NMR approach and prediction for the residual structures in the intrinsically disordered proteins

• Project/Area Number: 23590049
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Physical pharmacy
• Research Institution: Teikyo Heisei University
• Principal Investigator: NISHIMURA Chiaki 帝京平成大学, 薬学部, 教授 (70218197)
• Co-Investigator(Renkei-kenkyūsha): GOTO Yuji 大阪大学, 蛋白質研究所, 教授 (40153770)
• Project Period (FY): 2011-04-28 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2013: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2012: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 核磁気共鳴 / 天然変性蛋白質 / 残存構造 / ２次構造 / 緩和時間 / 化学シフト / 揺らぎ構造 / ウイルス / 蛋白質 / 生体分子 / 超分子化学 / 揺らぎ / 分子認識 / 薬学 / 核酸 / 感染症

Outline of Final Research Achievements

Residual and ensemble structures in intrinsically disordered proteins can be directly related to their functions. For alpha-synuclein, the N- and C-terminal domains were slightly more protected from the amide-proton exchange than the other regions monitored by CLEANEX-PM. Chemical shift studies and delta2d analyses were powerful tools to figure out the minor populations of the residual alpha- and beta-structures for the measles virus C-terminal domain Ntail of nucleoprotein. The amounts of residual structures in both proteins were very small.
HIV-1 p17 matrix protein and p24 capsid N-terminal domain fold in the physiological condition as globular proteins, although two proteins were predicted to be 50% unfolded based on the sequence. The order-parameter studies on p17 revealed that the more flexibility was included in helix 5 than in the other helices. For p24, the long-range effects by the addition of the unnecessary tag on the dynamics structures were observed at helices 4 and 6.

