(矢上), 講師 2014 – 2015: 慶應義塾大学, 理工学部, 講師 2012 – 2014: 慶應義塾大学, 理工学部, 助教
Review Section/Research Field	Principal Investigator Biological physics/Chemical physics/Soft matter physics / Basic Section 13040:Biophysics, chemical physics and soft matter physics-related / Biomolecular chemistry and related fields / Science and Engineering / Biological Sciences Except Principal Investigator Broad Section B
Keywords	Principal Investigator 分子動力学シミュレーション / 水和構造 / 溶液X線散乱 / 生体分子 / MDシミュレーション / 構造アンサンブル / 蛋白質 / 溶媒和自由エネルギー / X線散乱回折実験 / 蛋白質ダイナミックス … More / 分子力場 / 機能的構造揺らぎ / 自由エネルギー地形 / 動的構造 / 水素結合 / 蛋白質分子力場 / X線溶液散乱 / 構造アンサンブル最適化 / 溶液Ｘ線散乱 / 情報量空間 / 構造アンサンブル最適化法 / 蛋白質-水分子間相互作用 / 蛋白質構造の自由エネルギー地形 / 蛋白質分子 / X線回折散乱実験 / 生体分子の機能発揮機構 / ベイズ統計 / 溶液散乱実験 / 機能的構造変化 / 電子－電子二重共鳴計測 / 中性子溶液散乱 / 蛋白質の機能的構造揺らぎ / 分子クラウディング環境 / 電子―電子二重共鳴計測 / 溶液X戦散乱 / 溶液中性子散乱 / 蛋白質ダイナミクス / 分子クラウディング / グルタミン酸脱水素酵素 / ダイナミックス / 低温X線結晶構造解析 / 水素結合ネットワーク / 構造サンプリング法 / マルチスケール構造サンプリング / 原子間力顕微鏡 / DNA結合蛋白質 / 天然変性領域 / MD-SAXS / 構造サンプリング / 核磁気共鳴法 / 天然変性タンパク質 … More Except Principal Investigator 蛋白質ダイナミクス / 租視化分子動力学計算 / 中性子準弾性散乱 / MD連携解析 / 蛋白質階層間連携ダイナミクス / 蛋白質重水素化 / 階層関連ダイナミクス / 分子動力学計算 / ドメイン選択重水素化 / 新世代中性子構造生物学 / 計算機連携解析 / ドメインライゲーション / タンパク質重水素化 / 中性子溶液散乱 / 階層間連携ダイナミクス / 分子動力学シミュレーション / 重水素化 / 生体高分子ダイナミクス / 中性子散乱 Less

Development of force field considering hydrogen-bond directionalityPrincipal Investigator
- Principal Investigator
  
  Oroguchi Tomotaka
- Project Period (FY)
  2021 – 2023
- Research Category
  
  Grant-in-Aid for Scientific Research (C)
- Review Section
  
  Basic Section 13040:Biophysics, chemical physics and soft matter physics-related
- Research Institution
  Keio University
Neutron Structural Biology for New Generation
- Principal Investigator
  
  Sugiyama Masaaki
- Project Period (FY)
  2018 – 2022
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Review Section
  
  Broad Section B
- Research Institution
  Kyoto University
Visualization of protein dynamics in molecular crowding environmentPrincipal Investigator
- Principal Investigator
  
  Oroguchi Tomotaka
- Project Period (FY)
  2017 – 2019
- Research Category
  
  Grant-in-Aid for Challenging Research (Exploratory)
- Research Field
  
  Biomolecular chemistry and related fields
- Research Institution
  Keio University
Elucidation of thermodynamic roles of hydration structure in protein functionsPrincipal Investigator
- Principal Investigator
  
  Oroguchi Tomotaka
- Project Period (FY)
  2017 – 2020
- Research Category
  
  Grant-in-Aid for Young Scientists (A)
- Research Field
  
  Biological physics/Chemical physics/Soft matter physics
- Research Institution
  Keio University
X線回折散乱実験と分子シミュレーションを用いた生体分子の動的構造の解析Principal Investigator
- Principal Investigator
  
  苙口友隆
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Science and Engineering
- Research Institution
  Keio University
Role of water molecules in biomolecular functions and interactionsPrincipal Investigator
- Principal Investigator
  
  Tomotaka Oroguchi
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Young Scientists (B)
- Research Field
  
  Biological physics/Chemical physics/Soft matter physics
- Research Institution
  Keio University
天然変性蛋白質の動的構造及び基質認識機構の原子レベルでの解明Principal Investigator
- Principal Investigator
  
