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Masahiko Taguchi

Section

Institute of Multidisciplinary Research for Advanced Materials

Job title

Assistant Professor

Degree

PhD (Science) (University of Tsukuba)

researchmap

https://researchmap.jp/masahiko_taguchi

J-GLOBAL ID

202301011378686008

e-Rad No.

60879930

Profile

　学位取得までは超伝導体ナノ構造などを対象とした物理学の理論研究を行っておりました。その後、物理学で発展した概念や手法を用いて生物科学を研究する生物物理学に惹かれ、特に生体内化学反応やタンパク質ダイナミクスに着目した計算科学研究に従事して参りました。
　現在は、構造生物学の研究室で主に時分割構造データを活用した分子モデリング・シミュレーション研究に取り組んでおります。

Research History 5

2026/04 - Present

University of Tsukuba　Faculty of Pure and Applied Sciences
2025/11 - Present

RIKEN　Center for Computational Science　Visiting Scientist
2023/04 - Present

Tohoku University　Institute of Multidisciplinary Research for Advanced Materials　Assistant professor
2020/04 - 2023/03

National Institutes for Quantum Science and Technology　Institute for Quantum Life Science　Postdoctoral Fellow
2016/04 - 2020/03

Kyoto University　Graduate School of Science　Program-Specific Researcher

Education 5

University of Tsukuba　Graduate School of Pure and Applied Sciences　Doctoral Program in Nano-Science and Nano-Technology

2013/04 - 2016/03
Laboratoire de Physique et Modélisation des Milieux Condensés, Centre national de la recherche scientifique (LPMMC, CNRS)

2014/01 - 2014/05
University of Tsukuba　Graduate School of Pure and Applied Sciences　Department of Physics

2010/04 - 2013/03
University of Tsukuba　First Cluster of Colleges,College of Natural Sciences

2006/04 - 2010/03
高崎経済大学附属高等学校　普通科

2003/04 - 2006/03

Committee Memberships 1

東北大学多元物質科学研究所同窓会(多友会)　幹事

2025/09 - Present

Professional Memberships 4

Quantum Life Science Society
Protein Science Society of Japan
The Biophysical Society of Japan
The Antibody Society of Japan

Research Interests 3

Integration of Structural Biology Data
Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Method
Bio-molecular modeling and simulation

Research Areas 2

Life sciences / Biophysics /
Life sciences / Structural biochemistry /

Awards 4

量子生命科学会第7回大会 Best Presentation 賞

2025/05　ハイブリッド量子古典シミュレーションによる光活性化アデニル酸シクラーゼの光活性化機構の解明
つくばアクションプロジェクト表彰「優秀賞」

2014/03　筑波大学　プレゼンひろば（企画番号：13034A）
つくばアクションプロジェクト表彰「特別賞」

2013/03　筑波大学　雙峰祭学内研究企画エリア拡充プロジェクト（企画番号：12005A）
つくばアクションプロジェクト表彰「優秀賞」

2012/03　筑波大学　院生プレゼンバトル（企画番号：11013A）

Papers 11

Switchbody, an Antigen‐Responsive Enzyme Switch Based on Antibody and Its Working Principle International-journal Peer-reviewed

Takanobu Yasuda, Yoshiyuki Ueno, Masahiko Taguchi, Naoya Tochio, Hiromasa Yagi, Shuma Yazaki, Ryoichi Arai, Bo Zhu, Takanori Kigawa, Hiroshi Ueda, Tetsuya Kitaguchi

