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Development of protein sequence data mining method to design total sequence of artificial amino acid metabolism enzymes

Research Project

Project/Area Number 18K14391
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 38030:Applied biochemistry-related
Research InstitutionUniversity of Shizuoka

Principal Investigator

Nakano Shogo  静岡県立大学, 食品栄養科学部, 助教 (80748541)

Project Period (FY) 2018-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2018: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
KeywordsL-アミノ酸酸化酵素 / 祖先型設計 / D-アミノ酸 / 光学分割 / 基質特異性 / アミノ酸酸化酵素 / L-アミノ酸 / タンパク質工学 / 人工タンパク質 / アミノ酸代謝関連酵素 / 祖先型設計法
Outline of Final Research Achievements

In this study, we try to develop a method to curate protein sequence data and increase succession rate for the design of highly functional artificial enzymes. By applying the method to the design of two enzymes belonging to L-amino acid oxidase family (L-arginine oxidase and L-amino acid oxidase), we can generate artificial enzymes bearing high stability, solubility and reactivity with ancestral sequence reconstruction.

Academic Significance and Societal Importance of the Research Achievements

データベースに登録されるアミノ酸配列データは今後も際限なく拡大していくと予測されている。本手法は拡大を続ける配列データベースから必要な情報を選抜し、高機能化した人工酵素配列の設計を可能にするなど、配列データベースの持つ潜在能力を引き出すことができる。また本研究で得られた人工酵素群の機能は、自然界のものより優れており、産業応用への展開が期待できるものも多かった。本成果は人工酵素は自然界由来の酵素より機能が劣るという、一般論を覆すものであると考えている。

Report

(3 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • Research Products

    (19 results)

All 2020 2019 2018

All Journal Article (14 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 12 results,  Open Access: 7 results) Presentation (4 results) (of which Int'l Joint Research: 2 results,  Invited: 3 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] Elucidation of Molecular Mechanism of a Selective PPARα Modulator, Pemafibrate, through Combinational Approaches of X-ray Crystallography, Thermodynamic Analysis, and First-Principle Calculations2020

    • Author(s)
      Kawasaki Mayu、Kambe Akira、Yamamoto Yuta、Arulmozhiraja Sundaram、Ito Sohei、Nakagawa Yoshimi、Tokiwa Hiroaki、Nakano Shogo、Shimano Hitoshi
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 21 Issue: 1 Pages: 361-361

    • DOI

      10.3390/ijms21010361

    • NAID

      120007132701

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Deracemization and Stereoinversion to Aromatic d-Amino Acid Derivatives with Ancestral l-Amino Acid Oxidase2019

    • Author(s)
      Nakano Shogo、Minamino Yuki、Hasebe Fumihito、Ito Sohei
    • Journal Title

      ACS Catalysis

      Volume: 9 Issue: 11 Pages: 10152-10158

    • DOI

      10.1021/acscatal.9b03418

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Competitive Binding Assay with an Umbelliferone-Based Fluorescent Rexinoid for Retinoid X Receptor Ligand Screening2019

    • Author(s)
      Yamada Shoya、Kawasaki Mayu、Fujihara Michiko、Watanabe Masaki、Takamura Yuta、Takioku Maho、Nishioka Hiromi、Takeuchi Yasuo、Makishima Makoto、Motoyama Tomoharu、Ito Sohei、Tokiwa Hiroaki、Nakano Shogo、Kakuta Hiroki
    • Journal Title

      Journal of Medicinal Chemistry

      Volume: 62 Issue: 19 Pages: 8809-8818

    • DOI

      10.1021/acs.jmedchem.9b00995

    • NAID

      120006882792

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Kinetics-based structural requirements of human immunoglobulin G binding peptides2019

    • Author(s)
      Kyohei Muguruma, Konomi Fujita, Akane Fukuda, Satoshi Kishimoto, Soichiro Sakamoto, Risako Arima, Mayu Ito, Mayu Kawasaki, Shogo Nakano, Sohei Ito, Kanade Shimizu, Akihiro Taguchi, Kentaro Takayama, Atsuhiko Taniguchi, Yuji Ito, Yoshio Hayashi
    • Journal Title

      ACS Omega

      Volume: 4 Issue: 11 Pages: 14390-14397

    • DOI

      10.1021/acsomega.9b01104

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Following the Evolutionary Track of a Highly Specific L-Arginine Oxidase by Reconstruction and Biochemical Analysis of Ancestral and Native Enzymes2019

    • Author(s)
      Nakano Shogo、Niwa Masazumi、Asano Yasuhisa、Ito Sohei
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 10 Issue: 12 Pages: 00459-00459

    • DOI

      10.1128/aem.00459-19

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Development of analysis toolkit to visualize interaction energies generated by fragment molecular orbital calculations2018

    • Author(s)
      Takaki Tokiwa, Shogo Nakano, Yuta Yamamoto, Takeshi Ishikawa, Sohei Ito, Vladimir Sladek, Kaori Fukuzawa, Yuji Mochizuki, Hiroaki Tokiwa, Fuminori Misaizu, and Yasuteru Shigeta
    • Journal Title

