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Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules

Planned Research

Project AreaNovel measurement techniques for visualizing 'live' protein molecules at work
Project/Area Number 26119002
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionKyushu University

Principal Investigator

Kohda Daisuke  九州大学, 生体防御医学研究所, 教授 (80186618)

Co-Investigator(Kenkyū-buntansha) 稲垣 冬彦  公益財団法人微生物化学研究会, 微生物化学研究所, 客員研究員 (70011757)
Project Period (FY) 2014-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥225,290,000 (Direct Cost: ¥173,300,000、Indirect Cost: ¥51,990,000)
Fiscal Year 2018: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2017: ¥37,960,000 (Direct Cost: ¥29,200,000、Indirect Cost: ¥8,760,000)
Fiscal Year 2016: ¥52,260,000 (Direct Cost: ¥40,200,000、Indirect Cost: ¥12,060,000)
Fiscal Year 2015: ¥80,470,000 (Direct Cost: ¥61,900,000、Indirect Cost: ¥18,570,000)
Fiscal Year 2014: ¥16,640,000 (Direct Cost: ¥12,800,000、Indirect Cost: ¥3,840,000)
Keywordsタンパク質結晶 / 動的構造 / 結晶コンタクト / 融合タンパク質 / MBP / Tom20 / Tim21 / タンパク質 / X線結晶解析 / X線小角散乱 / X線結晶解析 / 電子顕微鏡 / 高速AFM / シグナル配列 / X線小角散乱 / 電子顕微鏡単粒子解析 / 高速AFM / 蛋白質 / 核磁気共鳴法 / オリゴ糖転移酵素 / ミトコンドリア
Outline of Final Research Achievements

We developed a fusion protein method to create crystal contact-free space (CCFS) in protein crystals and to place the mobile parts or ligands in the CCFS. The mobile parts/ligands appear as smeared electron densities in the CCFS in the difference electron density map. We applied the CCFS method to visualize the movement of a highly mobile presequence peptide as bound to the mitochondrial import receptor, Tom20, and to estimate the solution conformation of a flexible loop segment in another mitochondrial import protein, Tim21, which was distorted in the conventional crystals by the crystal contacts.

Academic Significance and Societal Importance of the Research Achievements

蛋白質の結晶中では分子同士が接触して3次元の結晶格子を作っている.蛋白質の中には一部の構造が柔らかく創られているために,結晶中では結晶コンタクトにより容易に変形し,正しい形(溶液中の平衡状態)をとっていない可能性がある.柔らかく動的な部分の構造変化は蛋白質の機能と密接に関連していることが少なくないことを考えると,「柔動構造の変形・固定問題」を真剣にとらえ,実験的に解決する手段を考案することは重要である.

Report

(6 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (46 results)

All 2019 2018 2017 2016 2015 2014 Other

All Journal Article (12 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 12 results,  Open Access: 1 results,  Acknowledgement Compliant: 6 results) Presentation (25 results) (of which Int'l Joint Research: 10 results,  Invited: 13 results) Book (1 results) Remarks (8 results)

  • [Journal Article] A Radioisotope-free Oligosaccharyltransferase Assay Method2019

    • Author(s)
      Yamasaki Takahiro、Kohda Daisuke
    • Journal Title

      BIO-PROTOCOL

      Volume: 9 Issue: 5

    • DOI

      10.21769/bioprotoc.3186

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computational investigation of the conformational dynamics in Tom20-mitochondrial presequence tethered complexes2018

    • Author(s)
      Srivastava Arpita、Tama Florence、Kohda Daisuke、Miyashita Osamu
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: 87 Issue: 1 Pages: 81-90

    • DOI

      10.1002/prot.25625

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states2018

    • Author(s)
      Fujinami Daisuke、-Mahin Abdullah-Al、Elsayed Khaled M.、Islam Mohammad R.、Nagao Jun-ichi、Roy Urmi、Momin Sabrina、Zendo Takeshi、Kohda Daisuke、Sonomoto Kenji
    • Journal Title

      Communications Biology

      Volume: 1 Issue: 1 Pages: 150-150

    • DOI

      10.1038/s42003-018-0150-3

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] “Multiple partial recognitions in dynamic equilibrium” in the binding sites of proteins form the molecular basis of promiscuous recognition of structurally diverse ligands2018

    • Author(s)
      Kohda Daisuke
    • Journal Title

      Biophysical Reviews

      Volume: 10 Issue: 2 Pages: 421-433

    • DOI

      10.1007/s12551-017-0365-4

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural Basis of Protein Asn-Glycosylation by Oligosaccharyltransferases2018

    • Author(s)
      Kohda Daisuke
    • Journal Title

      Adv Exp Med Biol.

