Fragment molecular orbital studies for the carbohydrate-recognition of bio-molecules.

• Project/Area Number: 21700333
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Tokai University
• Principal Investigator: Aida-Hyugaji Sachiko 東海大学, 情報教育センター, 講師 (70317824)
• Project Period (FY): 2009-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2011: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2010: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2009: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: 分子軌道法 / 糖鎖 / 生体分子間相互作用 / フラグメント分子軌道法 / 分子認識 / 糖構造 / 分子間相互作用 / 生体高分子 / 高精度量子化学計算

Outline of Final Research Achievements

Antibodies are expected to be used as potential anticancer drugs. Recently, it is reported that recombinant antibody, 5A3 recognizes Man3. However, only amino acid sequences of 5A3 were already investigated.
In this study, fragment molecular orbital (FMO) calculations were performed to get insight into the mechanism of Man3-recognition of 5A3. Prior to the FMO calculations, 3D structures of the complex was investigated using induced-fit docking simulations between six structures of 5A3 and 141 conformers of Man3. Finally, amino acid residues of 5A3 contributing to Man3-recognition were proposed.

Research Products

• [Presentation] リガンドに依存した核内受容体の構造変化に対する線型応答理論による解析 (2010)
  • Author(s): 渡邉千鶴, 合田(日向寺)祥子, 渡邉博文, 田中成典
  • Organizer: 第65回日本物理学会年次大会(日本物理学会)
  • Place of Presentation: 岡山大学(岡山県)
  • Year and Date: 2010-03-20
• [Presentation] 大学における創薬インフォマティクス教育の試み (2009)
  • Author(s): 合田(日向寺)祥子
  • Organizer: BiWO2009(CBRC)
  • Place of Presentation: 生命情報工学研究センター(東京都)
  • Year and Date: 2009-12-03
• [Presentation] Intramolecular lnteraction of Human Estrogen Receptor Ligand Binding Domain with Different Helixl2 Positions Studied by Ab initio Fragment Molecular Orbital Method (2009)
  • Author(s): Chiduru Watanabe, Sachiko Aida-Hyugaji, Kaori Fukuzawa
  • Organizer: BioInfo2009 CBI-KSBSB Joint Conference (CBI, KSBSB)
  • Place of Presentation: Busan, Korea
  • Year and Date: 2009-11-04
• [Presentation] Theoretical Analysis of Binding Affinity of Human Mannose-Binding Protein Carbohvdate Recoenition Domain to Mannose (2009)
  • Author(s): Zhenxia Zhu, Sachiko Aida-Hyu gaji
  • Organizer: BioInfo2009 CBI-KSBSB Joint Conference (CBI, KSBSB)
  • Place of Presentation: Busan, Korea
  • Year and Date: 2009-11-04
• [Presentation] フラグメント分子軌道法によるエストロゲン受容体αの分子内相互作用解析
  • Author(s): 合田（日向寺）祥子
  • Organizer: 第６回分子科学討論会
  • Place of Presentation: 東京大学 本郷キャンパス