Theoretical study of the electronic structure of the active site of metalloproteins

2008 Fiscal Year Final Research Report

• Project/Area Number: 18750011
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Physical chemistry
• Research Institution: Osaka University
• Principal Investigator: TAKANO Yu Osaka University, 蛋白質研究所, 助教 (30403017)
• Project Period (FY): 2006 – 2008
• Keywords: 電子状態 / 量子化学 / 生体分子 / 遷移金属

Research Abstract

遷移金属蛋白質の機能制御機構を明らかにするため、多核遷移金属中心をもつ酸素運搬蛋白質であるヘモシアニンおよびヘムエリスリンに対して理論計算(密度汎関数法)を用いて、周りの蛋白質により活性中心の電子構造がどのように制御されているかを調べた。その結果、蛋白質により誘起される活性中心の構造ゆがみ、活性中心に配位するアミノ酸残基の電子構造の双方が電子構造を制御し、そのバランスにより機能発現に至っていることを明らかにした。

Research Products

• [Journal Article] Theoretical studies on electronic structure and magnetic properties of mixed-valence uteroferrin active site (2009)
  • Author(s): K. Koizumi, K. Yamaguchi, H. Nakamura, Y. Takano
  • Journal Title: Int. J. Quantum Chem. (in press)
  • Peer Reviewed
• [Journal Article] Electronic structures of heme a of cytochrome c oxidase in the redox states -Roles of Propionate and Formyl Groups in Electron Transfer- (2009)
  • Author(s): Y. Takano, H. Nakamura
  • Journal Title: J. Comput. Chem. (in press)
  • Peer Reviewed
• [Journal Article] Theoretical studies of the magnetic couplings and the chemical indices of the biomimetic models of oxyhemocyanin and oxytyrosinase (2009)
  • Author(s): Y. Takano, K. Koizumi, H. Nakamura
  • Journal Title: Inorg. Chim Acta (in press)
  • Peer Reviewed
• [Journal Article] Hybrid-DFT study on electronic structures of the active site of sweet potato purple acid phosphatase -The origin of stronger antiferromagnetic couplings than other purple acid phosphatase- (2009)
  • Author(s): K. Koizumi, K. Yamaguchi, H. Nakamura, Y. Takano
  • Journal Title: J. Phys. Chem. A 113 Pages: 5099-5104
  • Peer Reviewed
• [Journal Article] Theoretical investigation of the electronic assymetry of the special pair cation radical in the photosynthetic type-II reaction center (2008)
  • Author(s): H. Yamasaki, Y. Takano, H. Nakamura
  • Journal Title: J. Phys. Chem. B 112 Pages: 13923-13933
  • Peer Reviewed
• [Journal Article] A Theoretical Approach to a Novel Pathway of Proton Translocation of Cytochrome c Oxidase (2008)
  • Author(s): Y. Takano, H. Nakamura
  • Journal Title: AIP Conf. Proc. 1046 Pages: 60-63
• [Journal Article] Theoretical studies on electronic structures and chemical indices of the active site in oxygenated and deoxygenated hemerythrin (2008)
  • Author(s): Y. Takano, H. Isobe, K. Yamaguchi
  • Journal Title: Bull. Chem. Soc. Jpn. 81 Pages: 91-92
  • Peer Reviewed
• [Journal Article] Theoretical analysis of the electronic asymmetry of the special pair in the photosynthetic reaction center: Effect of the protein environment and structural asymmetry (2007)
  • Author(s): H. Yamasaki, H. Nakamura, Y. Takano
  • Journal Title: Chem. Phys. Lett. 447 Pages: 324-329
  • Peer Reviewed
• [Journal Article] Theory of chemical bonds in metalloenzymes. IX. Theoretical study on the active site of the ribonucleotide reductase and the related species (2007)
  • Author(s): M. Shoji, H. Isobe, Y. Takano, Y. Kitagawa, S. Yamanaka, M. Okumura, K. Yamaguchi
  • Journal Title: Int. J. Quant. Chem. 107 Pages: 3250-3265
  • Peer Reviewed
• [Journal Article] Hybrid density functional study of ligand coordination effects on the magnetic couplings and the dioxygen binding of the models of hemocyanin (2007)
  • Author(s): Y. Takano, K. Yamaguchi
  • Journal Title: Int. J. Quant. Chem. 107 Pages: 3103-3119
  • Peer Reviewed
• [Journal Article] Quantum mechanical study of the proton transfer via a peptide bond in the novel pathway of proton translocation of cytochrome c oxidase (2006)
