Okuda Aya 奥田綾

… Alternative Names

奥田綾オクダアヤ

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Researcher Number	80825646
Other IDs
Affiliation (Current)	2025: 京都大学, 複合原子力科学研究所, 准教授
Affiliation (based on the past Project Information) *help	2023: 京都大学, 複合原子力科学研究所, 准教授 2020 – 2022: 京都大学, 複合原子力科学研究所, 助教 2019: 京都大学, 複合原子力科学研究所, 研究員
Review Section/Research Field	Principal Investigator Basic Section 38030:Applied biochemistry-related Except Principal Investigator Medium-sized Section 14:Plasma science and related fields
Keywords	Principal Investigator 中性子小角散乱法 / マルチドメインタンパク質 / 区分同位体標識 / タンパク質ライゲーション Except Principal Investigator X線・中性子小角散乱同時測定 / SAXS/SANS同時測定 / 部分重水素化 / 小角中性子散乱 / マルチドメインタンパク質 / 重水素化 / 中性子散乱

Establishment of the enzymatic protein ligation technique for the preparation of segmental deuterated proteinsPrincipal Investigator
- Principal Investigator
  
  奥田綾
- Project Period (FY)
  2023 – 2024
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 38030:Applied biochemistry-related
- Research Institution
  Kyoto University
Correlated quantum beam analyzes to explore the structure and dynamics of biomacromolecules
- Principal Investigator
  
  Inoue Rintaro
- Project Period (FY)
  2019 – 2023
- Research Category
  
  Fund for the Promotion of Joint International Research (Fostering Joint International Research (B))
- Review Section
  
  Medium-sized Section 14:Plasma science and related fields
- Research Institution
  Kyoto University

All 2024 2023 2022 2021 2020 2019

All Journal Article Presentation

[Journal Article] Mechanistic Modeling of Amyloid Oligomer and Protofibril Formation in Bovine Insulin2024
- Author(s)
  Yuzu Keisuke、Imamura Hiroshi、Nozaki Takuro、Fujii Yuki、Badawy Shaymaa Mohamed Mohamed、Morishima Ken、Okuda Aya、Inoue Rintaro、Sugiyama Masaaki、Chatani Eri
- Journal Title
  
  Journal of Molecular Biology
  
  Volume: 436 Issue: 6 Pages: 168461-168461
- DOI
  10.1016/j.jmb.2024.168461
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-21K06503, KAKENHI-PROJECT-22KJ2255, KAKENHI-PROJECT-19KK0071, KAKENHI-PROJECT-20H03224
[Journal Article] Characterization of K-binding factor involved in water-soluble complex of menaquinone-7 produced by <i>Bacillus subtilis natto</i>2023
- Author(s)
  Chatake Toshiyuki、Yanagisawa Yasuhide、Murakami Risa、Ohsugi Tadanori、Sumi Hiroyuki、Takata Takumi、Okuda Aya、Morishima Ken、Inoue Rintaro、Sugiyama Masaaki
- Journal Title
  
  The Journal of Biochemistry
  
  Volume: 174 Issue: 4 Pages: 383-389
- DOI
  10.1093/jb/mvad051
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-21K15051, KAKENHI-PROJECT-19KK0071
[Journal Article] Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach2022
- Author(s)
  Yunoki Yasuhiro、Matsumoto Atsushi、Morishima Ken、Martel Anne、Porcar Lionel、Sato Nobuhiro、Yogo Rina、Tominaga Taiki、Inoue Rintaro、Yagi-Utsumi Maho、Okuda Aya、Shimizu Masahiro、Urade Reiko、Terauchi Kazuki、Kono Hidetoshi、Yagi Hirokazu、Kato Koichi、Sugiyama Masaaki
- Journal Title
  
  Communications Biology
  
  Volume: 5 Issue: 1 Pages: 184-184
- DOI
  10.1038/s42003-022-03143-z
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-19K05833, KAKENHI-PROJECT-20K06579, KAKENHI-PROJECT-19KK0071, KAKENHI-PROJECT-21K15051, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-20K22629
[Journal Article] Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations2022
- Author(s)
  Shimizu Masahiro、Okuda Aya、Morishima Ken、Inoue Rintaro、Sato Nobuhiro、Yunoki Yasuhiro、Urade Reiko、Sugiyama Masaaki
- Journal Title
  
