Study of the self-assembling nano-fibrils by protein design approach

• Project/Area Number: 20870043
• Research Category: Grant-in-Aid for Young Scientists (Start-up)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities
• Principal Investigator: MAKABE Koki National Institutes of Natural Sciences Okazaki Research Facilities, 岡崎統合バイオサイエンスセンター, 助教 (20508072)
• Project Period (FY): 2008 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥3,302,000 (Direct Cost: ¥2,540,000、Indirect Cost: ¥762,000); Fiscal Year 2009: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2008: ¥1,742,000 (Direct Cost: ¥1,340,000、Indirect Cost: ¥402,000)
• Keywords: 蛋白質デザイン / βシート / アミロイド / フォールディング / 生物物理 / ナノ繊維 / X線結晶構造解析 / 自己組織化

Research Abstract

Using OspA as a model system for beta-sheet study, we successfully determined the X-ray crystal structure of the mutants. We also found that OspA folds through an on-pathway intermediate.

Research Products

• [Journal Article] Minimalist design of water-soluble cross-beta architecture. (2010)
  • Author(s): Biancalana M, Makabe K, Koide S.
  • Journal Title: Proc Natl Acad Sci U S A. 107 Pages: 3469-3474
  • Peer Reviewed
• [Journal Article] Different Folding Pathways Taken by Highly Homologous Proteins, Goat alpha-Lactalbumin and Canine Milk Lysozyme. (2010)
  • Author(s): Nakamura T, Makabe K, Tomoyori K, Maki K, Mukaiyama A, Kuwajima K.
  • Journal Title: J Mol Biol. 396 Pages: 1361-1378
  • Peer Reviewed
• [Journal Article] Flexible recognition of the tRNA G18 methylation target site by TrmH methyltransferase through first binding and induced fit processes. (2010)
  • Author(s): Ochi A, Makabe K, Kuwajima K, Hori H.
  • Journal Title: J Biol Chem. 285 Pages: 9018-9029
  • Peer Reviewed
• [Journal Article] Minimalist design of water-soluble cross-beta architecture (2010)
  • Author(s): Biancalana M, Makabe K, Koide S.
  • Journal Title: Proc Natl Acad Sci USA 107 Pages: 3469-3474
  • Peer Reviewed
• [Journal Article] Different folding pathways taken by highly homologous proteins, goat alpha-lactalbumin and canine milk lysozyme (2010)
  • Author(s): Nakamura T, Makabe K, Tomoyori K, Maki K, Mukaiyama A, Kuwajima K.
  • Journal Title: J Mol Biol. 396 Pages: 1361-1378
  • Peer Reviewed
• [Journal Article] Structural Basis for Exquisite Specificity of Affinity Clamps, Synthetic Binding Proteins Generated through Directed Domain-interface Evolution. (2009)
  • Author(s): Huang J, Makabe K, Biancalana M, Koide A, Koide S.
  • Journal Title: J Mol Biol. 392 Pages: 1221-1231
  • Peer Reviewed
• [Journal Article] Molecular Mechanism of Thioflavin-T Binding to the Surface of beta-Rich Peptide Self-Assemblies. (2009)
  • Author(s): Biancalana M, Makabe K, Koide A, Koide S.
  • Journal Title: J Mol Biol. 385 Pages: 1052-1063
  • Peer Reviewed
• [Journal Article] Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution (2009)
  • Author(s): Huang J, Makabe K, Biancalana M, Koide A, Koide S.
  • Journal Title: J Mol Biol. 392 Pages: 1221-1231
  • Peer Reviewed
• [Journal Article] Molecular mechanism of thioflavin-T binding to the surface of beta-rich peptide self-assemblies (2009)
  • Author(s): Biancalana M, Makabe K, Koide A, Koide S.
  • Journal Title: J Mol Biol. 385 Pages: 1052-1063
  • Peer Reviewed
• [Journal Article] The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion. (2008)
  • Author(s): Makabe K, Koide S.
  • Journal Title: J Am Chem Soc. 130 Pages: 14370-14371
  • Peer Reviewed
• [Journal Article] The promiscuity of beta-strand pairing allows for rational design of beta-sheet face inversion (2008)
  • Author(s): Makabe K, Koide S.
  • Journal Title: J Am Chem Soc. 130 Pages: 14370-14371
  • Peer Reviewed
• [Presentation] βシート蛋白質の構造形成機構 (2010)
  • Author(s): 真壁幸樹, 小出昌平, 桑島邦博
  • Organizer: 生物物理学会中部支部講演会
• [Presentation] Protein design approach for beta-sheet characterization (2009)
  • Author(s): Koki Makabe
  • Organizer: 北海道大学-Mahidol 大学若手合同シンポジウム
  • Place of Presentation: 北海道大学(北海道)
  • Year and Date: 2009-05-12
• [Presentation] Structures of β-Sheet Self-Assembly Mimics (2009)
  • Author(s): Makabe K
  • Organizer: First Korea-Japan Seminars on Biomolecular Sciences-Experiments and Simulations
  • Place of Presentation: KIAS, Seoul, Korea
  • Year and Date: 2009-02-27
• [Presentation] -シート形成における主鎖水素結合の役割 (2009)
  • Author(s): 真壁幸樹, 小出昌平, 桑島邦博
  • Organizer: 蛋白質科学会
  • Place of Presentation: 熊本
• [Presentation] Protein design approach for β-sheet characterization (2009)
  • Author(s): Koki Makabe
  • Organizer: 北海道大学-Mahidol大学若手合同シンポジウム
• [Presentation] Structures of β-Sheet Self-Assembly Mimics (2009)
  • Author(s): Koki Makabe, Shohei Koide, Kunihiro Kuwajima
  • Organizer: Asia Core
  • Place of Presentation: 韓国, ソウル
• [Remarks] 桑島研究室ホームページ
  • URL: http://gagliano.ims.ac.jp/