  苙口友隆
- Project Period (FY)
  2012 – 2013
- Research Category
  
  Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
- Review Section
  
  Biological Sciences
- Research Institution
  Keio University

All 2023 2022 2021 2020 2019 2018 2017 2016 2015 2014 2013 2012 Other

All Journal Article Presentation

[Journal Article] Internal dynamics of multidomain protein as revealed by an optimized neutron spin echo measurement and all-atom molecular dynamics simulation2023
- Author(s)
  Inoue Rintaro、Oroguchi Tomotaka、Oda Takashi、Farago Bela、Martel Anne、Porcar Lionel、Sato Mamoru、Sugiyama Masaaki
- Journal Title
  
  Physical Review Research
  
  Volume: 5 Issue: 4 Pages: 043154-043154
- DOI
  10.1103/physrevresearch.5.043154
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K06527, KAKENHI-PROJECT-21K03489, KAKENHI-PROJECT-19KK0071
[Journal Article] Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser2021
- Author(s)
  Kobayashi Amane、Takayama Yuki、Hirakawa Takeshi、Okajima Koji、Oide Mao、Oroguchi Tomotaka、Inui Yayoi、Yamamoto Masaki、Matsunaga Sachihiro、Nakasako Masayoshi
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 3877-3877
- DOI
  10.1038/s41598-021-83401-y
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-19H05783, KAKENHI-PROJECT-19H03259, KAKENHI-PROJECT-20K14434, KAKENHI-PLANNED-20H05911, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-21H01050, KAKENHI-PROJECT-21K03489
[Journal Article] Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy2020
- Author(s)
  Oide Mao、Kato Takayuki、Oroguchi Tomotaka、Nakasako Masayoshi
- Journal Title
  
  The FEBS Journal
  
  Volume: - Issue: 16 Pages: 3472-3493
- DOI
  10.1111/febs.15224
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-18J11653, KAKENHI-PROJECT-17K19209
[Journal Article] Dipole?dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme2020
- Author(s)
  Fukuda Asahi、Oroguchi Tomotaka、Nakasako Masayoshi
- Journal Title
  
  Biochimica et Biophysica Acta (BBA) - General Subjects
  
  Volume: 1864 Issue: 2 Pages: 129406-129406
- DOI
  10.1016/j.bbagen.2019.07.015
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-17K19209
[Journal Article] Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data of Hyper-thermostable Glutamate Dehydrogenase2020
- Author(s)
  Oroguchi Tomotaka、Oide Mao、Wakabayashi Taiki、Nakasako Masayoshi
- Journal Title
  
  The Journal of Physical Chemistry B
  
  Volume: 124 Issue: 39 Pages: 8479-8494
- DOI
  10.1021/acs.jpcb.0c04464
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-18H05229
[Journal Article] Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments2019
- Author(s)
  Ekimoto T, Kokabu Y, Oroguchi T, Ikeguchi M
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 16 Issue: 0 Pages: 377-390
- DOI
  10.2142/biophysico.16.0_377
- NAID
  130007752757
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-18H05426, KAKENHI-PROJECT-17K19209
[Journal Article] Molecular shape under far-red light and red light-induced association of Arabidopsis phytochrome B2019
- Author(s)
  Mao Oide, Takaaki Hikima, Tomotaka Oroguchi, Takayuki Kato, Yuhki Yamaguchi, Shizue Yoshihara, Masaki Yamamoto, Masayoshi Nakasako, Koji Okajima.
- Journal Title
  
  FEBS Journal
  
  Volume: 287 Issue: 8 Pages: 1612-1625
- DOI
  10.1111/febs.15095
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-18J11653, KAKENHI-PROJECT-17K19209
[Journal Article] Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser2018
- Author(s)
  Tomotaka Oroguchi, Takashi Yoshidome, Takahiro Yamamoto, Masayoshi Nakasako
- Journal Title
  
  Nano Letters
  
  Volume: 18 Issue: 8 Pages: 5192-5197
- DOI
  10.1021/acs.nanolett.8b02153
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PUBLICLY-17H05891, KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-17H04854
[Journal Article] Classification of ab initio models of proteins restored from small-angle X-ray scattering2018
- Author(s)
  Mao Oide, Yuki Sekiguchi, Asahi Fukuda, Koji Okajima, Tomotaka Oroguchi, Masayoshi Nakasako
- Journal Title
  
