KEIO RESEARCHERS INFORMATION SYSTEM

Career 【 Display / hide 】

Career 【 Display / hide 】

• 1992.10

  -

  2002.09

  鐘淵化学工業（株）生物化学研究所（現ライフサイエンス研究所） ,研究員

• 2006.08

  -

  2007.08

  ドイツGreifswald大学（博士研究員）

Academic Background 【 Display / hide 】

Academic Background 【 Display / hide 】

• 1988.03

  Keio University, Faculty of Science and Engineering, 化学科

  University, Graduated

• 1990.03

  Keio University, Graduate School, Division of Science and Engineeri, 化学専攻

  Graduate School, Completed, Master's course

• 1992.09

  Keio University, Graduate School, Division of Science and Engineeri, 化学専攻

  Graduate School, Completed, Doctoral course

Academic Degrees 【 Display / hide 】

Academic Degrees 【 Display / hide 】

• 理学, Keio University, 1992.09

Research Areas 【 Display / hide 】

Research Areas 【 Display / hide 】

• Nanotechnology/Materials / Green sustainable chemistry and environmental chemistry

• Nanotechnology/Materials / Bio chemistry (微生物変換)

Research Keywords 【 Display / hide 】

Research Keywords 【 Display / hide 】

• プラスチック分解菌

• 微生物

• 有機化学

• 遺伝子

• 酵素

Books 【 Display / hide 】

Books 【 Display / hide 】

• Dual Modification of Artificial Protein Cage

  Kawakami N., Nasu E., Miyamoto K., Methods in Molecular Biology, 2023

  　View Summary

  Chemical modifications of proteins confer new functions on them or modulate their original functions. Although various approaches are developed for modifications, modifications of the two different reactive sites of proteins by different chemicals are still challenging. In this chapter, we show a simple approach for selective modifications of both interior and exterior surfaces of protein nanocages by two different chemicals based on a molecular size filter effect of the surface pores.

  • Access to Document (DOI)

• 基礎から学ぶケイミカルバイオロジー

  上村大輔、袖岡幹子、阿部孝宏、闐闐孝介、中村和彦、宮本憲二, 共立出版, 2016

• Green Biocatalysis

  MIYAMOTO KENJI, Wiley, 2016

  Scope: Decarboxylation and racemization of unnatural compounds using artificial enzymes derived from arylmalonate decarboxylase

• 有機合成実験法ハンドブック

  MIYAMOTO KENJI, 有機合成化学協会, 2015.12

  Scope: 特殊環境からの新規酵素のスクリーニング

• Chemical Biology

  MIYAMOTO KENJI, INTECH, 2012.02

  Scope: 63-82

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Papers 【 Display / hide 】

Papers 【 Display / hide 】

• Cross-species gene redesign leveraging ortholog information and generative modeling

  Akiyama M., Tashiro M., Huang Y., Uehara M., Kanzaki T., Itaya M., Kataoka M., Miyamoto K., Sakakibara Y.

  Nature Communications 17 ( 1 )  2026.12

  　View Summary

  Conventional approaches to heterologous gene expression rely on codon optimization, which is limited to swapping synonymous codons and fails to capture deeper adaptive changes. In contrast, naturally evolved orthologous genes include non-synonymous mutations, insertions, and deletions that confer functional adaptation to different host contexts. Here we present OrthologTransformer, a Transformer-based deep learning model that converts orthologous genes between species by learning from large-scale orthologous gene datasets. The model recapitulates evolutionary differences—from synonymous codon swaps to amino acid-changing mutations and indels—to predict coding sequences optimized for target species while preserving protein function. In extensive tests across diverse bacterial species pairs, the model’s context-aware gene designs more closely resembled native host orthologs, preserved protein functionality, and achieved superior expression yields compared to codon-optimized sequences. As proof of concept, an OrthologTransformer-redesigned PETase expressed in Bacillus subtilis showed robust activity, producing approximately 10-fold more reaction product than the codon-optimized enzyme, and achieving higher expression levels, thereby demonstrating improved enzyme performance via AI-guided gene design.

