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Okuda, Aya
Institute for Integrated Radiation and Nuclear Science (KURNS) Associate Professor
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Last Updated :2026/08/31
Basic Information
Professional Memberships
- PROTEIN SCIENCE SOCIETY OF JAPAN
- THE JAPANESE BIOCHEMICAL SOCIETY
- JAPAN SOCIETY FOR BIOSCIENCE, BIOTECHNOLOGY, AND AGROCHEMISTRY
- 日本中性子科学会
Academic Degree
Academic Resume (Graduate Schools)
- Kyoto University, Graduate School of Agriculture, 修了
- Kyoto University, Graduate School of Agriculture, 修了
Academic Resume (Undergraduate School/Majors)
High School
High School
私立奈良学園高等学校
Research History
- From Oct. 2023, To PresentKyoto University, Institute for Integrated Radiation and Nuclear Science, 准教授
- From Feb. 2021, To Sep. 2023Kyoto University, Institute for Integrated Radiation and Nuclear Science, 助教
- From Apr. 2019, To Jan. 2021Kyoto University, Institute for Integrated Radiation and Nuclear Science, 研究員
- From Apr. 2018, To Mar. 2019Kyoto University, Graduate School of Agriculture, 特定助教
- From Apr. 2017, To Mar. 2018Kyoto University, Graduate School of Agriculture, 日本学術振興会 特別研究員 (PD)
- From Apr. 2016, To Mar. 2017Kyoto University, Graduate School of Agriculture, 日本学術振興会 特別研究員 (DC2)
ID,URL
J-Global ID
researchmap URL
list
Last Updated :2026/08/31
Research
Research Topics, Overview of the research
Research Topics
酸化的フォールディング酵素PDIファミリータンパク質の分子ダイナミクス解析Overview of the research
タンパク質の酸化的フォールディングを担う酵素群であるPDIファミリータンパク質の機能と構造ダイナミクスの相関関係を、生化学的手法とX線および中性子の小角散乱解析をはじめとした物理学的手法により明らかにする。
Research Areas
Papers
- Integrated analysis with iCM-SANS, SAXS and MD simulations for dynamics of multi-domain proteins.Aya Okuda; Rintaro Inoue; Minami Kurokawa; Anne Martel; Lionel Porcar; Rikuto Osaki; Kaori Fukuzawa; Kevin L Weiss; Sai Venkatesh Pingali; Reiko Urade; Masaaki SugiyamaJournal of applied crystallography, 01 Aug. 2026, Peer-reviewed, Lead author
- Mechanistic modeling of amyloid oligomer and protofibril formation in bovine insulinKeisuke Yuzu; Hiroshi Imamura; Takuro Nozaki; Yuki Fujii; Shaymaa Mohamed Mohamed Badawy; Ken Morishima; Aya Okuda; Rintaro Inoue; Masaaki Sugiyama; Eri ChataniJournal of Molecular Biology, Jan. 2024, Peer-reviewed
- Structural and Dynamical Changes of Nucleosome upon GATA3 Binding.Hisashi Ishida; Atsushi Matsumoto; Hiroki Tanaka; Aya Okuda; Ken Morishima; Paul A Wade; Hitoshi Kurumizaka; Masaaki Sugiyama; Hidetoshi KonoJournal of molecular biology, 05 Oct. 2023, Peer-reviewed
- Characterization of K-binding factor involved in water-soluble complex of menaquinone-7 produced by Bacillus subtilis nattoToshiyuki Chatake; Yasuhide Yanagisawa; Risa Murakami; Tadanori Ohsugi; Hiroyuki Sumi; Takumi Takata; Aya Okuda; Ken Morishima; Rintaro Inoue; Masaaki SugiyamaThe Journal of Biochemistry, 07 Jul. 2023, Peer-reviewed
- Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance.Aya Okuda; Masahiro Shimizu; Rintaro Inoue; Reiko Urade; Masaaki SugiyamaAngewandte Chemie (International ed. in English), 02 Jan. 2023, Peer-reviewed, Lead author
- Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulationsMasahiro Shimizu; Aya Okuda; Ken Morishima; Rintaro Inoue; Nobuhiro Sato; Yasuhiro Yunoki; Reiko Urade; Masaaki SugiyamaScientific Reports, Dec. 2022, Peer-reviewed
- Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach.Yasuhiro Yunoki; Atsushi Matsumoto; Ken Morishima; Anne Martel; Lionel Porcar; Nobuhiro Sato; Rina Yogo; Taiki Tominaga; Rintaro Inoue; Maho Yagi-Utsumi; Aya Okuda; Masahiro Shimizu; Reiko Urade; Kazuki Terauchi; Hidetoshi Kono; Hirokazu Yagi; Koichi Kato; Masaaki SugiyamaCommunications biology, 10 Mar. 2022, Peer-reviewed
- Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation.Aya Okuda; Masahiro Shimizu; Ken Morishima; Rintaro Inoue; Nobuhiro Sato; Reiko Urade; Masaaki SugiyamaScientific reports, 11 Mar. 2021, Peer-reviewed, Lead author
- Histone variant H2A.B-H2B dimers are spontaneously exchanged with canonical H2A-H2B in the nucleosome.Rina Hirano; Yasuhiro Arimura; Tomoya Kujirai; Mikihiro Shibata; Aya Okuda; Ken Morishima; Rintaro Inoue; Masaaki Sugiyama; Hitoshi KurumizakaCommunications biology, 12 Feb. 2021, Peer-reviewed
- Elucidation of the mechanism of subunit exchange in αB crystallin oligomers.Rintaro Inoue; Yusuke Sakamaki; Takumi Takata; Kathleen Wood; Ken Morishima; Nobuhiro Sato; Aya Okuda; Masahiro Shimizu; Reiko Urade; Noriko Fujii; Masaaki SugiyamaScientific reports, 28 Jan. 2021, Peer-reviewed
- Deuteration Aiming for Neutron ScatteringAya Okuda; Rintaro Inoue; Ken Morishima; Tomohide Saio; Yasuhiro Yunoki; Maho Yagi-Utsumi; Hirokazu Yagi; Masahiro Shimizu; Nobuhiro Sato; Reiko Urade; Koichi Kato; Masaaki SugiyamaBiophysics and Physicobiology, 2021, Peer-reviewed, Lead author
- Dynamics of proteins with different molecular structures under solution condition.Rintaro Inoue; Takashi Oda; Hiroshi Nakagawa; Taiki Tominaga; Tomohide Saio; Yukinobu Kawakita; Masahiro Shimizu; Aya Okuda; Ken Morishima; Nobuhiro Sato; Reiko Urade; Mamoru Sato; Masaaki SugiyamaScientific reports, 10 Dec. 2020, Peer-reviewed
- A novel soybean protein disulphide isomerase family protein possesses dithiol oxidation activity: identification and characterization of GmPDIL6.Aya Okuda; Motonori Matsusaki; Taro Masuda; Ken Morishima; Nobuhiro Sato; Rintaro Inoue; Masaaki Sugiyama; Reiko UradeJournal of biochemistry, 01 Oct. 2020, Peer-reviewed, Lead author
- Integral approach to biomacromolecular structure by analytical-ultracentrifugation and small-angle scattering.Ken Morishima; Aya Okuda; Rintaro Inoue; Nobuhiro Sato; Yosuke Miyamoto; Reiko Urade; Maho Yagi-Utsumi; Koichi Kato; Rina Hirano; Tomoya Kujirai; Hitoshi Kurumizaka; Masaaki SugiyamaCommunications biology, 08 Jun. 2020, Peer-reviewed
