Large scale MD simulation studies on quaternary structural changes of hemoglobin

• Project/Area Number: 20500268
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: Hirosaki University
• Principal Investigator: SAITO Minoru Hirosaki University, 大学院・理工学研究科, 教授 (60196011)
• Co-Investigator(Kenkyū-buntansha): 岡崎 功 弘前大学, 大学院・理工学研究科, 講師 (60332491)
• Research Collaborator: NAGAI Masako 法政大学, 工学研究科, 客員教授 (60019578)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2010: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2008: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 生体生命情報学 / ヘモグロビン / 四次構造変化 / シミュレーション / 並列計算機 / サブユニット

Research Abstract

I accelerated my software COSMOS90 by vectorization and parallelization on supercomputers and made it possible to perform long MD simulations for hemoglobin under the realistic condition, in water with all degrees of freedom and long-range Coulomb interactions included. I found quaternary structural changes and dynamics of hemoglobin.

Research Products

• [Journal Article] Force-field parameters of the Ψ and Φ aroud glycosidic bonds to oxygen and sulfur atoms (2009)
  • Author(s): Minoru Saito, Isao Okazaki
  • Journal Title: J.Comput.Chem. 30 Pages: 2656-2665
  • Peer Reviewed
• [Journal Article] Large Scale MD Simulations of Proteins on the Earth Simulator : Quaternary Structural Changes of Hemoglobin (2009)
  • Author(s): Minoru Saito
  • Journal Title: Annual Report of the Earth Simulator Cent er, April 2008-March 2009 (印刷中)
• [Journal Article] Large Scale MD Simulations of Proteins on the Earth Simulator : Quaternary Structural Changes of Hemoglobin (2008)
  • Author(s): Minoru Saito
  • Journal Title: Annual Report of the Earth Simulator Center Pages: 261-265
• [Presentation] MD simulations of hemoglobin in water with all degrees of freedom for different oxygen binding states and quaternary structures (2010)
  • Author(s): Minoru Saito
  • Organizer: The 48th Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Tohoku University (Sendai, Japan)
  • Year and Date: 2010-09-20
• [Presentation] MD simulations of hemoglobin in water with all degrees of freedom for different oxygen binding states and quaternary structures (2010)
  • Author(s): Minoru Saito
  • Organizer: The 48^<th> Annual Meeting of the Biophysical Society of Japan
  • Place of Presentation: Tohoku University (Sendai, Japan)
  • Year and Date: 2010-09-20
• [Presentation] 水中のヘモグロビンの四次構造変化のシミュレーション (2008)
  • Author(s): 斎藤稔
  • Organizer: 第46回日本生物物理学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-12
• [Remarks] ホームページ等
  • URL: http://www.si.hirosaki-u.ac.jp/~msaito/