Advanced Science　12　(44)　2025/09/15
Publisher: Wiley
DOI： 10.1002/advs.202508422 　

ISSN： 2198-3844

eISSN： 2198-3844

More details Close

Abstract An enzyme switch, termed “Switchbody”, is developed by fusing an antibody with a fragment of a split enzyme for the precise regulation of enzyme activity in response to an antigen. A luciferase‐based Switchbody is engineered by fusing the NanoLuc luciferase fragment HiBiT to the N‐terminus of an antibody. The enzyme activity of the Switchbody increases upon the addition of an antigen in a dose‐dependent manner in the presence of the complementary fragment LgBiT and its substrate furimazine, demonstrating the potential of the luciferase‐based Switchbody as a biosensor. As its working principle, ELISA shows that the interaction between HiBiT and LgBiT is facilitated by antigen binding. Moreover, X‐ray crystallography and NMR reveal the heterogeneous trapped state of the HiBiT region and an increasing motility of HiBiT region upon antigen binding, respectively. MD simulations and luminescence measurements show that antigen disrupted the trapping of HiBiT in the antibody, enabling its release. By applying this “Trap and Release” principle to Protein M, an antibody‐binding protein, label‐free IgG antibodies are successfully converted into bioluminescent Switchbodies. This adaptable Switchbody platform has the potential to expand switching technology beyond luciferase to various other enzymes in the future.
Unveiling the Photoactivation Mechanism of BLUF Photoreceptor Protein through Hybrid Quantum Mechanics/Molecular Mechanics Free-Energy Calculation International-journal Peer-reviewed

Masahiko Taguchi, Shun Sakuraba, Justin Chan, Hidetoshi Kono

ACS Physical Chemistry Au　4　(6)　647-659　2024/10/29
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acsphyschemau.4c00040 　

ISSN： 2694-2445

eISSN： 2694-2445
Hybrid QM/MM Free-Energy Evaluation of Drug-Resistant Mutational Effect on the Binding of an Inhibitor Indinavir to HIV-1 Protease International-journal Peer-reviewed

Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi

Journal of Chemical Information and Modeling　62　(5)　1328-1344　2022/02/25
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jcim.1c01193 　

ISSN： 1549-9596

eISSN： 1549-960X
Protein Structure Data and Precise Predictions Pave the Way for Molecular Design Peer-reviewed

Yusuke Yamada, Masahiko Taguchi, Eriko Nango

Journal of Synthetic Organic Chemistry, Japan　84　(5)　482-491　2026/05/01
Publisher: The Society of Synthetic Organic Chemistry, Japan
DOI： 10.5059/yukigoseikyokaishi.84.482 　

ISSN： 0037-9980

eISSN： 1883-6526
Self-Assembly of V-Shaped Polyaromatic Amphiphiles Studied by Molecular Dynamics Simulation International-journal Peer-reviewed

Yuki Yamamoto, Masahiko Taguchi, Daichi Tanaka, Yoshihiro Uchida, Shigehiko Hayashi

The Journal of Physical Chemistry B　129　(4)　1399-1414　2024/12/30
Publisher: American Chemical Society (ACS)
DOI： 10.1021/acs.jpcb.4c06937 　

ISSN： 1520-6106

eISSN： 1520-5207
HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks International-journal International-coauthorship Peer-reviewed

Effi Haque, Aamir Salam Teeli, Dawid Winiarczyk, Masahiko Taguchi, Shun Sakuraba, Hidetoshi Kono, Paweł Leszczyński, Mariusz Pierzchała, Hiroaki Taniguchi

