Prediction of "Functional Structure" of Intrinsically Disordered Proteins using High Pressure Vibrational Spectroscopy

• Project/Area Number: 26410187
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Bio-related chemistry
• Research Institution: Ritsumeikan University
• Principal Investigator: KATO MINORU 立命館大学, 生命科学部, 教授 (00241258)
• Project Period (FY): 2014-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: 天然変性蛋白質 / 圧力 / FTIR法 / ラマン分光 / ダイヤモンドアンビルセル / αヘリックス / 2次構造予測 / 圧力効果 / ラマン分光法 / βヘアピン / 水和

Outline of Final Research Achievements

For the first step to establish a method to experimentally predict the secondary structure of intrinsically disordered proteins (IDPs) bound to the target molecules, in this study we examined whether pressure induces helix formation of IDPs without the target proteins. As a model molecule we performed pressure effect on the secondary structure of pKID (phosphorylated kinase-inducible domain) using high pressure FTIR equipped with diamond anvil cell up to 1058 MPa. Increasing pressure increased the peak intensity of the amide I’ band due to solvated helix This indicated that pressure induced the helix formation of pKID. The present test experiment supports the availability of the use of pressure experiments without target molecules for prediction of helix formation of IDPs as bound to target molecules.

Academic Significance and Societal Importance of the Research Achievements

真核生物においては、蛋白質の約40%が天然変性タンパク質であるにも関わらず、対応する標的分子の多くが同定されていない。これが天然変性タンパク質研究の進展の阻害要因の一つになっている。標的分子を用いなくても実験的に機能時の構造予測ができれば、その学術的意義は大きい。本研究は、標的分子を用いない実験的予測法の一つとして高圧力を利用できる可能性を示すことができた。さらに検証を深めることにより新たな予測法の確立が期待できる。