  • Access to Document (DOI)

• Mechanistic Elucidation and Stereochemical Consequences of Alternative Binding of Alkenyl Substrates by Engineered Arylmalonate Decarboxylase

  van der Pol E., Schlatzer T., Hoffka G., Di Geronimo B., Eder J., Schweiger A.K., Karava M., Gross D., Fischer R.C., Kracher D., Kazlauskas R., Miyamoto K., Kamerlin S.C.L., Breinbauer R., Kourist R.

  Journal of the American Chemical Society 147 ( 43 ) 39271 - 39283 2025.10

  ISSN  00027863

  　View Summary

  The cofactor-free arylmalonate decarboxylase (AMDase) is a valuable biocatalyst for synthesizing α-aryl and α-alkenyl alkanoic acids with excellent stereoselectivity. We engineered a new hydrophobic pocket in (S)-selective AMDase mutants, creating AMDase ICPLLG with enhanced activity. For the investigation of the mechanism, we synthesized isotope-labeled, pseudochiral 2-methyl-2-vinyl malonate via an auxiliary-based asymmetric route using a chiral imidazolidinone to enable stereoselective bis-alkylation of malonates. Our results reveal striking substrate-dependent stereochemical behavior: AMDase ICPLLG decarboxylates prochiral aromatic malonates with retention of configuration at the α-carbon. The critical Cys residue adds a proton from the same face of the substrate as the leaving carboxylate. Interestingly, the same mutant decarboxylates the corresponding alkenyl malonate with inversion of configuration, i.e., with protonation from the opposite face. Kinetic isotope effect measurements and QM/MM metadynamics calculations suggest that alkenyl malonates adopt an alternative binding mode and undergo decarboxylation via a borderline concerted mechanism instead of a stepwise mechanism. This new pathway changes the stereochemical preference. We exploited this strategy to decarboxylate sterically hindered alkenyl malonates (substrates not converted by wild-type AMDase) with high stereoselectivity. The engineered hydrophobic pocket in (S)-selective AMDase mutants expands the substrate scope for synthesizing enantiomerically pure α-aryl and α-alkenyl butanoic acids. This work demonstrates a new approach (a mechanistic change) to engineer the substrate range and stereoselectivity of enzymes.

  • Access to Document (DOI)

• Fusion then fission: splitting and reassembly of an artificial fusion-protein nanocage

  Ohara N., Kawakami N., Arai R., Adachi N., Ikeda A., Senda T., Miyamoto K.

  Chemical Communications 60 ( 34 ) 4605 - 4608 2024.04

  ISSN  13597345

  　View Summary

  A split-protein system is a simple approach to introduce new termini which are useful as modification sites in protein engineering, but has been adapted mainly for monomeric proteins. Here we demonstrate the design of split subunits of the 60-mer artificial fusion-protein nanocage TIP60. The subunit fragments successfully reformed the cage structure in the same manner as prior to splitting. One of the newly introduced terminals at the interior surface can be modified using a tag peptide and green fluorescent protein. Therefore, the termini could serve as a versatile modification site for incorporating a wide variety of functional peptides and proteins.

  • Access to Document (DOI)

• Thermally Reversible Gel-Sol Transition of Hydrogels via Dissociation and Association of an Artificial Protein Nanocage

  Nasu E., Kawakami N., Takamura S., Hotta A., Arai R., Miyamoto K.

  Biomacromolecules 25 ( 4 ) 2358 - 2366 2024.04

  ISSN  15257797

  　View Summary

  Oligomeric protein nanocages often disassemble into their subunits and reassemble by external stimuli. Thus, using these nanocages as cross-linkers for hydrogel network structures is a promising approach to allow hydrogels to undergo stimuli-responsive gel-sol transitions or self-healing. Here, we report hydrogels that show a reversible gel-sol transition resulting from the heat-induced dissociation and reassociation of protein nanocages. The hydrogel contained the 60-mer artificial protein nanocage, TIP60, as a supramolecular cross-linker for polyethylene glycol network structures. The hydrogel showed a gel-to-sol transition upon heating at a temperature above the melting point of TIP60 and immediately returned to a gel state upon cooling to room temperature. During the heating and cooling treatment of the hydrogel, small-angle X-ray scattering analysis suggested the dissociation and reassociation of TIP60. Furthermore, we demonstrated redox-responsive cargo release from TIP60 in the hydrogel. These results showed the potential of TIP60 as a component of multi-stimuli-responsive hydrogels.