  Scientific Reports
  
  Volume: 12 Issue: 1 Pages: 9970-9970
- DOI
  10.1038/s41598-022-13982-9
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K15051, KAKENHI-PROJECT-19KK0071, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-20K06579, KAKENHI-PLANNED-18H05534
[Journal Article] Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance2022
- Author(s)
  Okuda Aya、Shimizu Masahiro、Inoue Rintaro、Urade Reiko、Sugiyama Masaaki
- Journal Title
  
  Angewandte Chemie International Edition
  
  Volume: 62 Issue: 1
- DOI
  10.1002/anie.202214412
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19KK0071, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-20K06579, KAKENHI-PLANNED-18H05534
[Journal Article] Elucidation of the mechanism of subunit exchange in αB crystallin oligomers2021
- Author(s)
  Inoue Rintaro、Sakamaki Yusuke、Takata Takumi、Wood Kathleen、Morishima Ken、Sato Nobuhiro、Okuda Aya、Shimizu Masahiro、Urade Reiko、Fujii Noriko、Sugiyama Masaaki
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 1-9
- DOI
  10.1038/s41598-021-82250-z
- NAID
  120006956390
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-20K06579, KAKENHI-PROJECT-20K11646, KAKENHI-PROJECT-19KK0071, KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-17K13221, KAKENHI-PROJECT-19K16088
[Journal Article] Deuteration Aiming for Neutron Scattering2021
- Author(s)
  Okuda Aya、Inoue Rintaro、Morishima Ken、Saio Tomohide、Yunoki Yasuhiro、Yagi-Utsumi Maho、Yagi Hirokazu、Shimizu Masahiro、Sato Nobuhiro、Urade Reiko、Kato Koichi、Sugiyama Masaaki
- Journal Title
  
  Biophysics and Physicobiology
  
  Volume: 18 Issue: 0 Pages: 16-27
- DOI
  10.2142/biophysico.bppb-v18.003
- NAID
  130008000165
- ISSN
  2189-4779
- Language
  English
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K06579, KAKENHI-PROJECT-20K22629, KAKENHI-PROJECT-19KK0071, KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-18J21063, KAKENHI-PROJECT-19K16088
[Journal Article] Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation2021
- Author(s)
  Okuda Aya、Shimizu Masahiro、Morishima Ken、Inoue Rintaro、Sato Nobuhiro、Urade Reiko、Sugiyama Masaaki
- Journal Title
  
  Scientific Reports
  
  Volume: 11 Issue: 1 Pages: 1-13
- DOI
  10.1038/s41598-021-85219-0
- NAID
  120006997066
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K06579, KAKENHI-PROJECT-20K22629, KAKENHI-PROJECT-19KK0071, KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-19K16088
[Journal Article] Dynamics of proteins with different molecular structures under solution condition2020
- Author(s)
  Inoue Rintaro、Oda Takashi、Nakagawa Hiroshi、Tominaga Taiki、Saio Tomohide、Kawakita Yukinobu、Shimizu Masahiro、Okuda Aya、Morishima Ken、Sato Nobuhiro、Urade Reiko、Sato Mamoru、Sugiyama Masaaki
- Journal Title
  
  Scientific Reports
  
  Volume: 10 Issue: 1 Pages: 21678-21678
- DOI
  10.1038/s41598-020-78311-4
- NAID
  120007193758
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K06527, KAKENHI-PROJECT-20K06579, KAKENHI-PROJECT-19KK0071, KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-18H02391, KAKENHI-PROJECT-20H02944, KAKENHI-PROJECT-19K16088, KAKENHI-PUBLICLY-19H04945
[Journal Article] Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS)2019
- Author(s)
  R. Inoue, T. Nakagawa, K. Morishima, N. Sato, A. Okuda, R. Urade, R. Yogo, S. Yanaka, M. Yagi-Utsumi, K. Kato, K. Omoto, K. Ito, M. Sugiyama
- Journal Title
  