Research Products

• [Journal Article] Pressure-induced structural changes of alanine oligopeptides in aqueous solutions (2019)
  • Author(s): Takahiro Takekiyo, Minoru Kato, Yukihiro Yoshimura
  • Journal Title: High Pressure Research Volume: 39 Issue: 2 Pages: 202-209
  • DOI: 10.1080/08957959.2019.1584195
  • Peer Reviewed
• [Journal Article] <b>Molecular Discrimination of Barbital Enantiomer at the Propofol Binding Site of the Human β₃ Homomeric GABA_A Receptor </b> (2018)
  • Author(s): Seto Tomoyoshi、Kato Minoru、Koyano Ken
  • Journal Title: Chem-Bio Informatics Journal Volume: 18 Issue: 0 Pages: 154-163
  • DOI: 10.1273/cbij.18.154
  • NAID: 130007522494
  • ISSN: 1347-0442, 1347-6297
  • Year and Date: 2018-11-28
  • Peer Reviewed / Open Access
• [Journal Article] Functional characterizations of polyethylene terephthalate-degrading cutinase-like enzyme Cut190 mutants using bis(2-hydroxyethyl) terephthalate as the model substrate (2018)
  • Author(s): Hantani Yoshiji, Imamura Hiroshi, Yamamoto Tsubasa, Senga Akane, Yamagami Yuri, Kato Minoru, Kawai Fusako, Oda Masayuki
  • Journal Title: AIMS Biophysics Volume: 5 Issue: 4 Pages: 290-302
  • DOI: 10.3934/biophy.2018.4.290
  • Peer Reviewed / Open Access
• [Journal Article] Interaction Site between the Protein Aggregates and Thiocyanate Ion in Aqueous Solution: A Case Study of 1-Butyl-3-methylimidazolium Thiocyanate (2015)
  • Author(s): T. Takekiyo, E. Yamaguchi, K., M. Kato, T. Yamaguchi, Y. Yoshimura
  • Journal Title: J. Phys. Chem. B. Volume: 119 Issue: 22 Pages: 6536-6544
  • DOI: 10.1021/acs.jpcb.5b01650
  • Peer Reviewed
• [Journal Article] A Raman spectroscopic study of the conformations of 1,4-dioxane in the pure liquid, methanol, and aqueous solution (2015)
  • Author(s): R. Wada, K.i Fujimoto, M. Kato
  • Journal Title: Chem. Phys. Lett. Volume: 641 Pages: 74-79
  • DOI: 10.1016/j.cplett.2015.10.036
  • Peer Reviewed
• [Journal Article] Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering (2015)
  • Author(s): 61.E. Chatani, R. Inoue, H. Imamura, M. Sugiyama, M. Kato, M. Yamamoto, K. Nishida and T. Kanaya
  • Journal Title: Scientific Report Volume: 5 Issue: 1 Pages: 15485-15498
  • DOI: 10.1038/srep15485
  • NAID: 120005672389
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Why is Poly(oxyethylene) Soluble in Water? Evidence from the Thermodynamic Profile of the Conformational Equilibria of 1,2-Dimethoxyethane and Dimethoxymethane Revealed by Raman Spectroscopy (2014)
  • Author(s): Ryoichi Wada, Kazushi Fujimoto, and Minoru Kato
  • Journal Title: J. Phys. Chem. B. Volume: 118 Issue: 42 Pages: 12223-12231
  • DOI: 10.1021/jp5048997
  • Peer Reviewed / Open Access
• [Presentation] Pressure effects on the secondary structure of an intrinsically disordered protein: pKID peptide (2018)
  • Author(s): Minoru Kato, Soichiro Kubota, Tsubara Yamamoto
  • Organizer: The 10th International Conference on High Pressure Bioscience and Biotechnology (HPBB2018)
  • Int'l Joint Research
• [Presentation] Free energy landscape for temperature-pressure denaturation of Ubiquitin (2018)
  • Author(s): Minoru Kato, Tsubasa Yamamoto
  • Organizer: Joint Conference of EMLG/JMLG Meeting 2018 and 41st Symposium on Solution Chemistry of Japan
  • Int'l Joint Research
• [Presentation] Do an intrinsically disordered peptide, pKID fold under high pressure? (2018)
  • Author(s): 加藤 稔，窪田 総一郎，山本 翼