  Journal of Synchrotron Radiation
  
  Volume: 25 Issue: 5 Pages: 1379-1388
- DOI
  10.1107/s1600577518010342
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PUBLICLY-17H05891, KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-18J11653
[Journal Article] Diffraction apparatus and procedure in tomography X-ray diffraction imaging for biological cells at cryogenic temperature using synchrotron X-ray radiation2018
- Author(s)
  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 Title
  
  Journal of Synchrotron Radiation
  
  Volume: 25 Issue: 6 Pages: 1803-1818
- DOI
  10.1107/s1600577518012687
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-19K21186
[Journal Article] Blue-light excited LOV1 and LOV2 domains cooperatively regulate the kinase activity of full-length phototropin2 from Arabidopsis2018
- Author(s)
  M. Oide, K. Okajima, H. Nakagami, T. Kato, Y. Sekiguchi, T. Oroguchi, T. Hikima, M. Yamamoto and M. Nakasako
- Journal Title
  
  The Journal of Biological Chemistry
  
  Volume: 293 Issue: 3 Pages: 963-972
- DOI
  10.1074/jbc.ra117.000324
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PUBLICLY-17H05891, KAKENHI-PROJECT-17H04854
[Journal Article] Shot-by-shot characterization of focused X-ray free electron laser pulses2018
- Author(s)
  A. Kobayashi, Y. Sekiguchi, T. Oroguchi, M. Yamamoto and M. Nakasako
- Journal Title
  
  Shot-by-shot characterization of focused X-ray free electron laser pulses
  
  Volume: 8 Issue: 1 Pages: 831-831
- DOI
  10.1038/s41598-018-19179-3
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-15J01831
[Journal Article] Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acids side chains in molecular dynamics simulation2017
- Author(s)
  T. Oroguchi and M. Nakasako
- Journal Title
  
  Scientific Reports
  
  Volume: 7 Issue: 1 Pages: 15859-15859
- DOI
  10.1038/s41598-017-16203-w
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PUBLICLY-17H05891, KAKENHI-PROJECT-17H04854
[Journal Article] 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 calculation2017
- Author(s)
  Y. Sekiguchi, S. Hashimoto, A. Kobayashi, T. Oroguchi and M. Nakasako
- Journal Title
  
  Journal of Synchrotron Radiation
  
  Volume: 24 Issue: 5 Pages: 1024-1038
- DOI
  10.1107/s1600577517008396
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-17K19209, KAKENHI-PUBLICLY-17H05891, KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-17H04854, KAKENHI-PROJECT-15J01831
[Journal Article] Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging2017
- Author(s)
  H. Kameda, S. Usugi, M. Kobayashi, N. Fukui, S. Lee, K. Hongo, T. Mizobata, Y.　Sekiguchi, Y. Masaki, A. Kobayashi, T. Oroguchi, M. Nakasako, Y. Takayama, M. Yamamoto, and Y. Kawata
- Journal Title
  
  Journal of Biochemistry (Tokyo)
  
  Volume: １６１ Issue: 1 Pages: 55-65
- DOI
  10.1093/jb/mvw052
- NAID
  40021091513
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-16H02218, KAKENHI-PROJECT-15J01707, KAKENHI-PROJECT-15J01831, KAKENHI-PROJECT-16K21621, KAKENHI-PROJECT-17K19209, KAKENHI-PROJECT-17H04854
[Journal Article] Classification and assessment of retrieved electron density maps in coherent X-ray diffraction imaging using multivariate statistics2016
- Author(s)
  Y. Sekiguchi, T. Oroguchi and M. Nakasako
- Journal Title
  
  Journal of Synchrotron Radiation
  
  Volume: 23 Issue: 1 Pages: 312-323
- DOI
  10.1107/s1600577515018202
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-15H01647, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-15J01707, KAKENHI-PROJECT-26800227
[Journal Article] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser.2015
- Author(s)
  Takayama, Y., Inui, Y., Sekiguchi, Y., Kobayashi, A., Oroguchi, T., Yamamoto, M., Matsunaga, S., and Nakasako, M.
- Journal Title
  
  PLANT AND CELL PHYSIOLOGY
  
  Volume: 未定 Issue: 7 Pages: 1-15
- DOI
  10.1093/pcp/pcv032
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PUBLICLY-25114514, KAKENHI-PUBLICLY-25120726, KAKENHI-PROJECT-25891033, KAKENHI-PROJECT-26291067, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-15J01831, KAKENHI-PROJECT-26800227
[Journal Article] Signal-enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects2015
- Author(s)
  Y. Takayama, S. Maki-Yonekura, T. Oroguchi, M. Nakasako and K. Yonekura
- Journal Title
  
  Sci. Rep.
  
