Masayuki Oda

Profile Information

Affiliation: Professor, Lab. Biophysical Chemistry, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University

Degree: Ph D

Researcher number: 20318231
J-GLOBAL ID: 200901080743630884
researchmap Member ID: 1000289205

External link: https://kpu-biophyschem.com/english/

Research Interests

Research Areas

Research History

Apr, 2018 - Present

Professor, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
Apr, 2020 - Mar, 2021

山陽小野田市立山口東京理科大学非常勤講師
Apr, 2019 - Mar, 2020

京都工芸繊維大学非常勤講師
Apr, 2008 - Mar, 2018

Associate Professor, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University
Apr, 2015 - Mar, 2016

名古屋工業大学非常勤講師
Jul, 2003 - Mar, 2008

Lecturer, Graduate School of Agriculture, Kyoto Prefectural University
Apr, 1999 - Jun, 2003

Research Associate, Research Institute of Biological Sciences, Tokyo University of Science
Oct, 1997 - Mar, 1999

Research Associate, Tokyo Research Laboratories, Kyowa Hakko Kogyo, Co. Ltd.
Apr, 1995 - Sep, 1997

Research Associate, Biomolecular Research Institute (BERI)
Jul, 1993 - Mar, 1995

Research Associate, Protein Engineering Research Institute (PERI)
Apr, 1991 - Jun, 1993

Research Associate, Tokyo Research Laboratories, Kyowa Hakko Kirin Co., Ltd.

Education

Apr, 1989 - Mar, 1991

Graduate School of Science, Kyoto University
Apr, 1985 - Mar, 1989

Faculty of Science, Kyoto University

Committee Memberships

Sep, 2020 - Present

評議員, 日本生化学会
Mar, 2018 - Present

president, Biomolecular Interaction Research Association (BIRA)
Oct, 2020 - Sep, 2022

委員, 日本熱測定学会
2007 - 2021

分野別編集委員, 日本生物物理学会
Oct, 2018 - Sep, 2019

編集委員長、編集幹事, 日本熱測定学会
Oct, 2017 - Sep, 2018

副編集委員長、編集幹事, 日本熱測定学会
Oct, 2016 - Sep, 2017

編集委員, 日本熱測定学会
2015 - 2016

和文誌編集委員, 日本生物物理学会
2014 - 2015

庶務幹事, 日本熱測定学会

Awards

2022

Editors' Choice Award, Biophysics and Physicobiology

Masayuki Oda
2006

Encourage Award, The Japan Society of Thermal Analysis and Calorimetry

Papers

143

Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking

Masayuki Oda

International Journal of Molecular Sciences, 24(18) 13717-13717, Sep 6, 2023 Peer-reviewedInvitedLead authorLast author
Elucidation of binding mechanism, affinity and complex structure between mWT1 tumor‐associated antigen peptide and HLA‐A*24:02

Gert‐Jan Bekker, Nobutaka Numoto, Maki Kawasaki, Takahiro Hayashi, Saaya Yabuno, Yuko Kozono, Takeyuki Shimizu, Haruo Kozono, Nobutoshi Ito, Masayuki Oda …

Protein Science, Sep 4, 2023 Peer-reviewed
Metal-binding and folding thermodynamics of Escherichia coli ribonuclease HI related to its catalytic function

Yumi Kitagawa, Zengwei Liao, Kosuke Morikawa, Masayuki Oda

Biophysical Chemistry, 295 106961-106961, Apr, 2023 Peer-reviewedLast authorCorresponding author
Regulation of CD28 binding to SH2 domains of Grb2 and PI3K by trisubstituted carboranes for T-cell activation

Shuhei Ogawa, Yasunobu Asawa, Momoka Iiyama, Atsushi Yoshimori, Hiroyuki Nakamura, Masayuki Oda

Bioorganic and Medicinal Chemistry Letters, 78 129049-129049, Dec, 2022 Peer-reviewedLast authorCorresponding author
Role of Cys residues of C-terminal SH2 domain of phosphoinositide 3-kinase in its conformational stability and CD28-binding ability

Momoka Iiyama, Yoshiji Hantani, Rene H. Wink, Masataka Kuroda, Masayuki Oda

Chemical Thermodynamics and Thermal Analysis, 8 100080-100080, Dec, 2022 Peer-reviewedLast authorCorresponding author
Structural dynamics of the N‐terminal SH2 domain of PI3K in its free and CD28‐bound states