Genes　13　(3)　413　2022/02/24
Publisher: MDPI AG
DOI： 10.3390/genes13030413 　

eISSN： 2073-4425

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Hepatocyte nuclear factor 1A (HNF1A) is the master regulator of liver homeostasis and organogenesis and regulates many aspects of hepatocyte functions. It acts as a tumor suppressor in the liver, evidenced by the increased proliferation in HNF1A knockout (KO) hepatocytes. Hence, we postulated that any loss-of-function variation in the gene structure or composition (mutation) could trigger dysfunction, including disrupted transcriptional networks in liver cells. From the International Cancer Genome Consortium (ICGC) database of cancer genomes, we identified several HNF1A mutations located in the functional Pit-Oct-Unc (POU) domain. In our biochemical analysis, we found that the HNF1A POU-domain mutations Y122C, R229Q and V259F suppressed HNF4A promoter activity and disrupted the binding of HNF1A to its target HNF4A promoter without any effect on the nuclear localization. Our results suggest that the decreased transcriptional activity of HNF1A mutants is due to impaired DNA binding. Through structural simulation analysis, we found that a V259F mutation was likely to affect DNA interaction by inducing large conformational changes in the N-terminal region of HNF1A. The results suggest that POU-domain mutations of HNF1A downregulate HNF4A gene expression. Therefore, to mimic the HNF1A mutation phenotype in transcription networks, we performed siRNA-mediated knockdown (KD) of HNF4A. Through RNA-Seq data analysis for the HNF4A KD, we found 748 differentially expressed genes (DEGs), of which 311 genes were downregulated (e.g., HNF1A, ApoB and SOAT2) and 437 genes were upregulated. Kyoto Encyclopedia of Genes and Genomes (KEGG) mapping revealed that the DEGs were involved in several signaling pathways (e.g., lipid and cholesterol metabolic pathways). Protein–protein network analysis suggested that the downregulated genes were related to lipid and cholesterol metabolism pathways, which are implicated in hepatocellular carcinoma (HCC) development. Our study demonstrates that mutations of HNF1A in the POU domain result in the downregulation of HNF1A target genes, including HNF4A, and this may trigger HCC development through the disruption of HNF4A–HNF1A transcriptional networks.
Interplay among transacting factors around promoter in the initial phases of transcription International-journal Invited Peer-reviewed

Amarjeet Kumar, Justin Chan, Masahiko Taguchi, Hidetoshi Kono

Current Opinion in Structural Biology　71　7-15　2021/12
Publisher: Elsevier BV
DOI： 10.1016/j.sbi.2021.04.008 　

ISSN： 0959-440X
Theory of coherent quantum phase slips in Josephson junction chains with periodic spatial modulations International-journal International-coauthorship Peer-reviewed

Aleksandr E. Svetogorov, Masahiko Taguchi, Yasuhiro Tokura, Denis M. Basko, Frank W. J. Hekking

Physical Review B　97　(10)　2018/03/29
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevb.97.104514 　

ISSN： 2469-9950

eISSN： 2469-9969
Quantum Adiabatic Pumping by Modulating Tunnel Phase in Quantum Dots Peer-reviewed

Masahiko Taguchi, Satoshi Nakajima, Toshihiro Kubo, Yasuhiro Tokura

Journal of the Physical Society of Japan　85　(8)　084704　2016/08/15
Publisher: Physical Society of Japan
DOI： 10.7566/jpsj.85.084704 　

ISSN： 0031-9015

eISSN： 1347-4073
Interaction effect on adiabatic pump of charge and spin in quantum dot International-journal Peer-reviewed

Satoshi Nakajima, Masahiko Taguchi, Toshihiro Kubo, Yasuhiro Tokura

Physical Review B　92　(19)　2015/11/19
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevb.92.195420 　

ISSN： 1098-0121

eISSN： 1550-235X
Mode engineering with a one-dimensional superconducting metamaterial International-journal International-coauthorship Peer-reviewed

Masahiko Taguchi, Denis M. Basko, Frank W. J. Hekking

Physical Review B　92　(2)　2015/07/10
Publisher: American Physical Society (APS)
DOI： 10.1103/physrevb.92.024507 　

ISSN： 1098-0121

eISSN： 1550-235X

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Misc. 2

物理モデルとAIモデル

田口真彦

生物工学会誌　104　(6)　252-252　2026/06

DOI： 10.34565/seibutsukogaku.104.6_252 　
Anfinsen's dogma

Journal of Synthetic Organic Chemistry, Japan　84　(5)　493-493　2026/05/01
Publisher: The Society of Synthetic Organic Chemistry, Japan
DOI： 10.5059/yukigoseikyokaishi.84.493 　