      Volume: 1104 Pages: 171-199

    • DOI

      10.1007/978-981-13-2158-0_9

    • ISBN
      9789811321573, 9789811321580
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Asn-linked oligosaccharide chain of a crenarchaeon, Pyrobaculum calidifontis, is reminiscent of the eukaryotic high-mannose-type glycan2017

    • Author(s)
      Fujinami Daisuke、Taguchi Yuya、Kohda Daisuke
    • Journal Title

      Glycobiology

      Volume: 27 Issue: 8 Pages: 701-712

    • DOI

      10.1093/glycob/cwx044

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tethering an N-Glycosylation Sequon-Containing Peptide Creates a Catalytically Competent Oligosaccharyltransferase Complex.2017

    • Author(s)
      Matsumoto S, Taguchi Y, Shimada A, Igura M, Kohda D.
    • Journal Title

      Biochemistry

      Volume: 56 Issue: 4 Pages: 602-611

    • DOI

      10.1021/acs.biochem.6b01089

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Comparative analysis of archaeal lipid-linked oligosaccharides that serve as oligosaccharide donors for Asn-glycosylation.2016

    • Author(s)
      Taguchi Y, Fujinami D, Kohda D
    • Journal Title

      J Biol Chem

      Volume: 291 Issue: 21 Pages: 11042-11054

    • DOI

      10.1074/jbc.m115.713156

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structural basis for the recognition of two consecutive mutually interacting DPF motifs by the SGIP1 μ homology domain2016

    • Author(s)
      Shimada A, Yamaguchi A, Kohda D
    • Journal Title

      Scietific Report

      Volume: 6 Issue: 1 Pages: 19565-19565

    • DOI

      10.1038/srep19565

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Comparative analysis of archaeal lipid-linked oligosaccharides that serve as oligosaccharide donors for Asn-glycosylation2016

    • Author(s)
      Taguchi Y, Fujinami D, Kohda D
    • Journal Title

      Journal Biological Chemistry

      Volume: in press

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structural elucidation of an asparagine-linked oligosaccharide from the hyperthermophilic archaeon, Archaeoglobus fulgidus.2015

    • Author(s)
      Fujinami D, Nyirenda J, Matsumoto S, Kohda D
    • Journal Title

      Carbohydrate Research

      Volume: 413 Pages: 55-62

    • DOI

      10.1016/j.carres.2015.05.010

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Rational design of crystal contact-free space in protein crystals for analyzing spatial distribution of motions within protein molecules.2015

    • Author(s)
      Matsuoka R, Shimada A, Komuro Y, Sugita Y, Kohda D
    • Journal Title

      Protein Science

      Volume: 25 Issue: 3 Pages: 754-768

    • DOI

      10.1002/pro.2867

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Visualization of the spatial distribution of a presequence peptide in the binding site of the mitochondrial presequence receptor, Tom20, using crystal contact-free space created in protein crystals2018

    • Author(s)
      韓喜玲,嶋田睦,神田大輔
    • Organizer
      日本生化学会九州支部例会
    • Related Report
      2018 Annual Research Report
  • [Presentation] The lantibiotic Nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states2018

    • Author(s)
      Daisuke Fujinami, Abdullah-Al-Mahin, Khaled M. Elsayed, Jun-ichi Nagao, Takeshi Zendo, Kenji Sonomoto, and Daisuke Kohda
    • Organizer
      XXVIIIth International Conference on Magnetic Resonance in Biological Systems (ICMRBS), アイルランド
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] NMRによる抗菌ペプチドnukacin ISK-1 の溶液構造決定と熱力学的解析2018