Yuhi Hosoe, Yohei Miyanoiri, Suyong Re, Saki Ochi, Yuya Asahina, Toru Kawakami, Masataka Kuroda, Kenji Mizuguchi, Masayuki Oda

The FEBS Journal, 290(9) 2366-2378, Nov 4, 2022 Peer-reviewedLast authorCorresponding author
Evaluation of multi-specificity of antibody G2 using its single-chain Fv and its covalently linked antigen peptides

Takahiro Hayashi, Yuji O. Kamatari, Masayuki Oda

Biophysical Chemistry, 290 106893-106893, Nov, 2022 Peer-reviewedLast authorCorresponding author
Structural, functional, and physiological properties of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during the course of affinity maturation

Masayuki Oda

Biophysical Reviews, Oct 20, 2022 Peer-reviewedInvitedLead authorLast authorCorresponding author
Interdomain interactions in Grb2 revealed by the conformational stability and CD28 binding analysis

Saki Ochi, Momoka Iiyama, Masayuki Oda

Biophysical Chemistry, 284 106792-106792, May, 2022 Peer-reviewedLast authorCorresponding author
A Trade-off Between Thermostability and Binding Affinity of Anti-(4-hydroxy-3-nitrophenyl)Acetyl Antibodies During the Course of Affinity Maturation

Akihiro Nishiguchi, Akikazu Murakami, Takachika Azuma, Masayuki Oda

The Protein Journal, Apr 30, 2022 Peer-reviewedLast authorCorresponding author
Pivotal role of a conserved histidine in Escherichia coli ribonuclease HI as proposed by X-ray crystallography

Zengwei Liao, Takuji Oyama, Yumi Kitagawa, Katsuo Katayanagi, Kosuke Morikawa, Masayuki Oda

Acta Crystallographica Section D Structural Biology, 78(3) 390-398, Mar 1, 2022 Peer-reviewedLast authorCorresponding author
Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH

Masayuki Oda, Tomoki Sano, Yuji O. Kamatari, Yoshito Abe, Teikichi Ikura, Nobutoshi Ito

The Protein Journal, 41(1) 71-78, Jan 30, 2022 Peer-reviewedLead authorCorresponding author
Varying the Directionality of Protein Catalysts for Aldol and Retro‐Aldol Reactions

Toshifumi Fujioka, Nobutaka Numoto, Hiroyuki Akama, Kola Shilpa, Michiko Oka, Prodip K. Roy, Yarkali Krishna, Nobutoshi Ito, David Baker, Masayuki Oda …

ChemBioChem, 23(2) e202100435, Jan 19, 2022 Peer-reviewedCorresponding author
Thermodynamics of nucleic acids

Drug Discovery System, 36(5) 232-238, Nov, 2021 Peer-reviewedInvitedLead authorLast authorCorresponding author
Structural dynamics of a DNA-binding protein analyzed using diffracted X-ray tracking

Yuhi Hosoe, Hiroshi Sekiguchi, Yuji C. Sasaki, Masayuki Oda

Biophysical Chemistry, 278 106669-106669, Nov, 2021 Peer-reviewedLast authorCorresponding author
Conformational changes of α-helical peptides with different hydrophobic residues induced by metal-ion binding

Masahiro Tanaka, Tatsuhisa Kato, Masayuki Oda

Biophysical Chemistry, 277 106661-106661, Oct, 2021 Peer-reviewedLast authorCorresponding author
Effects of chain length, temperature, and ionic strength on association and dissociation thermodynamics of DNA

Maki Kawasaki, Masayuki Oda

Chemical Thermodynamics and Thermal Analysis, 3-4 100015-100015, Sep, 2021 Peer-reviewedLast authorCorresponding author
Single-chain Fv antibody covalently linked to antigen peptides and its structural evaluation

Takahiro Hayashi, Maki Kawasaki, Yuji O. Kamatari, Masayuki Oda

Analytical Biochemistry, 629 114312-114312, Sep, 2021 Peer-reviewedLast authorCorresponding author
Structural basis for Ca²⁺-dependent catalysis of a cutinase-like enzyme and its engineering: application to enzymatic PET depolymerization