  Volume: 5 Issue: 1 Pages: 8074-8074
- DOI
  10.1038/srep08074
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-24657111, KAKENHI-PUBLICLY-25120725, KAKENHI-PROJECT-25891033, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-26800227
[Journal Article] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser2015
- Author(s)
  Yuki Takayama, Yayoi Inui Yuki Sekiguchi1, Amane Kobayashi, Tomotaka Oroguchi, Masaki Yamamoto, Sachihiro Matsunaga and Masayoshi Nakasako
- Journal Title
  
  PLANT CELL PHYSIOLOGY
  
  Volume: in press
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26800227
[Journal Article] Cryogenic coherent x-ray diffraction imaging for biological non-crystalline particles using the KOTOBUKI-1 diffraction apparatus at SACLA2015
- Author(s)
  Tomotaka Oroguchi, Yuki Sekiguchi, Amane Kobayashi,Yu Masaki, Asahi Fukuda, Saki Hashimoto, Masayoshi Nakasako, Yuichi Ichikawa, Hitoshi Kurumizaka, Mitsuhiro Shimizu et al.,
- Journal Title
  
  Journal of Physics B: Atomic, Molecular and Optical Physics
  
  Volume: 48 Issue: 18 Pages: 184003-184003
- DOI
  10.1088/0953-4075/48/18/184003
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-26430186, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-15J01707, KAKENHI-PROJECT-15J01831, KAKENHI-PROJECT-26800227, KAKENHI-PROJECT-25000013
[Journal Article] Coherent X-ray diffraction imaging of chloroplasts from Cyanidioschyzon merolae by using X-ray free electron laser2015
- Author(s)
  Yuki Takayama, Yayoi Inui Yuki Sekiguchi1, Amane Kobayashi, Tomotaka Oroguchi, Masaki Yamamoto, Sachihiro Matsunaga and Masayoshi Nakasako
- Journal Title
  
  PLANT CELL PHYSIOLOGY
  
  Volume: in press
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-26104535
[Journal Article] Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for X-ray free-electron laser diffraction imaging2015
- Author(s)
  T. Yoshidome, T. Oroguchi, M. Nakasako and M. Ikeguchi
- Journal Title
  
  Physical Review E
  
  Volume: 92 Issue: 3 Pages: 032710-032723
- DOI
  10.1103/physreve.92.032710
- Peer Reviewed / Acknowledgement Compliant / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-15H01647, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-26800227
[Journal Article] Dark-field phase retrieval under the constraint of the Friedel symmetry in coherent X-ray diffraction imaging2014
- Author(s)
  Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, and Masayoshi Nakasako
- Journal Title
  
  OPTICAL EXPRESS
  
  Volume: 22 Pages: 27892-27909
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-26104535
[Journal Article] Single shot three-dimensional imaging of high-index-faceted nanocrystals with femtosecond X-ray free electron laser pulses2014
- Author(s)
  R. Xu, H. Jiang, C. Song, Z. Huang, J. A. Rodriguez, C-C. Chen, D. Nam, J. Park, M. Gallagher-Jones, S. Kim, S. Kim, A. Suzuki, Y. Takayama, T. Oroguchi, Y. Takahashi, J. Fan, Y. Zou, T. Hatsui, Y. Inubushi, T. Kameshima, K. Yonekura et al.
- Journal Title
  
  Nat. Commun.
  
  Volume: 5 Issue: 1 Pages: 4061-4061
- DOI
  10.1038/ncomms5061
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-24657111, KAKENHI-PUBLICLY-25120725, KAKENHI-PROJECT-25891033, KAKENHI-PUBLICLY-26104535, KAKENHI-PROJECT-26800227
[Journal Article] IDATEN and G-SITENNO: GUI assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA2014
- Author(s)
  Yuki Sekiguchi, Masaki Yamamoto, Tomotaka Oroguchi, Yuki Takayama, Shigeyuki Suzuki and Masayoshi Nakasako
- Journal Title
  
  JOURNAL OF SYNCHROTRON RADIATION
  
  Volume: 21 Pages: 1378-1383
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PUBLICLY-26104535
[Journal Article] IDATEN and G-SITENNO: GUI assisted software for coherent X-ray diffraction imaging experiments and data analyses at SACLA2014
- Author(s)
  Yuki Sekiguchi, Masaki Yamamoto, Tomotaka Oroguchi, Yuki Takayama, Shigeyuki Suzuki and Masayoshi Nakasako
- Journal Title
  
