Molecular mechanism of the soft structure of proteins: Analysis of interior cavities and structural changes under pressure

2008 Fiscal Year Final Research Report

• Project/Area Number: 19500252
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Nagaoka University of Technology
• Principal Investigator: SODA Kunitsugu Nagaoka University of Technology, 工学部, 教授 (10011686)
• Co-Investigator(Kenkyū-buntansha): SEKI Yasutaka 長岡技術科学大, 工学部, 助教 (30377220)
• Project Period (FY): 2007 – 2008
• Keywords: 柔構造 / 分子動力学 / 原子充填密度 / 分子内空隙 / 圧力効果

Research Abstract

PDB (蛋白質立体構造データベース) に登録されている869種の蛋白質分子立体構造の網羅的解析により, 球状蛋白質は, これ迄広く認められていたよりも有意に低い原子充填密度を持つこと, 及び蛋白質分子水溶液への分子動力学模擬計算法の適用により, 球状蛋白質はTHz域に, 所謂Boson Peak に相当する振動モードを示すことを見出すと共に, その生成の分子機構を明らかにした。

Research Products

• [Journal Article] Global Structure Analysis of Acid-Unfolded Myoglobin with Consideration to Effects of Intermolecular Coulomb Repulsion on Solution X-ray Scattering (2007)
  • Author(s): Seki Y, Tomizawa T, Hiragi Y & Soda, K.
  • Journal Title: Biochemistry Pages: 234-244
  • Peer Reviewed
• [Presentation] J. Soft Structure of Proteins Analyzed by Atomic Packing Density and Volume Fluctuation Dynamics (2008)
  • Author(s): Soda, K, Seki, Y, Mori, K, Shimbo, Y, Matsumoto, H and Fujii
  • Organizer: International Conference on Protein Science and Human Proteome Organization.(PRICPS-AOHUPO 2008)
  • Place of Presentation: Cairns, Australia
  • Year and Date: 20080622-26
• [Presentation] Dynamics of Structural Fluctuations of Proteins and Hydration Effects (2008)
  • Author(s): Soda, K.
  • Organizer: Third International Workshop on Proteins under Pressure
  • Place of Presentation: Santa Fe, New Mexico, U.S.A.
  • Year and Date: 20080122-25
• [Presentation] Solvent- Reorganization Effects on Hydration Thermodynamic Quantities of Nonpolar Molecules by Molecular Dynamics Simulation (2008)
  • Author(s): Shimbo, Y & Soda, K
  • Organizer: Third International Workshop on Proteins under Pressure
  • Place of Presentation: Santa Fe, New Mexico, U.S.A.
  • Year and Date: 20080121-25
• [Book] 疎水効果, 水, 溶液X線散乱. タンパク質の事典(猪飼篤, 伏見譲, 卜部格, 上野川修一, 中村春木, 浜窪隆雄 編) (2008)
  • Author(s): 曽田 邦嗣
  • Total Pages: pp.511-515
  • Publisher: 朝倉書店
• [Book] 水と水和. 生物物理学ハンドブック(石渡信一, 桂勲, 桐野豊, 美宅成樹編) (2007)
  • Author(s): 曽田 邦嗣
  • Total Pages: pp. 12-15.
  • Publisher: 朝倉書店