Masayuki Oda

Biophysics and Physicobiology, 18 168-176, Jul, 2021 Peer-reviewedInvitedLead authorCorresponding author
Structural basis of mutants of PET ‐degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability

Miho Emori, Nobutaka Numoto, Akane Senga, Gert‐Jan Bekker, Narutoshi Kamiya, Yuma Kobayashi, Nobutoshi Ito, Fusako Kawai, Masayuki Oda

Proteins: Structure, Function, and Bioinformatics, 89(5) 502-511, May, 2021 Peer-reviewedLast authorCorresponding author

Misc.

抗原・抗体複合体の直接観察抗原の大きさ、結合価、及び抗体の結合親和性の影響(Direct observation of antigen-antibody complex: Effects of antigen size, valence, and binding affinity of antibody)

古賀舞子, 真柳浩太, 北井麻希, 村上明一, 東隆親, 織田昌幸

生物物理, 47(Suppl.1) S120-S120, Nov, 2007
Thermodynamic Analyses of Specific and Non-Spectific DNA Recognition Mechanisms by Transcriptional Factor c-Myb

ODA Masayuki

Seibutsu Butsuri, 39(5) 301-305, 1999 Peer-reviewedInvitedLead authorLast authorCorresponding author

Books and Other Publications

熱量測定・熱分析ハンドブック

日本熱測定学会 (Role: Joint author)

丸善出版, Aug, 2020 (ISBN: 9784621305072)
食品ハイドロコロイドの開発と応用Ⅱ

稲葉理美, 織田昌幸 (Role: Joint author, タンパク質の構造と熱物性)

シーエムシー出版, 2015
熱量測定・熱分析ハンドブック

織田昌幸 (Role: Joint author, 抗原・抗体相互作用)

丸善, 2010
ファルマシア

織田昌幸 (Role: Joint author, パーツをはめて薬を創る：NMRやカロリメトリーの利用.)

2008
等温滴定熱測定

織田昌幸

蛋白質科学プロトコール, 2008
Old and New Views of Protein Folding

Oda, M, Furukawa, K, Ogata, K, Sarai, A, Nakamura, H (Role: Joint author, Thermodynamic analysis of protein induced folding upon DNA binding)

Elsevier, 1999
Thermodynamic analysis of protoin induced folding upon DNA binding

Elsevier, 1999

Presentations

エンド‐1,3‐β‐グルカナーゼ触媒ドメインの機能構造解析

三木彩子, 稲葉理美, 櫻井一正, 池上貴久, 伊島理枝子, 織田昌幸

日本農芸化学会大会講演要旨集(Web), Mar 5, 2017
Generation of single-chain Fv antibody against (4-hydroxy-3-nitrophenyl)acetyl and analysis of its structural dynamics

Yusui Sato, Yusuke Tanaka, Hiroshi Sekiguchi, Satomi Inaba, Takahiro Maruno, Yuji C. Sasaki, Yuji Kobayashi, Takachika Azuma, Masayuki Oda

PROTEIN SCIENCE, Oct, 2015, WILEY-BLACKWELL
Structural and thermodynamic analysis of co-stimulation receptor CD28 phosphopeptide interactions with Grb2, Gads, and PI3-kinese SH2 domains

Satomi Inaba, Nobutaka Numoto, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito, Masayuki Oda

PROTEIN SCIENCE, Oct, 2015, WILEY-BLACKWELL
温度変化実験により明らかとなったc‐Myb DNA結合ドメイン構造揺らぎの特性

稲葉理美, 前野覚大, 櫻井一正, 池上貴久, 深田はるみ, 森井尚之, 赤坂一之, 織田昌幸

日本蛋白質科学会年会プログラム・要旨集, May 26, 2014
1P027 Insight into the antigen binding motion of germline and affinity-matured antibodies(Protein: Structure & Function,Poster,The 52th Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Yusui Sato, Yusuke Tanaka, Hiroshi Sekiguchi, Yuji C. Sasaki, Takachika Azuma, Masayuki Oda

Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association
2P055 Detection of conformational dynamics of protein antigen by antibody(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Shimizu Shohey, Abe Yoshito, Kamatari Yuji O., Ueda Tadashi, Azuma Takachika, Oda Masayuki

Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association
2P058 Variable temperature and pressure NMR studies on flexible conformation of c-Myb DNA-binding domain(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Inaba Satomi, Maeno Akihiro, Sakurai Kazumasa, Akasaka Kazuyuki, Oda Masayuki

Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association
2P065 Effects of pH and DNA-binding on conformational dynamics of protein with helix-turn-helix motif(01C. Protein: Property,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Inaba Satomi, Sekiguchi Hiroshi, Sasaki Yuji C., Oda Masayuki

Seibutsu Butsuri, 2014, The Biophysical Society of Japan General Incorporated Association
高圧NMRおよび蛍光法によるc‐Myb DNA結合ドメイン準安定励起構造の解析

稲葉理美, 前野覚大, 池上貴久, 赤坂一之, 織田昌幸

日本蛋白質科学会年会プログラム・要旨集, May 31, 2013
2SAA-03 Cavity-dependent conformational fluctuation and DNA-binding function of c-Myb R2R3(2SAA Searching for the origins of the dynamism of life - how do random fluctuations turn into biological motions?,Symposium,The 51th Annual Meeting of the Biophysical Society of Japan)

Oda Masayuki

Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association
1P050 Characterization of multispecific monoclonal antibody G2 directed against chicken prion protein(01C. Protein:Property,Poster)

Kamatari Yuji, Oda Masayuki, Maruno Takahiro, Kobayashi Yuji, Ishiguro Naotaka

Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association
3P013 Dynamic structural analysis of three-helix bundle formation induced by metal-ion binding(01A. Protein: Structure,Poster)

Komichi Nobutaka, Sekiguchi Hiroshi, Sasaki Yuji C., Tanaka Toshiki, Oda Masayuki

Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association
3P026 Substrate binding ability of the Trp introduced mutant of carbohydrate-binding module(01A. Protein: Structure,Poster)

Tamashiro Tomonari, Asada Hiromi, Maruno Takahiro, Kanaori Kenji, Kobayashi Yuji, Oda Masayuki

Seibutsu Butsuri, 2013, The Biophysical Society of Japan General Incorporated Association
Critical role of the alpha-repeat in carbohydrate-binding module of endo-1,3-beta-glucanase for complex formation with laminarin

Masayuki Oda, Tomonari Tamashiro, Yoichi Tanabe, Teikichi Ikura, Nobutoshi Ito

PROTEIN SCIENCE, Aug, 2012, WILEY-BLACKWELL
Thermodynamic effects of multiple conformations in a protein on its stability and binding function

Satomi Inaba, Takahiro Maruno, Harumi Fukada, Yuji Kobayashi, Masayuki Oda

PROTEIN SCIENCE, Aug, 2012, WILEY-BLACKWELL
3B0924 Dynamic structural and antigen binding analyses of antibody single-chain Fvs(Proteins:Structure & Function III:Dynamics and Circadian Rhythm,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Tanaka Yusuke, Sekiguchi Hiroshi, Sasaki Yuji C., Azuma Takachika, Oda Masayuki

Seibutsu Butsuri, 2012, The Biophysical Society of Japan General Incorporated Association
2E1522 Cavity-dependent dynamics of c-Myb R2R3 revealed by high-pressure fluorescence and NMR spectroscopy(Proteins:Property II,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Inaba Satomi, Maeno Akihiro, Morii Hisayuki, Fukada Harumi, Akasaka Kazuyuki, Oda Masayuki

Seibutsu Butsuri, 2012, The Biophysical Society of Japan General Incorporated Association
1PT130 Molecular dynamics simulations of endo-1,3-β-glucanase and oligosaccharide complex(The 50th Annual Meeting of the Biophysical Society of Japan)

Komichi Nobutaka, Kamiya Narutoshi, Nakamura Haruki, Oda Masayuki

Seibutsu Butsuri, 2012, The Biophysical Society of Japan General Incorporated Association
1C1522 Contribution of Trp273 in the a-repeat of the carbohydrate-binding module of endo-1,3-β-glucanase to laminarin binding(Proteins: Measurement, Analysis, Engineering,Oral Presentation,The 50th Annual Meeting of the Biophysical Society of Japan)