  JOURNAL OF SYNCHROTRON RADIATION
  
  Volume: 21 Pages: 1378-1383
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26800227
[Journal Article] 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.2014
- Author(s)
  Okajima, K., Y. Aihara, Y. Takayama, M. Nakajima, S. Kashojiya, T. Hikima, T. Oroguchi, A. Kobayashi, Y. Sekiguchi, M. Yamamoto, T. Suzuki, A. Nagatani, M. Nakasako and S. Tokutomi
- Journal Title
  
  J. Biol. Chem
  
  Volume: 289 Issue: 1 Pages: 413-422
- DOI
  10.1074/jbc.m113.515403
- Peer Reviewed
- Data Source
  KAKENHI-ORGANIZER-22120001, KAKENHI-PLANNED-22120002, KAKENHI-PLANNED-22120005, KAKENHI-PROJECT-22244054, KAKENHI-PROJECT-23770040, KAKENHI-PUBLICLY-24113723, KAKENHI-PUBLICLY-25120725
[Journal Article] Signal enhancement and Patterson-search phasing for high-spatial-resolution coherent X-ray diffraction imaging of biological objects2014
- Author(s)
  Amane Kobayashi, Yuki Sekiguchi, Yuki Takayama, Tomotaka Oroguchi, and Masayoshi Nakasako
- Journal Title
  
  OPTICAL EXPRESS
  
  Volume: 22 Pages: 27892-27909
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-26800227
[Journal Article] 蛋白質水和構造の実験研究2013
- Author(s)
  中迫雅由、苙口友隆、高山裕貴、中島真、松井夕花
- Journal Title
  
  アンサンブル
  
  Volume: 15 Pages: 7-18
- NAID
  130004566739
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging2013
- Author(s)
  Masayoshi Nakasako, Yuki Takayama, Tomotaka Oroguchi, et al.
- Journal Title
  
  Review of Scientific Instruments
  
  Volume: 84 Issue: 9 Pages: 93705-93705
- DOI
  10.1063/1.4822123
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723, KAKENHI-PROJECT-24657111, KAKENHI-PUBLICLY-25120725, KAKENHI-PUBLICLY-25120726, KAKENHI-PROJECT-26291011
[Journal Article] Protein dynamics investigated by small-angle x-ray scattering and molecular dynamics simulations2013
- Author(s)
  Tomotaka Oroguchi, Mitsunori Ikeguchi, Mamoru Sato
- Journal Title
  
  日本結晶学会誌
  
  Volume: 55 Pages: 24-31
- NAID
  10031156002
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] コヒーレントX線回折イメージング構造解析理論の開発と展望2013
- Author(s)
  中迫雅由、苙口友隆、高山裕貴、小林周、児玉渉、坂本啓太、吉留崇、池口満徳
- Journal Title
  
  放射光
  
  Volume: 26 Pages: 11-25
- NAID
  10031139080
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] Three-dimensional structure determination protocol for noncrystalline biomolecules using x-ray free-electron laser diffraction imaging2013
- Author(s)
  Tomotaka Oroguchi, Masayoshi Nakasako
- Journal Title
  
  Physical Review E
  
  Volume: 87 Pages: 022712-022712
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] MD-SAXS method with nonspherical boundaries2012
- Author(s)
  Tomotaka Oroguchi, Mitsunori Ikeguchi
- Journal Title
  
  Chemical Physics Letter
  
  Volume: 541 Pages: 117-121
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] 非結晶粒子のコヒーレントＸ線回折イメージング2012
- Author(s)
  中迫雅由，高山裕貴，苙口友隆，白濱圭也，関口優希，山本雅貴，米倉功治，引間孝明，眞木‐さおり，高橋幸生，鈴木明大，松永幸大，加藤翔一，星貴彦
- Journal Title
  
  レーザー研究
  
  Volume: 40 Pages: 680-686
- NAID
  10031004094
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Journal Article] Ｘ線自由電子レーザーを用いた非結晶粒子のコヒーレントＸ線回折イメージング実験2012
- Author(s)
  中迫雅由，高山裕貴，苙口友隆，白濱圭也，関口優希，山本雅貴，米倉功治，引間孝明，眞木‐さおり，高橋幸生，鈴木明大，松永幸大，加藤翔一，星貴彦
- Journal Title
  