  • Access to Document (DOI)

• Alcanivorax bacteria as important polypropylene degraders in mesopelagic environments

  Koike H., Miyamoto K., Teramoto M.

  Applied and Environmental Microbiology 89 ( 12 )  2023.12

  ISSN  00992240

  　View Summary

  Plastics are causing serious problems in the sea and settling even to abyssal depths. Polypropylene (PP) is the second most common plastic product and thus would constitute a large fraction of plastics in the sea. The biodegradation of PP has not been clearly shown. In this study, Alcanivorax bacteria (mainly Alcanivorax borkumensis) were indicated to be enriched most abundantly on liquid PP and on its structurally similar branched alkane, pristane, in mesopelagic water. An Alcanivorax isolate probably of A. borkumensis showed the highest liquid PP-degrading activity among the isolates. These results indicate that Alcanivorax bacteria could be major degraders of PP in mesopelagic environments. Alcanivorax bacteria did not use liquid PP as the sole carbon and energy source. Short PP was preferentially degraded, and PP of all lengths appeared to be degraded. Liquid PP was degraded more efficientlyat 10°C than at 20°C, and correspondingly, higher concentrations of another carbon source were required at 10°C. Regarding the degradation of solid PP, an initial degradation sign, oxidation, was detected, but a weight loss of at least 1% was not detected. By using this study as a model, various PP-degrading microbes would start to be clarified.

  • Access to Document (DOI)

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Papers, etc., Registered in KOARA 【 Display / hide 】

Papers, etc., Registered in KOARA 【 Display / hide 】

• Extinguishable garbage disposal container "Chiero" and comprehensive analysis of its microbial flora

  Miyamoto, Kenji

  Keio SFC journal (慶應SFC学会)  23 ( 2 ) 14 - 30 2023

  ISSN  13472828

• Exploration of persistent plastic-degrading bacteria and development of processing and recycling technologies using their functions

  Miyamoto, Kenji

  科学研究費補助金研究成果報告書 2022

• Thermally driven asymmetric reaction using a chiral space of a thermostable esterase

  Miyamoto, Kenji

  科学研究費補助金研究成果報告書 2014

• Bioactive substances from marine cyanobacteria

  Miyamoto, Kenji

  科学研究費補助金研究成果報告書 2014

• Modification of enzyme functions by integration of conformational information and function and sequence

  Miyamoto, Kenji

  科学研究費補助金研究成果報告書 2012

Reviews, Commentaries, etc. 【 Display / hide 】

Reviews, Commentaries, etc. 【 Display / hide 】

• A method to improve enzyme thermostability using support vector machines

  Tsubamoto, Hitomi; Sakakibara, Yasubumi; Yoshida, Shosuke; Miyamoto, Kenji

  Bio Industry 30 ( 8 ) 12 - 19 2013.08

  Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media), Joint Work

Presentations 【 Display / hide 】

Presentations 【 Display / hide 】

• PET樹脂を分解する酵素の発見と利用

  MIYAMOTO KENJI

  慶應テクノモール (東京国際フォーラム) , 

  2017.12

  , 

  Oral presentation (invited, special)

• PET樹脂を食べる微生物～その生い立ちと分解機構～

  MIYAMOTO KENJI

  [Domestic presentation]  化学最前線 (神奈川大学平塚キャンパス) , 

  2017.09

  , 

  Oral presentation (invited, special)

• PET 分解菌の発見と分解機構の解析

  MIYAMOTO KENJI

  [Domestic presentation]  第１回慶應ライフサイエンスシンポジウム (慶應義塾大学協生館) , 

  2017.08

  , 

  Oral presentation (invited, special)

• Thermally driven asymmetric decarboxylation using a thermostable esterase as a chiral space

  MIYAMOTO KENJI

  [International presentation]  18th Japanese-German Workshop on Enzyme Technology, 

  2015.09

  , 

  Oral presentation (invited, special)

• 酵素機能を合理的にデザインする

  MIYAMOTO KENJI

  [Domestic presentation]  公益社団法人　新化学技術推進協会ライフサイエンス技術部会・反応分科会　講演会, 

  2015.01

  , 

  Oral presentation (invited, special)

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Research Projects of Competitive Funds, etc. 【 Display / hide 】