ISSN： 0037-9980

eISSN： 1883-6526

Books and Other Publications 2

タンパク質の運動と機能発現

田口真彦, 河野秀俊

Precision Medicine 2025年6月号「量子生命科学の最前線」
タンパク質機能の計算科学的解析

田口真彦

Precision Medicine 2025年6月号「量子生命科学の最前線」

Presentations 27

ハイブリッド量子古典計算によるテルペン環化酵素の反応機構解明

田口真彦, 藤原孝彰, Atika Nur Rochmah, 葛山智久, 林重彦, 南後恵理子

量子生命科学会第8回大会　2026/05
Analyzing the photoactivation mechanism of photoactivated adenylate cyclase OaPAC by hybrid QM/MM simulation International-presentation

Masahiko Taguchi, Akiya Fukuda, Shun Sakuraba, Chan Wai-Soon, Eriko Nango, Hidetoshi Kono

Quantum Innovation 2025　2025/07
Insights into light-driven chloride ion pump mechanism of NM-R3 by molecular dynamics simulation International-presentation

Msahiko Taguchi, Akiya Moriuchi, Hinano Ogawa, Osamu Miyashita, Eriko Nango

20th International Conference on Retinal Proteins (ICRP2024)　2024/11
ハイブリッド量子古典シミュレーションによる光活性化アデニル酸シクラーゼの光活性化機構の解明

田口真彦, 福田諒哉, 櫻庭俊, Chan Wai-Soon, 南後恵理子, 河野秀俊

量子生命科学会第7回大会　2025/05
Unveiling the photoactivation mechanism of photoactivated adenylate cyclase OaPAC by hybrid QM/MM simulation International-presentation

Masahiko Taguchi, Akiya Fukuda, Shun Sakuraba, Chan Wai-Soon, Eriko Nango, Hidetoshi Kono

Quantum Innovation 2024　2024/10
Insights into light-driven chloride ion pump mechanism of NM-R3 and NpHR by molecular dynamics simulation International-presentation

Masahiko Taguchi, Akiya Moriuchi, Hinano Ogawa, Osamu Miyashita, Eriko Nango

International Union for Pure and Applied Biophysics (IUPAB) 2024　2024/06
Understanding of protein functional expression using hybrid QM/MM free energy method International-presentation

Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Cheng Cheng, Chika Higashimura, Yoshihiro Uchida, Shun Sakuraba, Chan Wai-Soon, Shigehiko Hayashi, Hidetoshi Kono

"Molecular Movies" International Symposium　2023/11
光受容タンパク質 OaPAC のダイナミクスと機能発現機構

田口真彦, 櫻庭俊, Chan Wai-Soon, 河野秀俊

量子生命科学会第5回大会　2023/05
QM/MM 分子シミュレーションによる光活性化酵素 PAC の機能解析

田口真彦, 櫻庭俊, Chan Wai-Soon, 河野秀俊

量子生命科学会第4回大会　2022/05
Molecular insight into photoactivation of BLUF photoreceptor from QM/MM free energy calculation

Masahiko Taguchi, Shun Sakuraba, Chan Wai-Soon, Hidetoshi Kono

第59回日本生物物理学会年会　2021/11
量子/古典混合シミュレーションによるBLUF光受容体の光活性化機構の解析

田口真彦, 櫻庭俊, Chan Wai-Soon, 河野秀俊

量子生命科学会第3回大会　2021/09
光活性化アデニル酸シクラーゼの古典/量子ハイブリッド分子シミュレーション

田口真彦, 櫻庭俊, Chan Wai-Soon, 河野秀俊

量子生命科学会第2回大会　2020/12
Binding Free Energy Calculations of HIV-1 Protease with Indinavir and Its Drug-Resistant Mutant

Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi

第58回日本生物物理学会年会　2020/09
V字型アントラセンパネルを持つ両親媒性分子から形成される分子カプセルのクラスタリング解析

田口真彦, 山本裕生, 田中大地, 林重彦

第13回分子科学討論会　2019/09
Determination of protonated states for native and mutant structures of HIV-1 protease with indinavir by free energy calculations