  • Organizer: 第56回日本生物物理学会年会
• [Presentation] ユビキチンの変性の圧力・温度軸自由エネルギー曲面 (2018)
  • Author(s): 加藤 稔，山本 翼
  • Organizer: 第59回高圧討論会
• [Presentation] 天然変性タンパク質pKID の2 次構造に及ぼす圧力効果 (2017)
  • Author(s): 窪田総一郎、加藤 稔
  • Organizer: 第11回バイオ関連化学シンポジウム
• [Presentation] 疎水性相互作用の及ぼす圧力効果：メタン会合系の自由エネルギー計算 (2017)
  • Author(s): 藤本和士、堀田優也、加藤 稔
  • Organizer: 第40回溶液化学シンポジウム
• [Presentation] タンパク質圧力変性モデルの再考：メタン会合系での圧力効果 (2017)
  • Author(s): 藤本和士、堀田優也、加藤 稔
  • Organizer: 第58回高圧討論会
• [Presentation] A pressure-jump FTIR study of the folding reaction of β-Lactoglobulin (2016)
  • Author(s): Satoshi Hayakawa, Tsubasa Yamamoto, Minoru Kato
  • Organizer: 第54回生物物理学会年会
  • Place of Presentation: つくば国際会議場（茨城県つくば市）
  • Year and Date: 2016-11-25
• [Presentation] βヘアピンは圧力によりリフォールドするか (2016)
  • Author(s): 加藤 稔，今村比呂志，土屋慶太，窪田総一郎
  • Organizer: 第57回高圧討論会
  • Place of Presentation: 筑波大学（茨城県つくば市）
  • Year and Date: 2016-10-28
• [Presentation] 蛋白質の圧力誘起リフォールディング：FTIR法による初めての直接観測 (2016)
  • Author(s): 加藤 稔，池内ゆず, 山本翼
  • Organizer: 第43回生体分子科学討論会2016
  • Place of Presentation: 名古屋大学（愛知県名古屋市）
  • Year and Date: 2016-06-24
• [Presentation] Cytochrome cの圧力誘起リフォールディング (2015)
  • Author(s): 加藤 稔，山本翼，池内ゆず
  • Organizer: 第56回高圧討論会
  • Place of Presentation: 広島県広島市
  • Year and Date: 2015-10-11
• [Presentation] GB1(41-56)ペプチドのβ ヘアピン構造に及ぼす圧力効果に関するFTIR・ラマン分光研究 (FTIR and Raman studies of pressure effects on the β-hairpin structure of GB1(41-56) peptides) (2015)
  • Author(s): Minoru Kato, Keita Tsuchiya
  • Organizer: 第53回生物物理学会年会
  • Place of Presentation: 石川県金沢市
  • Year and Date: 2015-09-13
• [Presentation] モデルペプチドの高圧力研究から見えてくるタンパク質の圧力変性機構 (2015)
  • Author(s): 加藤 稔
  • Organizer: 第15回日本蛋白質科学会年会
  • Place of Presentation: 徳島県徳島市
  • Year and Date: 2015-06-26
  • Invited
• [Presentation] 振動分光法を用いたβ-hairpinモデルペプチドの構造に対する圧力効果 (2014)
  • Author(s): 土屋慶太，和田竜一, 加藤稔
  • Organizer: 第55回高圧討論会
  • Place of Presentation: 徳島大学常三島キャンパス（徳島県）
  • Year and Date: 2014-11-22
• [Presentation] 分子動力学計算によるβ-hairpinモデルペプチドの高圧力下での構造安定性に関する研究 (2014)
  • Author(s): 辻井政統，藤本和士，加藤稔
  • Organizer: 第55回高圧討論会
  • Place of Presentation: 徳島大学常三島キャンパス（徳島県）
  • Year and Date: 2014-11-22
• [Presentation] 圧力ジャンプFTIR法によるRibonuclease AおよびUbiquitinのフォールディング・アンフォールディング反応の速度論解析 (2014)
  • Author(s): 加藤 稔，楠本裕士, 山本翼
  • Organizer: 第55回高圧討論会
  • Place of Presentation: 徳島大学常三島キャンパス（徳島県）
  • Year and Date: 2014-11-22
• [Presentation] Vibrational spectroscopic study of the pressure effect on beta-hairpin structure using model peptides: mutants of GB1 (41-56) (2014)
  • Author(s): Keita Tsuciya, Ryoichi Wada, and Minoru Kato
  • Organizer: The European Molecular Liquids Group and the Japanese Molecular Liquids Group (EMLG/JMLG) Annual Meeting 2014
  • Place of Presentation: Rome, Italy
  • Year and Date: 2014-09-09 – 2014-09-11
• [Presentation] The structure stability of beta-hairpin model peptide by molecular dynamics calculations (2014)
  • Author(s): Masanori Tsujii, Kazushi Fujimoto, and Minoru Kato
  • Organizer: The European Molecular Liquids Group and the Japanese Molecular Liquids Group (EMLG/JMLG) Annual Meeting 2014
  • Place of Presentation: Rome, Italy
  • Year and Date: 2014-09-09 – 2014-09-11
• [Book] 「極限環境の生体分子 過酷な環境下での機能を科学する」（CSJカレントレビュー17） 「タンパク質の圧力変性機構：現状とこれらの課題」 (2014)
  • Author(s): 加藤 稔、今村比呂志
  • Total Pages: 8
  • Publisher: 化学同人
• [Remarks] 生体物理化学研究室 トップページ
  • URL: http://www.ritsumei.ac.jp/se/rc/staff/kato/LAB.html