  Scientific Reports
  
  Volume: 9 Issue: 1 Pages: 1-12
- DOI
  10.1038/s41598-019-48911-w
- NAID
  120006799252
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-19K16088, KAKENHI-PROJECT-19KK0071, KAKENHI-PLANNED-18H05534, KAKENHI-PROJECT-18H05229, KAKENHI-PROJECT-19H01017, KAKENHI-PROJECT-19J15602, KAKENHI-PROJECT-17K07361, KAKENHI-PROJECT-18K14892
[Presentation] 小胞体における酸化的フォールディング酵素の機能・構造相関解析2024
- Author(s)
  奥田綾
- Organizer
  日本農芸化学会2024年度大会
- Invited
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] Development of efficient multiple domain ligation method for proteins2023
- Author(s)
  A. Okuda, M. Shimizu, R. Inoue, R. Urade, M. Sugiyama
- Organizer
  26th Congress and General Assembly of the International Union of Crystallography - IUCr 2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Analysis of solution structure of CYP105A1 with small angle X-ray scattering2023
- Author(s)
  A. Okuda, Y. Yunoki, M. Shimizu, R. Inoue, M. Sugiyama
- Organizer
  2023 International Joint Meeting of the 23rd International Conference on Cytochrome P450 and the 38th Annual Meeting of the Japanese Society for the Study of Xenobiotics - 2023 ICCP450/JSSX, Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] 区分同位体修飾のための酵素を用いた高効率タンパク質ライゲーション法の開発2023
- Author(s)
  奥田綾、清水将裕、井上倫太郎、裏出令子、杉山正明
- Organizer
  第23回日本蛋白質科学年会
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] 生化学実験と分子動力学計算の協働による酵素を用いたプロテインライゲーションの実現2023
- Author(s)
  奥田綾、清水将裕、井上倫太郎、裏出令子、杉山正明
- Organizer
  第96回日本生化学会大会
- Invited
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] 区分重水素化試料を用いた逆転コントラスト同調中性子小角散乱測定2023
- Author(s)
  奥田綾、清水将裕、井上倫太郎、裏出令子、杉山正明
- Organizer
  第23回日本中性子科学会年会
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] Development of efficient multiple domain ligation method for proteins2023
- Author(s)
  Aya Okuda, Masahiro Shimizu, Rintaro Inoue, Reiko Urade, Masaaki Sugiyama
- Organizer
  International Union of Crystallography (IUCr) 2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] Deuteration Aiming for Neutron Scattering (DANS) in KumatorI Deuteration Station (KIDS)2023
- Author(s)
  Aya Okuda, Rintaro Inoue, Ken Morishima, Masahiro Shimizu, Reiko Urade, Masaaki Sugiyama
- Organizer
  DeuNet 2023 Facility Meeting
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K13882
[Presentation] Integrated Method with Analytical Ultracentrifugation and Small-Angle Scattering (AUC-SAS) for the Structural Analysis of a Biomacromolecule in a Polydisperse Solution.2022
- Author(s)
  MORISHIMA, Ken; OKUDA, Aya; SATO, Nobuhiro; SHIMIZU, Masahiro; YUNOKI, Yasuhiro; INOUE, Rintaro; URADE, Reiko; SUGIYAMA, Masaaki
- Organizer
  SAS2022
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Domain Conformation of Multi-domain Protein ER-60 Studied with Hybrid Approach of Coarse-grained Simulations and Small-angle X-ray Scattering2022
- Author(s)
  SHIMIZU, Masahiro; OKUDA, Aya; MORISHIMA, Ken; SATO, Nobuhiro; INOUE, Rintaro; YUNOKI, Yasuhiro; URADE, Reiko; SUGIYAMA
- Organizer
  SAS2022
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Solution Structure Analysis of the Multi-domain Protein, ER-60 by Small Angle Scattering2022
- Author(s)
  OKUDA, Aya; SHIMIZU, Masahiro; MORISHIMA, Ken; INOUE, Rintaro; SATO, Nobuhiro; YUNOKI, Yasuhiro; URADE, Reiko; SUGIYAMA,
- Organizer
  SAS2022
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Establishment of basic techniques related to protein sample preparation for neutron scattering2021
- Author(s)
  Okuda, Aya; Inoue, Rintaro; Morishima, Ken; Yunoki, Yasuhiro; Shimizu, Masahiro; Sato, Nobuhiro; Urade, Reiko; Sugiyama, Masaaki
- Organizer
  IUCR2021
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] αB-クリスタリンのサブユニット交換機構2021
- Author(s)
  井上倫太郎、酒巻裕介、高田匠、Kathleen Wood, 守島健、奥田綾、清水将裕、佐藤信浩、裏出令子、藤井紀子、杉山正明
- Organizer
  量子ビームサイエンスフェスタ
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Subunit dynamics in alpha-crystallin through deuteration-assisted small-angle neutron scattering2021
- Author(s)
  Inoue, Rintaro; Sakamaki, Yusuke; Takata, Takumi; Morishima, Ken; Wood, Kathleen; Sato, Nobuhiro; Okuda, Aya; Shimizu, Masahiro; Urade, Reiko; Fujii, Noriko; Sugiyama, Masaaki
- Organizer
  IUCr 2021
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] 中性子散乱解析を目指したタンパク質試料調製技術の確立2021
- Author(s)
  奥田綾, 井上倫太郎, 守島健, 清水将裕, 佐藤信浩, 裏出令子, 杉山正明
- Organizer
  量子ビームサイエンスフェスタ
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] 超遠心分析とX線小角散乱の統合手法 (AUC -SAXS ) によるタンパク質複合体の構造解析2021
- Author(s)
  守島健、宮本洋祐、清水将裕、柚木康弘、奥田綾、佐藤信浩、井上倫太郎、裏出令子、矢木宏和、加藤晃一、杉山正明
- Organizer
  量子ビームサイエンスフェスタ
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] AUC-SAS: Integrated analysis of biomacromolecular structure with analytical ultracentrifugation (AUC) and small-angle scattering (SAS)2021
- Author(s)
  Morishima, Ken; Inoue, Rintaro; Shimizu, Masahiro; Okuda, Aya; Sato, Nobuhiro; Urade, Reiko; Sugiyama, Masaaki
- Organizer
  IUCR2021
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] 中性子散乱解析を目指したタンパク質ライゲーションの技術戦略2020
- Author(s)
  奥田綾, 清水将裕, 守島健, 佐藤信浩, 井上倫太郎, 裏出令子, 杉山正明
- Organizer
  第20回日本中性子科学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-19KK0071
[Presentation] Subunit dynamics in a-crystallin through deuteration-assisted small-angle neutron scattering2019
- Author(s)
  R. Inoue, Y. Sakamaki, K. Wood1, K. Morishima, T. Takumi, N. Sato, A. Okuda, R. Urade, N. Fujii, M. Sugiyama
- Organizer
  J-PARC symposium 2019
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-19KK0071

