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Regulation of the transition states of the enzymes for alkane production by controlling their conformational fluctuations

Research Project

Project/Area Number 15KT0139
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Transition State Control
Research InstitutionThe University of Tokyo

Principal Investigator

Arai Munehito  東京大学, 大学院総合文化研究科, 教授 (90302801)

Co-Investigator(Kenkyū-buntansha) 林 勇樹  東京大学, 大学院総合文化研究科, 助教 (90444059)
Project Period (FY) 2015-07-10 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsタンパク質 / 酵素反応 / 分子動力学 / NMR / バイオエネルギー
Outline of Final Research Achievements

Recent advances in protein chemistry have revealed that global conformational change of an enzyme is closely related to formation of the transition state and thus constitutes the rate-determining step in an enzyme reaction. Here, using two enzymes, acyl-ACP reductase (AAR) and aldehyde-deformylating oxygenase (ADO), which are indispensable for biofuel production, we detected conformational fluctuations of enzymes by molecular dynamics simulations (theory) and NMR relaxation measurements (experiment). We then searched for residues essential for controlling conformational fluctuations of the enzymes. Introduction of mutations at these residues resulted in changes of activities, indicating that regulation of the transition state of an enzyme is possible by such mutations. We also performed comprehensive mutational analysis including alanine-scanning mutagenesis on AAR and ADO by making more than 600 mutants and succeeded in identifying the residues important for controlling activities.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (39 results)

All 2018 2017 2016 2015 Other

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 4 results,  Acknowledgement Compliant: 1 results) Presentation (30 results) (of which Invited: 1 results) Remarks (2 results)

  • [Journal Article] Unified understanding of folding and binding mechanisms of globular and intrinsically disordered proteins2018

    • Author(s)
      M. Arai
    • Journal Title

      Biophysical Reviews

      Volume: 10 Issue: 2 Pages: 163-181

    • DOI

      10.1007/s12551-017-0346-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Interaction of the GntR-family transcription factor Sll1961 with thioredoxin in the cyanobacterium Synechocystis sp. PCC 68032018

    • Author(s)
      Kujirai, J., Nanba, S., Kadowaki, T., Oka, Y., Nishiyama, Y., Hayashi, Y., Arai, M. and Hihara, Y.
    • Journal Title

      Sci. Rep.

      Volume: 8 Issue: 1 Pages: 6666-6666

    • DOI

      10.1038/s41598-018-25077-5

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Formation of the chaperonin complex studied by 2D NMR spectroscopy2017

    • Author(s)
      Takenaka Toshio、Nakamura Takashi、Yanaka Saeko、Yagi-Utsumi Maho、Chandak Mahesh S.、Takahashi Kazunobu、Paul Subhankar、Makabe Koki、Arai Munehito、Kato Koichi、Kuwajima Kunihiro
    • Journal Title

      PLOS ONE

      Volume: 12 Issue: 10 Pages: 187022-187022

    • DOI

      10.1371/journal.pone.0187022

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Highly Heterogeneous Nature of the Native and Unfolded States of the B Domain of Protein A Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy2017

    • Author(s)
      Otosu Takuhiro、Ishii Kunihiko、Oikawa Hiroyuki、Arai Munehito、Takahashi Satoshi、Tahara Tahei
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 121 Issue: 22 Pages: 5463-5473

    • DOI

      10.1021/acs.jpcb.7b00546

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] ラン藻由来アルカン合成関連酵素の高活性化と軽油生産性の向上2017

    • Author(s)
      新井宗仁、林勇樹、工藤恒
    • Journal Title

      月刊ファインケミカル

      Volume: 46 Pages: 19-25

    • Related Report
      2016 Research-status Report
    • Acknowledgement Compliant
  • [Journal Article] 多彩な戦略で挑むシアノバクテリア由来の燃料生産 ― 持続可能な第三世代バイオ燃料生産の最前線2017

    • Author(s)
      日原由香子、朝山宗彦、蘆田弘樹、天尾豊、新井宗仁、粟井光一郎、得平茂樹、小山内崇、鞆達也、成川礼、蓮沼誠久、増川一
    • Journal Title

      化学と生物

      Volume: 55 Pages: 88-97

    • NAID

      130006316058

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Comparison of aldehyde-producing activities of cyanobacterial acyl-(acyl carrier protein) reductases2016

    • Author(s)
      Hisashi Kudo, Ryota Nawa, Yuuki Hayashi, & Munehito Arai
    • Journal Title

      Biotechnology for Biofuels

      Volume: 9 Issue: 1 Pages: 234-234

    • DOI

      10.1186/s13068-016-0644-5

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 進化分子工学によるフィチン酸加水分解酵素の低温活性向上2018