Tamashiro Tomonari, Tanabe Yoichi, Kanaori Kenji, Ikura Teikichi, Ito Nobutoshi, Oda Masayuki

Seibutsu Butsuri, 2012, The Biophysical Society of Japan General Incorporated Association
CD28細胞内領域とアダプター分子Gads SH2及びGrb2 SH2との分子間相互作用解析

肥後邦武, 砂橋朗進, 森井尚之, 池上貴久, 伊倉貞吉, 伊藤暢聡, 安部良, 織田昌幸

日本蛋白質科学会年会プログラム・要旨集, May 27, 2011

Teaching Experience

Professional Memberships

Research Projects

静的局所環境の学習によるタンパク質動的構造情報の抽出

科学研究費助成事業, 基盤研究(B), 日本学術振興会, Apr, 2022 - Mar, 2025

水口賢司, 織田昌幸, 李秀栄
クチナーゼCut190のCa2+結合に伴う動的構造変化とPET分解分子機構の解明

科学研究費助成事業基盤研究(B), 基盤研究(B), 日本学術振興会, Apr, 2021 - Mar, 2024

織田昌幸, 関口博史, 沼本修孝, 神谷成敏, 宮ノ入洋平
耐熱性放線菌由来ＰＥＴ分解酵素による廃棄ＰＥＴのケミカルリサイクルの実用化

A-STEP「産学共同（育成型）」, JST, Dec, 2020 - Mar, 2023
Complex structure and affinity prediction among cancer vaccine peptides and immune related proteins

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B), Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2020 - Mar, 2023
クラゲコラーゲンの３Ｄバイオインク利用

A-STEP「トライアウト」, JST, Nov, 2020 - Mar, 2022
CD28ファミリー細胞内領域SH2結合の特異的阻害剤の探索

橋渡し研究（シーズA）開発候補課題, AMED, Apr, 2020 - Mar, 2021
親和性成熟に着目した抗体の抗原認識機構と動的構造の解明

科学研究費補助金基盤研究（C）, 日本学術振興会, Apr, 2018 - Mar, 2021

織田昌幸
Transform the antibodies against DNA lesions into the repair-enhancing reagents of them

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B), Grant-in-Aid for Scientific Research (B), Japan Society for the Promotion of Science, Apr, 2016 - Mar, 2019

MORI Toshio, IWAMOTO Takaaki, HIGASHI Nobutake
PET分解酵素のstructure-based designによる高機能化と応用に関する研究

一般研究助成, 公益財団法人発酵研究所, Apr, 2017 - Mar, 2019

織田昌幸
Understanding of antigen recognition mechanism of multispecific antibodies

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2015 - Mar, 2018

KAMATARI Yuji, KUWATA Kazuo, ISHIGURO Naotaka, AKASAKA Kazuyuki
ヘリックスバンドル形成をモデルとした蛋白質の構造エントロピーの定量化

科学研究費補助金挑戦的萌芽研究, 日本学術振興会, Apr, 2014 - Mar, 2016

織田昌幸
Inhibition of a prion conversion by suppressing protein fluctuations using small-molecules

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2012 - Mar, 2015

KAMATARI Yuji O., KUWATA Kazuo, AKASAKA Kazuyuki, ODA Masayuki, ISHIKAWA Takeshi
抗原・抗体間相互作用におけるタンパク質の動的構造変化の解明

科学研究費補助金基盤研究（C）, 日本学術振興会, Apr, 2010 - Mar, 2013

織田昌幸
Elucidation of antigen recognition mechanism by antibody and conformational change of antibody upon antigen binding in correlation with protein fluctuation in solution

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2005 - 2008

ODA Masayuki
MHC/peptides stability and T cell activation-Biophysical bases of synapse formation

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2002 - 2003

KOZONO Haruo, AZUMA Takachika, ODA Masayuki
抗NP抗体の親和性成熟に伴う抗原認識機構の変化に関する構造生物学的研究

科学研究費助成事業奨励研究(A), 奨励研究(A), 日本学術振興会, 2000 - 2001

織田昌幸

Profile Information

Research Interests

Research Areas

Research History

Education

Committee Memberships

Awards

Papers

Misc.

Books and Other Publications

Presentations

Teaching Experience

Professional Memberships

Research Projects

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