  • Author(s): Y. Takano, H. Nakamura
  • Journal Title: Chem. Phys. Lett. 430 Pages: 149-155
  • Peer Reviewed
• [Presentation] ヘムエリスリンの活性中心の電子構造への蛋白場の影響 (2009)
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-21
• [Presentation] タンパク質がつくる静電場のヘムエリスリンの活性中心の電子構造への影響 (2009)
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: 日本化学会第89回春季年会
  • Place of Presentation: 日本大学
  • Year and Date: 2009-03-30
• [Presentation] Density functional study of the roles of heme side chains and axial ligands (2009)
  • Author(s): Yu Takano, Haruki Nakamura
  • Organizer: 49th Sanibel Symposium
  • Place of Presentation: The King and Prince Golf & Beach Resort, Georgia
  • Year and Date: 2009-02-27
• [Presentation] 酸素運搬タンパク質ヘムエリスリンの活性中心の電子構造に関する理論的研究 (2009)
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: スーパーコンピュータワークショップ2009
  • Place of Presentation: 分子科学研究所
  • Year and Date: 2009-01-19
• [Presentation] 金属蛋白質の多核活性中心の電子構造および化学結合様式に関する理論的研究-酸素運搬蛋白質ヘムエリスリンへの適用- (2008)
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: 日本生物物理学会第46回年会
  • Place of Presentation: 博多国際会議場
  • Year and Date: 2008-12-05
• [Presentation] ヘムエリスリンの活性中心の化学結合様式に関する理論的研究 (2008)
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: 第2回分子科学討論会2008福岡
  • Place of Presentation: 博多国際会議場
  • Year and Date: 2008-09-27
• [Presentation] 酸素運搬タンパク質ヘムエリスリンの活性中心の電子構造および化学結合様式に関する理論的研究 (2008)
  • Author(s): 鷹野優, 山口兆, 中村春木
  • Organizer: 第102回触媒討論会
  • Place of Presentation: 名古屋大学
  • Year and Date: 2008-09-25
• [Presentation] Electronic Structures and Chemical Indices of the Active Site of Oxygenated and Deoxygenated Hemerythrin (2008)
  • Author(s): Yu Takano, Kizashi Yamaguchi, Haruki Nakamura
  • Organizer: WATOC2008
  • Place of Presentation: Sydney
  • Year and Date: 2008-09-14
• [Presentation] ヘムエリスリンの活性中心の電子構造および化学結合様式に関する理論的研究 (2008)
  • Author(s): 鷹野優, 山口兆, 中村春木
  • Organizer: 第8回蛋白質科学会
  • Place of Presentation: タワーホール船堀
  • Year and Date: 2008-06-11
• [Presentation] Theoretical study of the roles of heme side chains and axial ligands (2008)
  • Author(s): Yu Takano, Haruki Nakamura
  • Organizer: 48th Sanibel Symposium
  • Place of Presentation: The King and Prince Golf & Beach Resort, Georgia
  • Year and Date: 2008-02-26
• [Presentation] Molecular orbital study of the proton transfer through a peptide bond -A theoretical approach to a novel pathway of proton translocation of cytochrome c oxidase- (2007)
  • Author(s): Yu Takano, Haruki Nakamura
  • Organizer: ICCMSE2007
  • Place of Presentation: Marbella Corfu Hotel, Greece
  • Year and Date: 2007-09-26
• [Presentation] チトクロムc酸化酵素のheme aの酸化還元における電子構造変化とプロトン移動との関係 (2007)
  • Author(s): 鷹野優, 中村春木
  • Organizer: 第1回分子科学討論会2007仙台
  • Place of Presentation: 東北大学
  • Year and Date: 2007-09-18
• [Presentation] The Nature of the Copper-Oxygen Bonds in Hemocyanin by Hybrid DFT Calculation of Effective Exchange Integrals and Dioxygen Binding Energy via Ligand Coordination Effects (2007)
  • Author(s): Yu Takano, Kizashi Yamaguchi
  • Organizer: 47th Sanibel Symposium
  • Place of Presentation: The King and Prince Golf & Beach Resort, Georgia
  • Year and Date: 2007-02-25
• [Presentation] 分子軌道法によるチトクロムc酸化酵素の新しいプロトン輸送経路の考察 (2006)
  • Author(s): 鷹野優, 中村春木
  • Organizer: 分子構造総合討論会2006
  • Place of Presentation: 静岡グランシップ
  • Year and Date: 2006-09-23
• [Presentation] Quantum mechanical approach to a novel pathway of proton translocation of cytochrome c oxidase (2006)
  • Author(s): Yu Takano, Haruki Nakamura
  • Organizer: Material-oriented Quantum Chemistry
  • Place of Presentation: Osaka
  • Year and Date: 2006-05-28
• [Presentation] 酸素運搬蛋白質ヘムエリスリンの化学結合様式に関する理論的研究
  • Author(s): 鷹野優, 小泉健一, 山口兆, 中村春木
  • Organizer: 次世代生命体統合シミュレーション研究開発プロジェクト分子スケール研究開発チーム成果発表会