    • Author(s)
      和田愛未、林勇樹、新井宗仁
    • Organizer
      日本農芸化学会2018年度大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] ラン藻由来アシルACP還元酵素の変異解析による炭化水素合成量の向上2018

    • Author(s)
      工藤恒、林勇樹、新井宗仁
    • Organizer
      第7回日本生物物理学会関東支部会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 細胞内GTP定量センサーの開発2018

    • Author(s)
      岡芳樹、竹内恒、林勇樹、新井宗仁
    • Organizer
      第4回筑波大-KEK連携セミナー「生命の機能とかたち」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] ラン藻由来アルカン合成関連酵素の機能解析2017

    • Author(s)
      工藤恒、名和良太、榛葉啓悟、林勇樹、新井宗仁
    • Organizer
      第6回日本生物物理学会関東支部会
    • Place of Presentation
      早稲田大学先端生命医科学センター(東京都新宿区)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Research-status Report
  • [Presentation] 進化分子工学によるフィチン酸塩加水分解酵素の活性向上2017

    • Author(s)
      和田愛未、林勇樹、新井宗仁
    • Organizer
      第6回日本生物物理学会関東支部会
    • Place of Presentation
      早稲田大学先端生命医科学センター(東京都新宿区)
    • Year and Date
      2017-03-13
    • Related Report
      2016 Research-status Report
  • [Presentation] In vivo real-time measurement of fatty aldehyde and its application2017

    • Author(s)
      Yuuki Hayashi, Munehito Arai
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 細胞内酵素活性の可視化によるアシルACP還元酵素の進化分子工学2017

    • Author(s)
      林勇樹、新井宗仁
    • Organizer
      第69回日本生物工学会大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 進化分子工学によるフィチン酸塩加水分解酵素の活性向上2017

    • Author(s)
      和田愛未、林勇樹、新井宗仁
    • Organizer
      第17回日本蛋白質科学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Structural and functional analysis of a cyanobacterial enzyme for alkane biosynthesis2016

    • Author(s)
      Hisashi Kudo, Ryota Nawa, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-26
    • Related Report
      2016 Research-status Report
  • [Presentation] Alanine scanning mutagenesis reveals functional roles of conserved residues in an enzyme for alkane biosynthesis2016

    • Author(s)
      Masashi Nomura, Hisashi Kudo, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-26
    • Related Report
      2016 Research-status Report
  • [Presentation] Improving activity of a phytate-hydrolyzing enzyme by directed evolution2016

    • Author(s)
      Manami Wada, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Structural dynamics of a cyanobacterial alkane synthase studied by NMR and molecular dynamics simulations2016

    • Author(s)
      Yuma Suematsu, Yuji O. Kamatari, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Search for the binding sites between two enzymes essential for cyanobacterial alkane biosynthesis2016

    • Author(s)
      Mari Chang, Keigo Shinba, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] Alanine scanning mutagenesis of a cyanobacterial alkane synthase2016

    • Author(s)
      Keigo Shimba, Fumitaka Yasugi, Yuuki Hayashi, Munehito Arai
    • Organizer
      第54回日本生物物理学会年会
    • Place of Presentation
      つくば国際会議場(茨城県つくば市)
    • Year and Date
      2016-11-25
    • Related Report
      2016 Research-status Report
  • [Presentation] ラン藻由来アルカン合成関連酵素を利用したバイオエネルギー生産2016

    • Author(s)
      工藤恒、名和良太、林勇樹、渡辺麻衣、池内昌彦、新井宗仁
    • Organizer
      酵素工学研究会 第76回講演会
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2016-10-07
    • Related Report
      2016 Research-status Report
  • [Presentation] 脂肪酸アシルACP還元酵素のin vivo迅速活性評価法の開発2016

    • Author(s)
      林勇樹、新井宗仁
    • Organizer
      第68回日本生物工学会年次大会
    • Place of Presentation
      富山国際会議場(富山県富山市)
    • Year and Date
      2016-09-30
    • Related Report
      2016 Research-status Report
  • [Presentation] ラン藻でのアルカン合成に必要な2つの酵素間の結合部位の探索2016

    • Author(s)
      張マリ、榛葉啓悟、林勇樹、新井宗仁
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Year and Date
      2016-06-08
    • Related Report
      2016 Research-status Report
  • [Presentation] アルカン合成酵素ADのNMRと分子動力学シミュレーションによるダイナミクス解析2016

    • Author(s)
      末松佑麿、鎌足雄司、林勇樹、新井宗仁
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Year and Date
      2016-06-08
    • Related Report
      2016 Research-status Report
  • [Presentation] ラン藻由来アルカン合成関連酵素の構造機能解析2016

    • Author(s)
      工藤恒、名和良太、林勇樹、新井宗仁
    • Organizer
      第16回日本蛋白質科学会年会
    • Place of Presentation
      福岡国際会議場(福岡県福岡市)
    • Year and Date
      2016-06-07
    • Related Report
      2016 Research-status Report
  • [Presentation] バイオエネルギーをつくる2016