- Regulation of plant ER oxidoreductin 1 (ERO1) activity for efficient oxidative protein foldingMatsusaki M; Okuda A; Matsuo K; Gekko K; Masuda T; Naruo Y; Hirose A; Kono K; Tsuchi Y; Urade RJournal of Biological Chemistry, Nov. 2019, Peer-reviewed, Lead author
- Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS).Inoue R; Nakagawa T; Morishima K; Sato N; Okuda A; Urade R; Yogo R; Yanaka S; Yagi-Utsumi M; Kato K; Omoto K; Ito K; Sugiyama MScientific reports, 2019, Peer-reviewed
- Identification and characterization of GmPDIL7, a soybean ER membrane-bound protein disulfide isomerase family proteinAya Okuda; Motonori Matsusaki; Taro Masuda; Reiko UradeFEBS JOURNAL, Feb. 2017, Peer-reviewed, Lead author
- Cooperative Protein Folding by Two Protein Thiol Disulfide Oxidoreductases and ERO1 in SoybeanMotonori Matsusaki; Aya Okuda; Taro Masuda; Katsunori Koishihara; Ryuta Mita; Kensuke Iwasaki; Kumiko Hara; Yurika Naruo; Akiho Hirose; Yuichiro Tsuchi; Reiko UradePLANT PHYSIOLOGY, Feb. 2016, Peer-reviewed
- Disulfide bond formation activity of soybean quiescin sulfhydryl oxidaseAya Okuda; Motonori Matsusaki; Yuki Higashino; Taro Masuda; Reiko UradeFEBS JOURNAL, Dec. 2014, Peer-reviewed, Lead author
Misc.
- アミロイド核形成に先立つインスリンの由来種に依存した初期凝集メカニズム柚佳祐; 今村比呂志; 野崎拓郎; 藤井悠生; 守島健; 奥田綾; 井上倫太郎; 杉山正明; 富永圭介; 富永圭介; 茶谷絵理日本生化学会大会(Web), 2021
- The molecular machine KaiC hexamer regulates circadian clock system柚木康弘; 児玉篤治; 矢木真穂; 矢木真穂; 矢木真穂; 守島健; 佐藤信浩; 奥田綾; 清水将裕; 井上倫太郎; 裏出令子; 矢木宏和; 加藤晃; 加藤晃; 加藤晃; 杉山正明KURNS-EKR (Web), 2022
- 小角散乱と超遠心分析の協奏的解析(AUC-SAS)による弱会合性タンパク質複合体の構造解析守島健; 矢木真穂; 矢木真穂; 矢木真穂; 井上倫太郎; 佐藤信浩; 奥田綾; 裏出令子; 加藤晃一; 加藤晃一; 加藤晃一; 杉山正明KURNS-EKR (Web), 2020
- Study of water-soluble vitamin K2 from Bacillus subtilis natto茶竹俊行; 柳澤泰任; 高田匠; 奥田綾; 守島健; 井上倫太郎; 杉山正明KURNS-EKR (Web), 2024
- ウシ由来インスリンのアミロイド核形成に見られるオリゴマーおよびプロトフィブリル形成機構柚佳祐; 今村比呂志; 野崎拓郎; 藤井悠生; 守島健; 奥田綾; 井上倫太郎; 杉山正明; 茶谷絵理日本蛋白質科学会年会プログラム・要旨集, 2023
- Overall structure of the fully assembled KaiABC complex in cyanobacterial circadian system analyzed by an integrated solution scattering-computational approach柚木康弘; 松本淳; 守島健; MARTEL Anne; PORCAR Lionel; 佐藤信浩; 與語理那; 與語理那; 與語理那; 富永大輝; 井上倫太郎; 矢木真穂; 矢木真穂; 矢木真穂; 奥田綾; 清水将裕; 裏出令子; 寺内一姫; 河野秀俊; 矢木宏和; 矢木宏和; 加藤晃一; 加藤晃一; 加藤晃一; 杉山正明時間生物学, 2022
- セラミド輸送タンパク質CERTの構造解析森田さより; 佐藤信浩; 守島健; 奥田綾; 杉木俊彦; 花田賢太郎; 杉山正明; 児嶋長次郎日本分子生物学会年会プログラム・要旨集(Web), 2020
- 小胞体分子シャペロンER-60によるペプチド結合様式裏出令子; 伊中浩治; 古林直樹; 東野ゆうき; 松崎元紀; 奥田綾; 加茂昌之SPring-8/SACLA利用研究成果集(Web), 2018
Media Coverage
External funds: Kakenhi
- Emerging approaches to protect biological systems from photoaging through molecular invisibilityGrant-in-Aid for Scientific Research (B)Basic Section 59040:Nutrition science and health science-relatedKyoto University高田 匠From 01 Apr. 2026, To 31 Mar. 2029, Grantedクリスタリン;分子シャペロン;蛋白質フォールディング;蛋白質ミスフォールディング;蛋白質の異常凝集