  オプトロニクス
  
  Volume: 368 Pages: 101-106
- Peer Reviewed
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] Optimization of MD-derived conformational ensemble in information content space and its application to experimental SAXS data2023
- Author(s)
  苙口友隆
- Organizer
  第61回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-21K03489
[Presentation] Optimization of MD-derived conformational ensemble in information content space and its application to experimental X-ray solution scattering data2023
- Author(s)
  T. Oroguchi
- Organizer
  TSRC Proten Dynamiccs Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K03489
[Presentation] Refinement of MD-derived conformational ensemble by referring to experimental SANXS data in framework of Bayesian statistics2022
- Author(s)
  苙口友隆
- Organizer
  第60回日本生物物理学会
- Data Source
  KAKENHI-PROJECT-21K03489
[Presentation] X線小角散乱と計算科学を用いた統合的解析による天然変性タンパク質の動的構造と機能の理解2022
- Author(s)
  小田隆, 大井里香, 古寺哲幸, 安藤敏夫, 小沼剛, 菅瀬謙治, 苙口友隆, 井上倫太郎, 杉山正明, 石野園子, 石野良純, 佐藤衛
- Organizer
  日本農芸化学会2022年度京都大会(JSBBA2022)
- Invited
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] 蛋白質の機能的動きに沿った溶媒和自由エネルギー変化の評価法開発2021
- Author(s)
  苙口友隆
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] 蛋白質の機能的動きに沿った溶媒和自由エネルギー変化の評価法開発2021
- Author(s)
  苙口友隆
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] MDシミュレーションと溶液散乱実験による蛋白質構造揺らぎの可視化: ベイズ学習の適用に向けて2021
- Author(s)
  苙口友隆
- Organizer
  CBI学会2021年大会
- Invited
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] MDシミュレーションと溶液散乱実験による蛋白質構造揺らぎの可視化: ベイズ学習の適用に向けて2021
- Author(s)
  苙口友隆
- Organizer
  CBI学会2021年大会
- Invited
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] 蛋白質の機能的動きに沿った溶媒和自由エネルギー変化の評価法開発2021
- Author(s)
  苙口友隆
- Organizer
  第59回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-21K03489
[Presentation] MDシミュレーションと溶液散乱実験による蛋白質構造揺らぎの可視化: ベイズ学習の適用に向けて2021
- Author(s)
  苙口友隆
- Organizer
  CBI学会2021年大会
- Invited
- Data Source
  KAKENHI-PROJECT-21K03489
[Presentation] 蛋白質の階層構造ダイナミクスの解明2020
- Author(s)
  中川洋、井上倫太郎、小田隆、矢木-内海真穂、斉尾智英、苙口友隆、長田裕也、杉山正明、佐藤衛、川北至信、岩瀬裕希、富永大輝、高田慎一
- Organizer
  量子ビームサイエンスフェスタ
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] Domain motion of Fv-fragment in antibody immunoglobulin G controls conformation of antigen-recognizing loop through hydration structure2019
- Author(s)
  T. Oroguchi, M. Nakasako
- Organizer
  第57回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] The structure and function of intrinsically disordered region of Hef that is associated with a DNA repair2019
- Author(s)
  T. Oda, A. Sekino, A. Murakami, R. Oi, M. Yoneyama, N. Kodera, T. Ando, T. Konuma, K. Sugase, T. Oroguchi, S. Ishino, Y. Ishino, and M. Sato
- Organizer
  第57回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] DNA修復にかかわるHefの天然変性領域の揺らいだ構造と機能2019
- Author(s)
  小田隆, 関野絢子, 村上綾香, 大井里香, 米山真紀, 古寺哲幸, 安藤敏夫, 小沼剛, 菅瀬謙治, 苙口友隆, 井上倫太郎, 杉山正明, 石野園子, 石野良純, 佐藤衛
- Organizer
  第4回LLPS研究会・ASUKA若手交流会2019
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] Domain motion of Fv-fragment in antibody immunoglobulin G controls conformation of antigen-recognizing loop through hydration structure2019
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第57回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] The dynamic structure and function of intrinsically disordered region of Hef that is associated with a DNA repair2019
- Author(s)
  T. Oda, A. Sekino, A. Murakami, R. Oi, M. Yoneyama, N. Kodera, T. Ando, T. Konuma, K. Sugase, T. Oroguchi, R. Inoue, M. Sugiyama, S. Ishino, Y. Ishino, M. Sato
- Organizer
  3rd Asia-Oceania Conference on Neutron Scattering (AOCNS 2019)
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-18H05229
[Presentation] Domain motion of Fv-fragment in antibody immunoglobulin G controls conformation of antigen-recognizing loop through hydration structure2019
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第57回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-17K19209
[Presentation] Domain motion of Fv-fragment in anti-dansyl immunoglobulin G controls conformation of its flexible antigen-binding region2018
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第56回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] Domain motion of Fv-fragment in anti-dansyl immunoglobulin G controls conformation of its flexible antigen-binding region2018
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第56回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-17K19209
[Presentation] Protein Structural Fluctuations Investigated by X-ray Solution Scattering and Molecular Dynamics Simulation2017
- Author(s)
  Tomotaka Oroguchi
- Organizer
  第55回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] Protein conformational fluctuations and hydration structures investigated by the combination of MD simulations and X-ray experiments2017
- Author(s)
  T. Oroguchi
- Organizer
  TSRC Protein Dynamics Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17K19209
