Doi, Nobuhide

写真a

Affiliation

Faculty of Science and Technology, Department of Biosciences and Informatics (Yagami)

Position

Professor

Related Websites

Profile Summary 【 Display / hide

  • '''''''This laboratory focuses on the biophysics/biotechnology of macromolecules, especially proteins, used to develop new methodologies for solving various biological problems that are resistant to conventional analytical approaches. Also studied is the development of new methods for in vitro selection and directed evolution of proteins, protein folding and design, origin and evolution of life, and high-throughput screening of protein interactions.'''''''

Career 【 Display / hide

  • 1997.04
    -
    2000.03

    三菱化学生命科学研究所

  • 2000.04
    -
    2002.03

    慶應義塾大学理工学部応用化学科 助手

  • 2002.04
    -
    2003.03

    慶應義塾大学理工学部生命情報学科 助手

  • 2003.04
    -
    2008.03

    慶應義塾大学理工学部生命情報学科 専任講師

  • 2005.10
    -
    2007.09

    兼慶應義塾大学理工学部生命情報学科 広報委員

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Academic Background 【 Display / hide

  • 1997.03

    Hokkaido University, Graduate School of Environmental Earth Sciences, 生態環境科学専攻

    Graduate School, Completed, Doctoral course

Academic Degrees 【 Display / hide

  • Environmental Science, Hokkaido University, 1997.03

 

Research Areas 【 Display / hide

  • Biomedical engineering/Biomaterial science and engineering (薬物送達システム)

  • Biofunction/Bioprocess (生物機能工学)

  • System genome science (蛋白質ネットワーク)

  • Molecular biology

  • Biophysics

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Research Keywords 【 Display / hide

  • Drug delivery system

  • Proteomics

  • Synthetic Biology

  • Antibody Engineering

  • Evolutionary Molecular Engineering

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Books 【 Display / hide

  • ドラッグデリバリーシステム - バイオ医薬品創成に向けた組織、細胞内、核内送達技術の開発-

    土居信英, シーエムシー出版, 2018.06

    Scope: pp.131-137

  • 医療・診断をささえるペプチド科学 - 再生医療・DDS・診断への応用 -

    土居信英, シーエムシー出版, 2017.10

    Scope: pp.232-238

  • ペプチド医薬品のスクリーニング・安定化・製剤化技術

    須藤慧,藤原慶,土居信英, 技術情報協会, 2017

  • 進化分子工学 ~高速分子進化によるタンパク質・核酸の開発~

    土居 信英、柳川弘志, NTS出版, 2013.10

    Scope: pp.275-286

  • 次世代医薬開発に向けた抗体工学の最前線

    土居信英, シーエムシー出版, 2012.12

    Scope: pp.66-73

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Papers 【 Display / hide

  • Cell-sized confinement controls generation and stability of a protein wave for spatiotemporal regulation in cells

    Kohyama S., Yoshinaga N., Yanagisawa M., Fujiwara K., Doi N.

    eLife (eLife)  8 2019.07

     View Summary

    © Kohyama et al. The Min system, a system that determines the bacterial cell division plane, uses changes in the localization of proteins (a Min wave) that emerges by reaction-diffusion coupling. Although previous studies have shown that space sizes and boundaries modulate the shape and speed of Min waves, their effects on wave emergence were still elusive. Here, by using a microsized fully confined space to mimic live cells, we revealed that confinement changes the conditions for the emergence of Min waves. In the microsized space, an increased surface-tovolume ratio changed the localization efficiency of proteins on membranes, and therefore, suppression of the localization change was necessary for the stable generation of Min waves. Furthermore, we showed that the cell-sized space strictly limits parameters for wave emergence because confinement inhibits both the instability and excitability of the system. These results show that confinement of reaction-diffusion systems has the potential to control spatiotemporal patterns in live cells.

  • A dual system using compartmentalized partnered replication for selection of arsenic-responsive transcriptional regulator

    Aye S., Fujiwara K., Doi N.

    J. Biochem. 164 ( 5 ) 341 - 348 2018.11

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  0021924X

  • Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication

    Aye, S.L., Fujiwara, K., Ueki, A., Doi, N.

    Biochem. Biophys. Res. Commun. (Biochemical and Biophysical Research Communications)  499 ( 2 ) 170 - 176 2018.05

    Research paper (scientific journal), Joint Work, Accepted,  ISSN  0006291X

     View Summary

    © 2018 Elsevier Inc. Although compartmentalized self-replication (CSR) and compartmentalized partnered replication (CPR) are powerful tools for directed evolution of proteins and gene circuits, limitations remain in the emulsion PCR process with the wild-type Taq DNA polymerase used so far, including long run times, low amounts of product, and false negative results due to inhibitors. In this study, we developed a high-efficiency mutant of DNA polymerase I from Thermus thermophilus HB27 (Tth pol) suited for CSR and CPR. We modified the wild-type Tth pol by (i) deletion of the N-terminal 5′ to 3′ exonuclease domain, (ii) fusion with the DNA-binding protein Sso7d, (iii) introduction of four known effective point mutations from other DNA polymerase mutants, and (iv) codon optimization to reduce the GC content. Consequently, we obtained a mutant that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, we performed four rounds of CSR selection with a randomly mutated library of this modified Tth pol and obtained mutants that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol.

  • Artificial cell fermentation as a platform for highly efficient cascade conversion

    Fujiwara, K., Adachi, T., Doi, N.