- 区分重水素化試料を用いた酸化的フォールディング酵素の機能・溶液構造相関解析Grant-in-Aid for Scientific Research (C)Basic Section 38030:Applied biochemistry-relatedKyoto University奥田 綾From 01 Apr. 2026, To 31 Mar. 2029, Grantedタンパク質ライゲーション;区分同位体標識;中性子小角散乱法;酸化的フォールディング酵素
- Correlated quantum beam analyzes to explore the structure and dynamics of biomacromoleculesFund for the Promotion of Joint International Research (Fostering Joint International Research (B))Medium-sized Section 14:Plasma science and related fieldsKyoto UniversityRintaro InoueFrom 07 Oct. 2019, To 31 Mar. 2024, Project Closed中性子散乱;重水素化;マルチドメインタンパク質;小角中性子散乱;部分重水素化;SAXS/SANS同時測定;X線・中性子小角散乱同時測定
- Establishment of the enzymatic protein ligation technique for the preparation of segmental deuterated proteinsGrant-in-Aid for Early-Career ScientistsBasic Section 38030:Applied biochemistry-relatedKyoto University奥田 綾From 01 Apr. 2023, To 31 Mar. 2026, Grantedタンパク質ライゲーション;区分同位体標識;マルチドメインタンパク質;中性子小角散乱法
External funds: others
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Last Updated :2026/08/31
Education
Teaching subject(s)
- From 01 Apr. 2026, To 31 Mar. 2027Advanced Radiation Chemistry ID7243, Fall, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Advanced Radiation Chemistry IC7242, Spring, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Advanced Radiation Chemistry IB7241, Fall, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Seminar on Radiation Chemistry IB7137, Fall, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Seminar on Radiation Chemistry IA7136, Spring, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Advanced Radiation Chemistry IA7240, Spring, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Seminar on Radiation Chemistry ID7139, Fall, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Seminar on Radiation Chemistry IC7138, Spring, Graduate School of Science, 1
- From 01 Apr. 2026, To 31 Mar. 2027Biochemistry IV4614, Spring, Faculty of Science, 2
- From 01 Apr. 2026, To 31 Mar. 2027Radiation Biochemistry II7013, Fall, Graduate School of Science, 2
- From 01 Apr. 2023, To 31 Mar. 2024Seminar on Macromolecular Structure D2066, Fall, Graduate School of Science, 2
- From 01 Apr. 2023, To 31 Mar. 2024Seminar on Macromolecular Structure C2065, Spring, Graduate School of Science, 2
- From 01 Apr. 2023, To 31 Mar. 2024Seminar on Macromolecular Structure B2064, Fall, Graduate School of Science, 2
- From 01 Apr. 2023, To 31 Mar. 2024Seminar on Macromolecular Structure A2063, Spring, Graduate School of Science, 2
- From 01 Apr. 2022, To 31 Mar. 2023Seminar on Macromolecular Structure C2065, Spring, Graduate School of Science, 2
- From 01 Apr. 2022, To 31 Mar. 2023Seminar on Macromolecular Structure D2066, Fall, Graduate School of Science, 2
- From 01 Apr. 2022, To 31 Mar. 2023Seminar on Macromolecular Structure A2063, Spring, Graduate School of Science, 2
- From 01 Apr. 2022, To 31 Mar. 2023Seminar on Macromolecular Structure B2064, Fall, Graduate School of Science, 2