Research Projects of Competitive Funds, etc. 【 Display / hide 】

• 低分子化プラスチック分解菌をプラットフォームとしたサーキュラーエコノミーの創造

  2025.04

  -

  2030.03

  基盤研究(A), Principal investigator

• 難分解性プラスチック分解菌の探索とその機能を利用した加工・リサイクル技術の開発

  2018.04

  -

  2023.03

  MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (A) , Principal investigator

• 好熱性酵素の活性部位を不斉反応場とした熱駆動型反応の実現

  2016.04

  -

  2017.03

  MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Principal investigator

Intellectual Property Rights, etc. 【 Display / hide 】

Intellectual Property Rights, etc. 【 Display / hide 】

• スルホン酸エステル誘導体とその製造方法及びその利用法

  Date applied： 国際出願特許ＷＯ９８／０５６３４  1998 

  Patent, Joint

• トリアゾール誘導体の製造法

  Date applied： 国際出願特許ＷＯ９５／２８３７４  1995 

  Patent, Joint

• 芳香族ポリエステル分解酵素及び該酵素を用いた芳香族ポリエステル分解方法

  Date applied： 特願2015-532867   

  Patent, Joint

• 光学活性4-(2-ハロ-1-ヒドロキシエチル)-2-トリフルオロメチルチアゾールの製造方法

  Date announced： 日本特許　特開平07-170996  1995 

  Patent, Joint

• （Ｒ）－４－（２－ハロ－１－ヒドロキシエチル）－２－トリフルオロメチルチアゾールの製造方法

  Date announced： 日本特許　特開平07-265095  1995 

  Patent, Joint

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Awards 【 Display / hide 】

Awards 【 Display / hide 】

• 第1回イムラ・ジャパン賞

  2017.02, 株式会社イム・ラジャパン

• 第1回イムラジャパン賞

  宮本憲二, 2017.02, 株式会社イムラジャパン, PET分解酵素の活性向上に関する研究

Courses Taught 【 Display / hide 】

Courses Taught 【 Display / hide 】

• BACHELOR'S THESIS

  2026

• ADVANCED SCIENCES FOR DRUG DISCOVERY

  2026

• SEMINAR IN BIOSCIENCES AND INFORMATICS 2

  2026

• INDEPENDENT STUDY ON FUNDAMENTAL SCIENCE AND TECHNOLOGY

  2026

• ADVANCED LABORATORY COURSE IN BIOSCIENCES AND INFORMATICS D

  2026

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Courses Previously Taught 【 Display / hide 】

Courses Previously Taught 【 Display / hide 】

• 生化学

  慶應義塾大学理工学部

  2018.04

  -

  2019.03

• 分子細胞生物学の基礎

  慶應義塾大学理工学部

  2018.04

  -

  2019.03

• 自然化学実験

  慶應義塾大学理工学部

  2018.04

  -

  2019.03

• 生体反応論第2

  慶應義塾大学

  2018.04

  -

  2019.03

• 生物有機化学

  Keio University

  2017.04

  -

  2018.03

  , 

  Spring Semester, Lecture, Within own ｆaculty

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Social Activities 【 Display / hide 】

Social Activities 【 Display / hide 】

• Biocatalysis and Biotransformation

  2007.11

  -

  Present

Memberships in Academic Societies 【 Display / hide 】

Memberships in Academic Societies 【 Display / hide 】

• 酵素工学研究会, 

  2010.04

  -

  Present

• 日本ケミカルバイオロジー学会, 

  2010.04

  -

  Present

• 生体触媒化学研究会, 

  2009.04

  -

  Present

• バイオインダストリー協会, 

  2007.10

  -

  Present

• 有機合成化学協会, 

  1992.04

  -

  2014.03

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Committee Experiences 【 Display / hide 】

Committee Experiences 【 Display / hide 】

• 2013.04

  -

  2015.03

  関東支部幹事, 日本農芸化学会

• 2012.04

  -

  Present

  ATP小委員会員, 日本化学会

• 2010.04

  -

  Present

  幹事, 新規素材探索研究会

• 2010.04

  -

  Present

  会員, 日本ケミカルバイオロジー学会

• 2010.04

  -

  Present

  Member, 酵素工学研究会

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