    ACS Synth. Biol. (ACS Synthetic Biology)  7 ( 2 ) 363 - 370 2018.02

    Research paper (scientific journal), Joint Work, Accepted

     View Summary

    © 2017 American Chemical Society. Because of its high specificity and stereoselectivity, cascade reactions using enzymes have been attracting attention as a platform for chemical synthesis. However, the sensitivity of enzymes outside their optimum conditions and their rapid decrease of activity upon dilution are drawbacks of the system. In this study, we developed a system for cascade enzymatic conversion in bacteria-shaped liposomes formed by hypertonic treatment, and demonstrated that the system can overcome the drawbacks of the enzymatic cascade reactions in bulk. This system produced final products at a level equivalent to the maximum concentration of the bulk system (0.10 M, e.g., 4.6 g/L), and worked even under conditions where enzymes normally lose their function. Under diluted conditions, the conversion rate of the artificial cell system was remarkably higher than that in the bulk system. Our results indicate that artificial cells can behave as a platform to perform fermentative production like microorganisms.

  • In vitro transcription–translation using bacterial genome as a template to reconstitute intracellular profile

    Fujiwara, K., Sawamura, T., Niwa, T., Deyama, T., Nomura, S.M., Taguchi, H., Doi, N.

    Nucleic Acids Res. 45 ( 19 ) 11449 - 11458 2017.11

    Research paper (scientific journal), Joint Work, Accepted

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

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Reviews, Commentaries, etc. 【 Display / hide

  • mRNAディスプレイによる翻訳アレスト配列の大規模探索

    濱野理,土居信英

    生物工学 (日本生物工学会)  97 ( 8 ) 10 - 12 2019.08

    Introduction and explanation (scientific journal), Joint Work

  • ヒト由来膜融合ペプチドによるバイオ医薬のDDS

    土居 信英

    細胞 49 ( 12 ) 602 - 605 2017.10

    Introduction and explanation (scientific journal), Single Work

  • マイクロカプセルを利用した制限酵素および受容体リガンドの試験管内選択法

    土居 信英, 柳川 弘志

    バイオテクノロジージャーナル 1 ( 1-2 ) 84 - 86 2005.01

    Introduction and explanation (scientific journal), Joint Work

  • 生命の理解と制御に向けた遺伝子ネットワーク解析

    土居 信英, 柳川 弘志

    Bioベンチャー 4 ( 4 ) 54 - 56 2004.07

    Introduction and explanation (scientific journal), Joint Work

  • タンパク質相互作用のハイスループット解析に向けて―新しい蛍光標識法とマイクロアレイ技術の融合

    土居 信英, 柳川 弘志

    Bioベンチャー 2   102 - 105 2002.06

    Introduction and explanation (scientific journal), Joint Work

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Presentations 【 Display / hide

  • Application of a human-derived fusogenic peptide to intracellular delivery of therapeutic peptides

    Kikuchi, M., Iwaki, K., Fujiwara, K., Doi, N.

    The Cold Spring Harbor Asia conference on Chemical Biology and Drug Discovery (Suzhou, China) , 2019.10, Poster (general)

  • ヒト由来膜透過促進ペプチドS19を利用したsiRNAデリバリー

    中村桃子,藤原慶,土居信英

    第35回日本DDS学会学術集会, 2019.07, Oral Presentation(general)

  • ヒト・シンシチン1由来膜透過促進ペプチドのアラニンスキャニング変異解析

    鈴木麻友子,岩城洸汰,須藤慧,藤原慶,土居信英

    第35回日本DDS学会学術集会, 2019.07, Poster (general)

  • LDL受容体を標的とする細胞選択的なタンパク質のデリバリーのためのヒト由来膜透過促進ペプチドの最適化

    前村帆南,岩城洸汰,藤原慶,土居信英

    第35回日本DDS学会学術集会, 2019.07, Oral Presentation(general)

  • ペプチド医薬の細胞質送達に向けたヒト由来膜透過促進ペプチドの応用

    菊地萌希,岩城洸汰,藤原慶,土居信英

    第35回日本DDS学会学術集会, 2019.07, Poster (general)

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

  • 細胞内の創薬ターゲットに対するがん細胞選択的な膜透過抗体医薬の開発

    2020.04
    -
    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, 土居 信英, Grant-in-Aid for Scientific Research (B), Principal Investigator

Intellectual Property Rights, etc. 【 Display / hide

  • 融合タンパク質又は複合タンパク質,細胞内送達用担体,部分ペプチド,細胞膜透過促進剤,DNA,及びベクター

    Application No.: PCT/JP2016/066455  2015.06 

    Patent, Joint, PCT international application

 

Courses Taught 【 Display / hide

  • TOPICS IN BIOSCIENCES AND INFORMATICS 1

    2020

  • SEMINAR IN BIOSCIENCES AND INFORMATICS

    2020

  • MOLECULAR BIOLOGY 2

    2020

  • MOLECULAR BIOLOGY 1

    2020

  • METHODOLOGY FOR POST-GENOME BIOSCIENCES

    2020

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Courses Previously Taught 【 Display / hide

  • 微生物学

    Keio University, 2015, Spring Semester, General education subject, Lecture

 

Memberships in Academic Societies 【 Display / hide

  • 日本生物工学会, 

    2014
    -
    Present
  • 日本DDS学会, 

    2014
    -
    Present
  • 細胞を創る研究会, 

    2013
    -
    Present
  • 日本癌学会, 

    2010
    -
    Present
  • 日本分子生物学会, 

    1994
    -
    Present

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Committee Experiences 【 Display / hide

  • 2018.01
    -
    Present

    JB編集委員会 編集委員 (Associate Editor), 日本生化学会