1. Inoue Rintaro (80563840)

# of Collaborated Projects: 1 results

# of Collaborated Products: 16 results
2. 杉山正明 (10253395)

# of Collaborated Projects: 1 results

# of Collaborated Products: 17 results
3. 守島健 (40812087)

# of Collaborated Projects: 1 results

# of Collaborated Products: 14 results
4. 小田隆

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
5. 今村比呂志

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
6. 河野秀俊

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Okuda Aya 奥田 綾

奥田 綾 オクダ アヤ

Research Projects

Research Products

Co-Researchers

Establishment of the enzymatic protein ligation technique for the preparation of segmental deuterated proteinsPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Correlated quantum beam analyzes to explore the structure and dynamics of biomacromolecules

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Journal Article] Mechanistic Modeling of Amyloid Oligomer and Protofibril Formation in Bovine Insulin2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Characterization of K-binding factor involved in water-soluble complex of menaquinone-7 produced by <i>Bacillus subtilis natto</i>2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Overall structure of fully assembled cyanobacterial KaiABC circadian clock complex by an integrated experimental-computational approach2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Extracting time series matching a small-angle X-ray scattering profile from trajectories of molecular dynamics simulations2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Elucidation of the mechanism of subunit exchange in αB crystallin oligomers2021

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] Deuteration Aiming for Neutron Scattering2021

Author(s)

Journal Title

DOI

NAID

ISSN

Language

Data Source

[Journal Article] Solution structure of multi-domain protein ER-60 studied by aggregation-free SAXS and coarse-grained-MD simulation2021

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] Dynamics of proteins with different molecular structures under solution condition2020

Author(s)

Journal Title

DOI

NAID

Data Source

[Journal Article] Newly developed Laboratory-based Size exclusion chromatography Small-angle x-ray scattering System (La-SSS)2019

Author(s)

Journal Title

DOI

NAID

Data Source

[Presentation] 小胞体における酸化的フォールディング酵素の機能・構造相関解析2024

Author(s)

Organizer

Data Source

[Presentation] Development of efficient multiple domain ligation method for proteins2023

Author(s)

Okuda Aya 奥田綾

奥田綾オクダアヤ