Research Products

• [Journal Article] Comparison of residual alpha- and beta-structures between two intrinsically disordered proteins by using NMR (2015)
  • Author(s): Ono, Y., Miyashita, M., Ono, Y., Okazaki, H., Watanabe, S., Tochio, N., Kigawa, T., and Nishimura, C. *
  • Journal Title: Biochimica et Biophysica Acta, Proteins and Proteomics Volume: 1854 Issue: 3 Pages: 229-238
  • DOI: 10.1016/j.bbapap.2014.12.007
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Probing the non-native H helix translocation in apomyoglobin folding (2014)
  • Author(s): Aoto, P.C., Nishimura, C., Dyson, H.J., and Wright, P.E. Two authors (P.C.A. and C.N.) contribute equally.
  • Journal Title: Biochemistry Volume: 53 Issue: 23 Pages: 3767-3780
  • DOI: 10.1021/bi500478m
  • Peer Reviewed
• [Journal Article] Long-range effects of tag sequence on marginally stabilized structure in HIV-1 p24 capsid protein monitored using NMR (2014)
  • Author(s): Okazaki, H., Kaneko, C., Hirahara, M., Watanabe, S., Tochio, N., Kigawa, T., and Nishimura, C.*
  • Journal Title: Biochimica et Biophysica Acta, Proteins and Proteomics Volume: 1844 Issue: 9 Pages: 1638-1647
  • DOI: 10.1016/j.bbapap.2014.06.009
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Flexible and rigid structures in HIV-1 p17 matrix protein monitored by relaxation and amide proton exchange using NMR (2014)
  • Author(s): Ohori, Y., Okazaki, H., Watanabe, S., Tochio, N., Arai, M., Kigawa, T., and Nishimura, C.*
  • Journal Title: Biochimica et Biophysica Acta Volume: 1844 Issue: 3 Pages: 520-526
  • DOI: 10.1016/j.bbapap.2013.12.010
  • Peer Reviewed
• [Journal Article] Remaining structures at the N- and C-terminal regions of alpha-synuclein accurately elucidated by amide-proton exchange NMR with fitting (2013)
  • Author(s): Okazaki, H., Ohori, Y., Komoto, M., Lee, Y-H, Goto, Y., Tochio, N., and Nishimura, C.*
  • Journal Title: FEBS Letters Volume: 587 Issue: 22 Pages: 3709-3714
  • DOI: 10.1016/j.febslet.2013.09.039
  • Peer Reviewed
• [Journal Article] Consequence of stabilizing the natively disordered F helix for the folding pathway of apomyoglobin (2011)
  • Author(s): Nishimura, C., Dyson, H.J., Wright, P.E.
  • Journal Title: J.Mol.Biol. Volume: 411 Issue: 1 Pages: 248-263
  • DOI: 10.1016/j.jmb.2011.05.028
  • Peer Reviewed
• [Presentation] Dynamic structures of the intrinsically disordered proteins and folding intermediates (2014)
  • Author(s): Nishimura, C
  • Organizer: 7th Korea-Japan Joint Seminars on Biomolecular Sciences: Experiments and Simulations
  • Place of Presentation: Korea Institute for Advanced Study, Seoul, Korea
  • Year and Date: 2014-11-26 – 2014-11-28
  • Invited
• [Presentation] 天然変性蛋白質の段階的なNMR解析 (2014)
  • Author(s): 大野悠一、宮下真奈美、大野優美、岡崎萌花、渡部暁、栃尾尚哉、西村千秋
  • Organizer: 第53回NMR討論会
  • Place of Presentation: 大阪大学コンベンションセンター（大阪府吹田市）
  • Year and Date: 2014-11-04 – 2014-11-06
• [Presentation] 天然変性蛋白質の段階的なNMR解析 (2014)
  • Author(s): 大野悠一、宮下真奈美、大野優美、岡崎萌花、渡部暁、栃尾尚哉、西村千秋
  • Organizer: 第58回日本薬学会関東支部会
  • Place of Presentation: 昭和薬科大学（東京都町田市）
  • Year and Date: 2014-10-04
• [Presentation] アポミオグロビン折り畳み中間体に存在する非天然的なHへリックス領域構造 (2014)
  • Author(s): 西村 千秋
  • Organizer: 第52回日本生物物理学会年会
  • Place of Presentation: 札幌コンベンションセンター（北海道札幌市）
  • Year and Date: 2014-09-25 – 2014-09-27
• [Presentation] パルスラベル重水素交換法によるフォールディング中間体の解析 (2014)
  • Author(s): 西村 千秋
  • Organizer: 第14回日本蛋白質科学会年会アーカイブWS
  • Place of Presentation: ワークピア横浜/横浜産貿ホールマリネリア（神奈川県横浜市）
  • Year and Date: 2014-06-25 – 2014-06-27
  • Invited
• [Presentation] Protein unfolding and disassembly monitored by amide proton exchange (2014)
  • Author(s): Nishimura,C., Watanabe,S. and Wright, P.E.
  • Organizer: The 2th International Symposium：Dynamical Ordering of Biomolecular Systems for Creation of Integrated Functions
  • Place of Presentation: Kyoto
• [Presentation] パルスラベル重水素交換法によるフォールディング中間体の解析 (2014)
  • Author(s): 西村千秋
  • Organizer: 第14回日本蛋白質科学会年会：アーカイブWS
  • Place of Presentation: 横浜
• [Presentation] 天然変性タンパク質のNMRによる揺らぎ構造解析 (2013)
  • Author(s): 岡崎萌花、大堀由佳、幸元雅也、渡部暁、栃尾尚哉、西村千秋
  • Organizer: 第52回NMR討論会
  • Place of Presentation: 金沢
• [Presentation] 水との交換を指標としたアルファーシヌクレインなど蛋白質の揺らぎ構造解析 (2012)
  • Author(s): 西村千秋
  • Organizer: 新学術領域「揺らぎと生体機能」「水和とATP」合同公開シンポジューム
  • Place of Presentation: 大阪ガーデンパレス
• [Presentation] Transient Structure of the Kinetic Intermediate of Apomyoglobin Monitored by Quench-Flow HD Exchange NMR (2012)
  • Author(s): C. Nishimura
  • Organizer: The 51st Annual Meeting of the Nuclear Magnetic Resonance Society of Japan
  • Place of Presentation: 名古屋
• [Presentation] Fluctuating and Remaining Structure in the Intrinsically Disordered Protein Monitored by NMR (2012)
  • Author(s): C. Nishimura
  • Organizer: The 6th International Symposium：Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 京都テルサ
• [Presentation] NMR studies on the protein containing the intrinsically disordered region (2012)
  • Author(s): Nishimura, C., Tochio, N., Akikawa, H., Kaneko, C., Ishii, A., Hayashi, N., Hirahara, M., Sato, M., Abe, S., and Orikasa, T.
  • Organizer: The 5th International Symposium of Molecular Science of Fluctuations toward Biological Functions
  • Place of Presentation: 東大寺総合文化センター（奈良県）
• [Presentation] Fluctuating structures during the folding events of apomyoglobin: Non-native structure in the intermediate (2012)
  • Author(s): Nishimura, C and Wright, P.E.
  • Organizer: 4th Japan-Korea Seminar on Biomolecular Sciences: Experiments and Simulations(招待講演)
  • Place of Presentation: 東大寺総合文化センター（奈良県）
• [Presentation] 天然揺らぎ構造のNMR解析 (2011)
  • Author(s): 西村 千秋
  • Organizer: 第49回日本生物物理学会年会シンポジューム(招待講演)
  • Place of Presentation: 兵庫県立大学（兵庫県）
• [Presentation] NMRで見たアポミオグロビン過渡的折りたたみ中間体の構築原理 (2011)
  • Author(s): 西村 千秋
  • Organizer: 日本物理学会2011年秋季大会シンポジューム、生物物理（領域12）(招待講演)
  • Place of Presentation: 富山大学（富山県）
• [Presentation] 天然変性蛋白質のNMRによる揺らぎ構造解析
  • Author(s): 岡崎萌花、大堀由佳、幸元雅也、渡部暁、栃尾尚哉、西村千秋
  • Organizer: 第57回日本薬学会関東支部大会
  • Place of Presentation: 板橋
• [Book] Organic solvents: properties, toxicity, and industrial effects (2011)
  • Author(s): Ohtake, S., Kita, Y., Nishimura, C. , and Arakawa, T.
  • Publisher: Nova Science Publishers, Editor Ryan E. Carter