Masahiko Taguchi, Ryo Oyama, Masahiro Kaneso, Shigehiko Hayashi

第57回日本生物物理学会年会シンポジウム（ポスト「京」始動を見据えた計算創薬の新展開）　2019/09
Photoactivation Intermediate of AsLOV2 Photoreceptor Protein Investigated by a Hybrid Molecular Simulation International-presentation

Masahiko Taguchi, Cheng Cheng, Chika Higashimura, Shigehiko Hayashi

FUKUI 2018 Satellite Symposium　2018/10
V字型アントラセンパネルを持つ両親媒性分子の分子動力学シミュレーション

田口真彦, 山本裕生, 田中大地, 林重彦

第12回分子科学討論会　2018/09
Molecular simulation on light-activation mechanism of LOV photoreceptor protein

Masahiko Taguchi, Cheng Cheng, Chika Higashimura, Shigehiko Hayashi

第56回日本生物物理学会年会　2018/09
HIV-1 proteaseの基質および反応阻害剤に関する分子シミュレーションと水溶性光受容タンパク質の光活性化機構に関する分子シミュレーション

田口真彦, 金曽将弘, 小山糧, 成鋮, 東村智佳, 林重彦

第5回ポスト京重点課題1 ワークショップ　2018/08
QM/MM study on HIV-1 protease with inhibitor International-presentation

Masahiko Taguchi, Masahiro Kaneso, Shigehiko Hayashi

IWR School Mathematical Methods for Quantum Chemistry　2017/11
Numerical study on the electric field response of superconducting nanowires

Masahiko Taguchi, Yasuhiro Tokura, Shiro Kawabata

2016/03
Normal mode engineering for quantum phase fluctuations of an inhomogeneous superconducting loop International-presentation

Masahiko Taguchi, Denis M. Basko, Frank W. J. Hekking

Frontiers of Quantum and Mesoscopic Thermodynamics (FQMT)　2015/07
Mode engineering with a one-dimensional superconducting metamaterial International-presentation

Masahiko Taguchi, Denis M. Basko, Frank W., J. Hekking

New Perspectives in Spintronics and Mesoscopic Physics (NPSMP)　2015/06
Quantum Adiabatic Pumping with Tunneling Phase in Quantum Dot System International-presentation

Masahiko Taguchi, Satoshi Nakajima, Toshihiro Kubo, Yasuhiro Tokura

International Conference on Physics of Semiconductor (ICPS)　2014/08
Quantum Fluctuations of a Superconducting Loop Embedded in an Inhomogeneous Electromagnetic Environment International-presentation

Masahiko Taguchi, Denis M. Basko, Frank W. J. Hekking, Yasuhiro Tokura

Frontiers of Condensed Matter　2014/08
Quantum pumping in quantum dot system International-presentation

Masahiko Taguchi, Satoshi Nakajima, Toshihiro Kubo, Yasuhiro Tokura

International Symposium on Nano-scale Transport and Technology (ISNTT)　2013/11
Theoretical investigation on the absorption spectrum of photosystem as a biomarker of extrasolar planets International-presentation

Masahiko Taguchi, Yu Komatsu, Akimasa Sato, Mitsuo Shoji, Megumi Kayanuma, Katsumasa Kamiya, Kenji Shiraishi, Kazuhiro Yabana, Masayuki Umemura

The VIIIth Congress of the International Society of Theoretical Chemical Physics (ISTCP)　2013/08

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Research Projects 15

時分割構造データと連携した計算科学による蛋白質の構造機能解析

田口真彦

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 基盤研究(C)

Institution: 東北大学

2026/04 - 2029/03
タンパク質の蛍光ラベル化を可能にするアミノ酸配列の新規デザイン手法の開発

伊藤優志, 田口真彦, 南後恵理子, 高橋聡

Offer Organization: 東北大学多元物質科学研究所

System: 多元研プロジェクト(学内若手共同研究)