    • Author(s)
      藤浪大輔,Abdullah Al Mahin,Khaled M Elsayed,永尾潤ー,善藤 威史,園元謙二,神田大輔
    • Organizer
      第57回NMR討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Creating crystal contact-free space in protein crystals makes the spatial distribution of a presequence peptide in the binding site of the mitochondrial presequence receptor, Tom20, visible2018

    • Author(s)
      韓喜玲,嶋田睦,神田大輔
    • Organizer
      第91回日本生化学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Integrative approach combining electron microscopy and high-speed AFM revealed the dynamic conformational exchange of the oligosaccharyltransferase in lipid bilayers2018

    • Author(s)
      Yuki Kawasaki, Kouta Mayanagi, Ashutosh Srivastava, Hirotaka Ariyama, Florence Tama, Toshio Ando, and Daisuke Kohda
    • Organizer
      第13回研究所ネットワーク国際シンポジウム
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Integrative approach combining electron microscopy and high-speed AFM revealed the dynamic conformational exchange of the oligosaccharyltransferase in lipid bilayers2018

    • Author(s)
      Yuki Kawasaki
    • Organizer
      Workshop “Trends in Computational Molecular Biophysics”
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation2018

    • Author(s)
      Daisuke Kohda
    • Organizer
      The Japanese Biochemical Society Bio-Frontier Symposium, International symposium on ER stress, glycosylation, homeostasis and diseases (埼玉)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation2017

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 10th Anniversary of Protein & Peptide Conference (PepCon-2017)
    • Place of Presentation
      Fukuoka
    • Year and Date
      2017-03-22
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 蛋白質のN型糖鎖転移反応理解のための統合的構造生物学アプローチ2017

    • Author(s)
      神田大輔
    • Organizer
      第44回生体分子科学討論会(秋田)
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Archaeal Glycobiology by MS and NMR2017

    • Author(s)
      Yuya Taguchi, Daisuke Fujinami, and 〇Daisuke Kohda
    • Organizer
      2017 Taiwan-Japan Biomedical Symposium on Magnetic Resonance (Tainan, Taiwan)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] アスパラギン結合型糖鎖転移反応の理解のための統合的構造生物学アプローチ2017

    • Author(s)
      神田大輔
    • Organizer
      第15回糖鎖科学コンソーシアム(JCGG)シンポジウム(福岡)
    • Related Report
      2017 Annual Research Report
  • [Presentation] Integrative Structural Biology Approach to Understand the Structural and Dynamic Basis of Asn-Glycosylation2017

    • Author(s)
      Daisuke Kohda
    • Organizer
      2nd Joint International Symposium of NSRRC and IPR (Hsinchu, Taiwan)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] アスパラギン結合型糖鎖転移反応の理解のための統合的構造生物学アプローチ2016

    • Author(s)
      神田大輔
    • Organizer
      第55回NMR討論会
    • Place of Presentation
      広島
    • Year and Date
      2016-11-18
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Integrative structural biology approach to decipher the molecular mechanism of Asn-glycosylation2016

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 42nd Naito Conference
    • Place of Presentation
      Sapporo
    • Year and Date
      2016-10-07
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Application of “crystal contact-free space” to the study of protein dynamics2015

    • Author(s)
      Daisuke Kohda
    • Organizer
      The 25th Hot Spring Harbor International Symposium
    • Place of Presentation
      九州大学
    • Year and Date
      2015-11-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Crystal contact-free space for analyzing spatial distribution of protein internal motions2015

    • Author(s)
      Daisuke Kohda
    • Organizer
      第53回日本生物物理学会年会シンポジウム
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-13
    • Related Report
      2015 Annual Research Report
  • [Presentation] オリゴ糖転移酵素の結晶構造解析が明らかにするアスパラギン糖鎖修飾反応のダイナミクス2015

    • Author(s)
      神田大輔
    • Organizer
      大阪大学蛋白研セミナー
    • Place of Presentation
      大阪大学
    • Year and Date
      2015-08-28
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Integrative structural biology approach to understand the structural and dynamical basis of Asn-glycosylation2015

    • Author(s)
      Daisuke Kohda
    • Organizer
      the 6th Asia-Pacific NMR Symposium (APNMR6)
    • Place of Presentation
      香港科技大学
    • Year and Date
      2015-08-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] “結晶コンタクトフリー空間“を利用する新しい結晶解析技術を用いて蛋白質分子の内部運動の空間分布を視覚化する2015