    • Author(s)
      新井宗仁
    • Organizer
      東京大学教養学部統合自然科学科 駒場サイエンス倶楽部
    • Place of Presentation
      東京大学(東京都目黒区)
    • Year and Date
      2016-05-20
    • Related Report
      2016 Research-status Report
  • [Presentation] タンパク質のフォールディングとデザイン2016

    • Author(s)
      新井宗仁
    • Organizer
      東京大学 大学院理学系研究科 物理学専攻 A7サブコース 第3回シンポジウム「生物物理の新展開」
    • Place of Presentation
      東京大学(東京都文京区)
    • Year and Date
      2016-05-20
    • Related Report
      2016 Research-status Report
  • [Presentation] ラン藻由来アルカン合成関連酵素の構造機能解析とバイオエネルギー生産への応用2016

    • Author(s)
      工藤恒、名和良太、林勇樹、渡辺麻衣、池内昌彦、新井宗仁
    • Organizer
      第16回 東京大学生命科学シンポジウム
    • Place of Presentation
      東京大学(東京都目黒区)
    • Year and Date
      2016-04-23
    • Related Report
      2016 Research-status Report
  • [Presentation] シアノバクテリアSynechocystis sp. PCC 6803における転写因子Sll1961とチオレドキシンとの相互作用解析2016

    • Author(s)
      鯨井 純一、門脇太朗、新井宗仁、久堀徹、日原由香子
    • Organizer
      第57回日本植物生理学会年会
    • Place of Presentation
      岩手大学(岩手県盛岡市)
    • Year and Date
      2016-03-19
    • Related Report
      2015 Research-status Report
  • [Presentation] ラン藻由来アルカン合成関連酵素の構造機能解析とバイオエネルギー生産への応用2016

    • Author(s)
      工藤恒、名和良太、林勇樹、渡辺麻衣、池内昌彦、新井宗仁
    • Organizer
      第5回日本生物物理学会関東支部会
    • Place of Presentation
      桐生地域地場産業振興センター(群馬県桐生市)
    • Year and Date
      2016-03-11
    • Related Report
      2015 Research-status Report
  • [Presentation] ラン藻でのアルカン合成に必要な2つの酵素間の結合部位の探索2016

    • Author(s)
      張マリ、榛葉啓悟、林勇樹、新井宗仁
    • Organizer
      第5回日本生物物理学会関東支部会
    • Place of Presentation
      桐生地域地場産業振興センター(群馬県桐生市)
    • Year and Date
      2016-03-10
    • Related Report
      2015 Research-status Report
  • [Presentation] シアノバクテリア由来アルカン合成関連酵素の機能解析及びバイオエネルギー生産への応用2015

    • Author(s)
      工藤恒、名和良太、林勇樹、渡辺麻衣、池内昌彦、新井宗仁
    • Organizer
      藍藻の分子生物学2015
    • Place of Presentation
      かずさアカデミアホール(千葉県木更津市)
    • Year and Date
      2015-11-16
    • Related Report
      2015 Research-status Report
  • [Presentation] Functional analysis of the cyanobacterial enzyme for alkane biosynthesis and its application for bioenergy production2015

    • Author(s)
      Hisashi Kudo, Ryota Nawa, Yuuki Hayashi, Mai Watanabe, Masahiko Ikeuchi, Munehito Arai
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-14
    • Related Report
      2015 Research-status Report
  • [Presentation] Structural dynamics of a cyanobacterial alkane-producing enzyme, aldehyde deformylating oxygenase, studied by NMR and MD simulations2015

    • Author(s)
      Yuuma Suematsu, Yuuki Hayashi, Munehito Arai
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-14
    • Related Report
      2015 Research-status Report
  • [Presentation] The search for the binding sites between two enzymes essential for cyanobacterial alkane biosynthesis2015

    • Author(s)
      Mari Chang, Yuuki Hayashi, Munehito Arai
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] Residues essential for the alkane producing activity of aldehyde deformylating oxygenase revealed by alanine scanning mutagenesis2015

    • Author(s)
      Keigo Shimba, Fumitaka Yasugi, Yuuki Hayashi, Munehito Arai
    • Organizer
      第53回日本生物物理学会年会
    • Place of Presentation
      金沢大学(石川県金沢市)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Remarks] 新井研究室のホームページ

    • URL

      http://folding.c.u-tokyo.ac.jp

    • Related Report
      2017 Annual Research Report
  • [Remarks] 新井研究室のホームページ

    • URL

      http://folding.c.u-tokyo.ac.jp/

    • Related Report
      2016 Research-status Report 2015 Research-status Report

URL: 

Published: 2015-07-14   Modified: 2019-03-29  

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