[Presentation] Protein Structural Fluctuations Investigated by X-ray Solution Scattering and Molecular Dynamics Simulation2017
- Author(s)
  T. Oroguchi
- Organizer
  第55回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-17K19209
[Presentation] MDシミュレーションと溶液X線小角散乱で探る蛋白質の構造揺らぎ2017
- Author(s)
  苙口友隆、大出真央、岡島公司、中迫雅由、引間孝明、山本雅貴
- Organizer
  第17回日本蛋白質科学会
- Invited
- Data Source
  KAKENHI-PROJECT-17K19209
[Presentation] Protein conformational fluctuations and hydration structures investigated by the combination of MD simulations and X-ray experiments2017
- Author(s)
  Tomotaka Oroguchi
- Organizer
  TSRC Protein Dynamics Workshop
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] MDシミュレーションと溶液X線散乱で探る2017
- Author(s)
  苙口友隆、大出真央、岡島公司、中迫雅由、引間孝明、山本雅貴
- Organizer
  第17回日本蛋白質科学会
- Invited
- Data Source
  KAKENHI-PROJECT-17H04854
[Presentation] Nanoscale wetting and drying processes work as a switch for protein functional motions2016
- Author(s)
  苙口友隆
- Organizer
  日本化学会第96春季年会
- Place of Presentation
  同志社大学 (京都府・京田辺市)
- Year and Date
  2016-03-24
- Invited
- Data Source
  KAKENHI-PUBLICLY-26104535
[Presentation] Nanoscale wetting and drying processes dominate protein functional motions2016
- Author(s)
  Tomotaka Oroguchi
- Organizer
  TSRC Protein Dynamics Workshop
- Place of Presentation
  Telluride (USA)
- Year and Date
  2016-08-03
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-26800227
[Presentation] Nanoscale wetting and drying processes work as a switch for protein functional motions2016
- Author(s)
  苙口友隆
- Organizer
  日本化学会第96春季年会
- Place of Presentation
  同志社大学 (京都府・京田辺市)
- Year and Date
  2016-03-24
- Invited
- Data Source
  KAKENHI-PROJECT-26800227
[Presentation] Nanoscale wetting and drying processes dominate protein functional motions2015
- Author(s)
  Tomotaka Oroguchi
- Organizer
  TSRC Protein Dynamics Workshop
- Place of Presentation
  Telluride (USA)
- Year and Date
  2015-08-03
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PUBLICLY-26104535
[Presentation] X線溶液散乱と分子動力学シミュレーションで探る蛋白質の機能的構造揺らぎ2014
- Author(s)
  苙口友隆
- Organizer
  第2回 Neutrons in Biology 研究会
- Place of Presentation
  日本原子力研究開発機構原子力科学研究所
- Invited
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] 実験と分子シミュレーションを用いた天然変性蛋白質の動的構造解析2014
- Author(s)
  苙口友隆
- Organizer
  新学術領域研究「天然変性タンパク質の分子認識機構と機能発現」第3回公開シンポジウム
- Place of Presentation
  九州大学医学部百年講堂
- Invited
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] Ｘ線溶液散乱と分子動力学シミュレーションで探る蛋白質の構造揺らぎ2013
- Author(s)
  苙口友隆、池口満徳
- Organizer
  第51回生物物理学会年会
- Place of Presentation
  国立京都国際会館
- Invited
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] Protein dynamics investigated by small-angle x-ray solution scattering and molecular dynamics simulation2013
- Author(s)
  Tomotaka Oroguchi
- Organizer
  4-th Japan-France Joint Seminar
- Place of Presentation
  播磨
- Invited
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] A protocol for structure analysis of non-crystalline particles with X-ray free electron laser2012
- Author(s)
  Tomotaka Oroguchi, Masayoshi Nakasako
- Organizer
  生物物理学会　第50年会
- Place of Presentation
  名古屋
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] Protein dynamics investigated by small-angle X-ray solution scattering and molecular dynamics simulations2012
- Author(s)
  Tomotaka Oroguchi
- Organizer
  15th International Small-Angle Scattering Conference 2012
- Place of Presentation
  Sydney, Australia
- Invited
- Data Source
  KAKENHI-PUBLICLY-24113723
[Presentation] Nanoscale wetting and drying processes control protein functional motions
- Author(s)
  苙口友隆
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学（石川県、金沢市）
- Year and Date
  2015-09-13 – 2015-09-15
- Invited
- Data Source
  KAKENHI-PUBLICLY-26104535
[Presentation] グルタミン酸脱水素酵素のドメイン運動に協奏した水和構造変化
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター　（北海道、札幌市）
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PROJECT-26800227
[Presentation] Nanoscale wetting and drying processes control protein functional motions
- Author(s)
  苙口友隆
- Organizer
  第53回日本生物物理学会年会
- Place of Presentation
  金沢大学　（石川県、金沢市）
- Year and Date
  2015-09-13 – 2015-09-15
- Invited
- Data Source
  KAKENHI-PROJECT-26800227
[Presentation] グルタミン酸脱水素酵素のドメイン運動に協奏した水和構造変化
- Author(s)
  苙口友隆、中迫雅由
- Organizer
  第52回日本生物物理学会年会
- Place of Presentation
  札幌コンベンションセンター（北海道、札幌市）
- Year and Date
  2014-09-25 – 2014-09-27
- Data Source
  KAKENHI-PUBLICLY-26104535
[Presentation] Nanoscale wetting and drying processes control protein functional motions
- Author(s)
  苙口友隆
- Organizer
  The 2015 TSRC workshop on Protein Dynamics
- Place of Presentation
  Telluride, USA
- Year and Date
  2015-08-03 – 2015-08-07
- Invited
- Data Source
  KAKENHI-PROJECT-26800227
[Presentation] Nanoscale wetting and drying processes control protein functional motions
- Author(s)
  苙口友隆
- Organizer
  The 2015 TSRC workshop on Protein Dynamics
- Place of Presentation
  Telluride, USA
- Year and Date
  2015-08-03 – 2015-08-07
- Invited
- Data Source
  KAKENHI-PUBLICLY-26104535