2026/05 - 2027/03
光活性化アデニル酸シクラーゼの活性制御機構の解明

平野美奈子 (受入研究者: 田口真彦)

Offer Organization: 物質・デバイス領域共同研究拠点

System: 基盤共同研究課題

2026/04 - 2027/03
Rational design of biosensor based on computational science and biochemical experiment

2025/04 - 2027/03
分⼦デザインを⽬指したテルペン環化酵素の反応機構解明 Competitive

田口真彦

Offer Organization: 株式会社モルシス

System: 第4回 MOLSIS-CCG GRANT

2025/10 - 2026/09
量子コンピュータを活用した生体内化学反応の計算プロトコルの探索的研究

田口真彦

Offer Organization: 東北大学附置研究所・センター連携体(若⼿アンサンブルプロジェクト)

System: 2025年度量子コンピュータ未来活用

2025/12 - 2026/03
分子シミュレーションによる光駆動塩化物イオンポンプロドプシン類のダイナミクス解析

田口真彦

Offer Organization: 東北大学多元物質科学研究所

System: 多元研プロジェクト(一般テーマ)

2025/05 - 2026/03
光活性化アデニル酸シクラーゼの活性制御機構の解明

平野美奈子 (受入研究者: 田口真彦)

Offer Organization: 物質・デバイス領域共同研究拠点

System: 基盤共同研究課題

2025/04 - 2026/03
Construction of Versatile Bioluminescent Immunosensor Based on “Trap & Release” of Peptide-tag

2024/04 - 2026/03
ハイブリッド分子シミュレーションによる光活性化アデニル酸シクラーゼの動態解析

田口真彦

Offer Organization: 日本学術振興会

System: 科学研究費助成事業

Category: 若手研究

Institution: 東北大学

2023/04 - 2026/03
AI-assisted and structural analysis-boosted ultra-high-throughput screening platform for switch-type antibody-drug conjugates

2024/04 - 2025/03
超伝導ナノ細線を用いた電荷センサーに関する理論研究

田口真彦 (受入研究者: 川畑史郎博士)

Offer Organization: 産業技術総合研究所ナノエレクトロニクス研究部門

System: リサーチアシスタント

2015/09 - 2016/03
半導体量子ドットに関する理論研究（スピントロニクス分野）

田口真彦 (指導教員: 都倉康弘教授)

Offer Organization: 筑波大学

System: つくばナノテク拠点産学独連携人材育成プログラム（Honors program）

2013/05 - 2015/03
超伝導細線における量子位相滑りについての理論研究

田口真彦 (受入研究者: Frank W. J. Hekking 教授)

Offer Organization: 筑波大学

System: 戦略イニシアティブ推進機構第 2 回若手研究者海外派遣制度

Institution: フランス国立科学研究センター凝縮系理論物理学研究所（CNRS LPMMC）

2015/01 - 2015/02
超伝導細線の物性制御についての理論研究

田口真彦 (受入研究者: Frank W. J. Hekking 教授)

Offer Organization: 筑波大学

System: 戦略イニシアティブ推進機構第 1 回若手研究者海外派遣制度

Institution: フランス国立科学研究センター凝縮系理論物理学研究所（CNRS LPMMC）

2014/09 - 2014/11

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Teaching Experience 6

生命科学B（分担）　東北大学全学講義 Undergraduate (liberal arts)
化学一般実験B（分担）　東北大学理学部化学科留学生コース Undergraduate (specialized)
物理化学演習A（分担）　東北大学理学部化学科留学生コース Undergraduate (specialized)
物理化学演習B（分担）　東北大学理学部化学科留学生コース Undergraduate (specialized)
修了生によるオムニバス講座（分担）　筑波大学数理物質科学研究群
基礎化学実験（分担）　東北大学理学部化学科留学生コース Undergraduate (specialized)

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