    • Author(s)
      神田大輔
    • Organizer
      第15回日本蛋白質科学会
    • Place of Presentation
      徳島市
    • Year and Date
      2015-06-26
    • Related Report
      2015 Annual Research Report
  • [Presentation] 蛋白質のアスパラギン残基に糖鎖を転移するオリゴ糖転移酵素の構造生物学-超好熱性古細菌由来の蛋白質の安定性を最大限に活かす-2015

    • Author(s)
      神田大輔
    • Organizer
      平成27年度日本生化学会九州支部例会
    • Place of Presentation
      九州大学
    • Year and Date
      2015-05-16
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 蛋白質結晶中に隙間を創り出す新しいX線結晶解析を用いて蛋白質分子内部の動きを観る2015

    • Author(s)
      神田大輔
    • Organizer
      日本生物物理学会九州支部・熊本大学イメージングセミナー
    • Place of Presentation
      熊本大学
    • Year and Date
      2015-05-07
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] X線結晶解析から分子の動的情報を得るための方法2014

    • Author(s)
      松岡礼, 小室靖明, 杉田有治, 神田大輔
    • Organizer
      立体視プロジェクションシステムを使った分子科学研究講演会
    • Place of Presentation
      飯塚,福岡
    • Year and Date
      2014-12-05 – 2014-12-06
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural and dynamic basis for mitochondrial presequence recognition by Tom202014

    • Author(s)
      Rei Matsuoka, Daisuke Kohda
    • Organizer
      The 5th Japan-Taiwan bilateral NMR symposium
    • Place of Presentation
      札幌
    • Year and Date
      2014-09-29 – 2014-09-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Structural and dynamic basis for mitochondrial presequence recognition by Tom202014

    • Author(s)
      Daisuke Kohda
    • Organizer
      ISN 2014 Special Neurochemistry Conference
    • Place of Presentation
      東京
    • Year and Date
      2014-09-20 – 2014-09-22
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Intentional crystal-contact-free space in protein crystal2014

    • Author(s)
      Rei Matsuoka, Yasuaki Komuro, Yuji Sugita, Daisuke Kohda
    • Organizer
      23rd congress and general assembly of the international union of crystallography (IUCr2014)
    • Place of Presentation
      Montreal
    • Year and Date
      2014-08-05 – 2014-08-12
    • Related Report
      2014 Annual Research Report
  • [Book] Experimental approaches of NMR spectroscopy -Methodology and application to life science and materials science-2018

    • Author(s)
      Hidekazu Hiroaki, Daisuke Kohda,Chapter 21, Protein-Ligand Interactions Studied by NMRを担当.
    • Total Pages
      636
    • Publisher
      Springer Nature, Singapore.
    • ISBN
      9789811059650
    • Related Report
      2017 Annual Research Report
  • [Remarks] 動的構造生命ホーム

    • URL

      http://ugoku-tanpaku.jp

    • Related Report
      2018 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所構造生物学分野

    • URL

      http://www.bioreg.kyushu-u.ac.jp/vsb/index.html

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
  • [Remarks] 動的構造生命ホームページ

    • URL

      http://ugoku-tanpaku.jp

    • Related Report
      2017 Annual Research Report
  • [Remarks] 動的構造生命 ホーム

    • URL

      http://ugoku-tanpaku.jp

    • Related Report
      2016 Annual Research Report
  • [Remarks] 新学術領域「動的構造生命」

    • URL

      http://ugoku-tanpaku.jp

    • Related Report
      2015 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所構造生物学分野の研究内容

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/Research/research_frame_content_jp.html

    • Related Report
      2015 Annual Research Report
  • [Remarks] 新学術領域「動的構造生命科学」ホームページ

    • URL

      http://ugoku-tanpaku.jp

    • Related Report
      2014 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所構造生物学分野研究内容

    • URL

      http://vsb.bmr.kyushu-u.ac.jp/VSB/Research/research_frame_content_jp.html

    • Related Report
      2014 Annual Research Report

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Published: 2014-11-20   Modified: 2020-03-30  

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