1. Sugiyama Masaaki (10253395)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
2. 中川洋 (20379598)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
3. 矢木真穂 (40608999)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
4. 富永大輝 (50513694)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
5. 佐藤衛 (60170784)

# of Collaborated Projects: 1 results

# of Collaborated Products: 5 results
6. 井上倫太郎 (80563840)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
7. 齋尾智英 (80740802)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
8. 小田隆 (00573164)

# of Collaborated Projects: 1 results

# of Collaborated Products: 6 results
9. YONEKURA Koji

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
10. MAKI-YONEKURA Saori

# of Collaborated Projects: 0 results

# of Collaborated Products: 2 results
11. KURUMIZAKA Hitoshi

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
12. 山本雅貴

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
13. 松永幸大

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
14. 中迫雅由

# of Collaborated Projects: 0 results

# of Collaborated Products: 3 results
15. 清水光弘

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
16. 西村いくこ

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
17. 長谷あきら

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
18. 徳富哲

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Oroguchi Tomotaka 苙口 友隆

Tomotaka Oroguchi 苙口 友隆

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Development of force field considering hydrogen-bond directionalityPrincipal Investigator

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Neutron Structural Biology for New Generation

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Visualization of protein dynamics in molecular crowding environmentPrincipal Investigator

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Elucidation of thermodynamic roles of hydration structure in protein functionsPrincipal Investigator

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X線回折散乱実験と分子シミュレーションを用いた生体分子の動的構造の解析Principal Investigator

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Role of water molecules in biomolecular functions and interactionsPrincipal Investigator

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天然変性蛋白質の動的構造及び基質認識機構の原子レベルでの解明Principal Investigator

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[Journal Article] Internal dynamics of multidomain protein as revealed by an optimized neutron spin echo measurement and all-atom molecular dynamics simulation2023

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[Journal Article] Common architectures in cyanobacteria Prochlorococcus cells visualized by X-ray diffraction imaging using X-ray free electron laser2021

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[Journal Article] Energy landscape of domain motion in glutamate dehydrogenase deduced from cryo‐electron microscopy2020

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[Journal Article] Dipole?dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme2020

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[Journal Article] Assessment of Force Field Accuracy Using Cryogenic Electron Microscopy Data of Hyper-thermostable Glutamate Dehydrogenase2020

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[Journal Article] Combination of coarse-grained molecular dynamics simulations and small-angle X-ray scattering experiments2019

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Oroguchi Tomotaka 苙口友隆

Tomotaka Oroguchi 苙口友隆