      J. Chem. Info. Model

      Volume: 59(1) Issue: 1 Pages: 25-30

    • DOI

      10.1021/acs.jcim.8b00649

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα)2018

    • Author(s)
      Miyashita Yurina、Numoto Nobutaka、Arulmozhiraja Sundaram、Nakano Shogo、Matsuo Naoya、Shimizu Kanade、Shibahara Osamu、Fujihara Michiko、Kakuta Hiroki、Ito Sohei、Ikura Teikichi、Ito Nobutoshi、Tokiwa Hiroaki
    • Journal Title

      FEBS Letters

      Volume: 593 Issue: 2 Pages: 242-250

    • DOI

      10.1002/1873-3468.13301

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Improvement of ST0452 N-Acetylglucosamine-1-Phosphate Uridyltransferase Activity by the Cooperative Effect of Two Single Mutations Identified through Structure-Based Protein Engineering2018

    • Author(s)
      Honda Yuki、Nakano Shogo、Ito Sohei、Dadashipour Mohammad、Zhang Zilian、Kawarabayasi Yutaka
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 84 Issue: 24

    • DOI

      10.1128/aem.02213-18

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Computational Molecular Docking and X-ray Crystallographic Studies of Catechins in New Drug Design Strategies2018

    • Author(s)
      Nakano Shogo、Megro Shin-ichi、Hase Tadashi、Suzuki Takuji、Isemura Mamoru、Nakamura Yoriyuki、Ito Sohei
    • Journal Title

      Molecules

      Volume: 23 Issue: 8 Pages: 2020-2020

    • DOI

      10.3390/molecules23082020

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] In Vitro and In Silico Studies of the Molecular Interactions of Epigallocatechin-3-O-gallate (EGCG) with Proteins That Explain the Health Benefits of Green Tea2018

    • Author(s)
      Saeki Koichi、Hayakawa Sumio、Nakano Shogo、Ito Sohei、Oishi Yumiko、Suzuki Yasuo、Isemura Mamoru
    • Journal Title

      Molecules

      Volume: 23 Issue: 6 Pages: 1295-1295

    • DOI

      10.3390/molecules23061295

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Binding of Catechins to Staphylococcal Enterotoxin A2018

    • Author(s)
      2.Shimamura, Y., Utsumi, M., Hirai, C., Nakano, S., Ito, S., Tsuji, A., Ishii, T., Hosoya, T., Kan, T., Ohashi, N., Masuda. S
    • Journal Title

      Molecules

      Volume: 23(5) Issue: 5 Pages: 1125-1125

    • DOI

      10.3390/molecules23051125

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Benchmark analysis of native and artificial NAD+-dependent enzymes generated by a sequence based design method with or without phylogenetic data2018

    • Author(s)
      Shogo Nakano, Tomoharu Motoyama, Yurina Miyashita, Yuki Ishizuka, Naoya Matsuo, Hiroaki Tokiwa, Suguru Shinoda, Yasuhisa Asano, and Sohei Ito
    • Journal Title

      Biochemistry

      Volume: 57(26) Issue: 26 Pages: 3722-3732

    • DOI

      10.1021/acs.biochem.8b00339

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] 新規アミノ酸配列解析手法の開発とタンパク質工学への応用2018

    • Author(s)
      中野 祥吾
    • Journal Title

      生物工学会誌

      Volume: 96 Pages: 573-577

    • Related Report
      2018 Research-status Report
  • [Journal Article] タンパク質の二次構造とアミノ酸の疎水性度に基づいた凝集に関連するホットスポットの合理的同定法2018

    • Author(s)
      松井 大亮, 中野 祥吾, Mohammad Dadashipour, 浅野 泰久
    • Journal Title

      酵素工学ニュース

      Volume: 80

    • Related Report
      2018 Research-status Report
  • [Presentation] In silicoでタンパク質を創る2019

    • Author(s)
      中野 祥吾
    • Organizer
      細胞を創る研究会12.0
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Reconstruction of ancestral L-amino acid oxidase to broaden substrate selectivity2019

    • Author(s)
      Shogo Nakano
    • Organizer
      Enzyme Engineering XXV
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Filling a gap between computational and experimental researches through sequence-based protein design2018

    • Author(s)
      Shogo Nakano
    • Organizer
      The 4th International Conference on Pharma and Food (ICPF) 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 新規アミノ酸配列解析手法、INTMSAlign の開発と応用2018

    • Author(s)
      中野 祥吾
    • Organizer
      第138回日本薬学会大会
    • Related Report
      2018 Research-status Report
    • Invited
  • [Patent(Industrial Property Rights)] 糖鎖結合性一本鎖抗体およびその作製方法2019

    • Inventor(s)
      隅田泰生,常盤広明,伊藤創平,中野祥吾,新地浩之
    • Industrial Property Rights Holder
      隅田泰生,常盤広明,伊藤創平,中野祥吾,新地浩之
    • Industrial Property Rights Type
      特許
    • Patent Publication Number
      2019-199472
    • Filing Date
      2019
    • Related Report
      2019 Annual Research Report

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Published: 2018-04-23   Modified: 2021-02-19  

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