栗田典之

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所属豊橋科学技術大学
知識情報工学系
分子情報工学講座
職位准教授
専門分野量子生物学
計算科学
生命情報科学
学位筑波大学
所属学会物理学会
生物物理学会
E-mail
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研究紹介

 DNA、タンパク質等の生体高分子が生体内で果たしている生命維持のための機能を理解するためには、それらの構造を決定するだけでは不十分であり、量子化学計算により、生体高分子の電子状態、化学反応性を明らかにする必要があります。しかし、複雑な生体高分子を十分にモデル化した分子に対し、信頼性の高い計算結果を得ることは、最新のスーパーコンピュータを用いても容易ではありません。

 本研究では、これまでに、大規模分子の電子状態解析に有効な密度汎関数法とフラグメント分子軌道法に基づく電子状態計算手法を開発し、水和したDNA2重鎖、タンパク質とリガンドの複合体、癌転移抑制剤として開発されたキメラタンパク質などの安定構造と電子状態を高精度に解析して来ました。現在、国内外の研究者、医学部の先生らと共同で、以下の研究テーマに取り組んでいます。

(1)遺伝情報のRNAへの転写機構を制御する転写制御タンパク質(ラクト-スリプレッサー、カタボライト活性化タンパク質)とリガンド及びDNAとの特異的相互作用機構の解明

(2)分子シミュレーションに基づく副作用の少ない癌転移抑制剤の提案

(3)DNA及びDNA類似の人工核酸中の電荷移動機構の解明、新規バイオチップの提案

(4)環境ホルモン物質と核内受容体タンパク質との特異的相互作用機構の解明

研究業績

国際学術雑誌に発表した論文(最新の20件)

  1. "Specific interactions between androgen receptor and its ligand: ab initio molecular orbital calculations in water",
    I. Kobayashi, R. Takeda, R. suzuki, K. Shimamura, H. Ishimura, R. Kadoya, N. Kurita, K. Kawai, M. Takimoto-Kamimura,
    Journal of Molecular Graphics and Modelling, 2017, 75, 383-389.
  2. "Molecular dynamics and ab initio FMO calculations on the effect of water molecules on the interactions between androgen receptor and its ligand and cofactor",
    K. Shimamura, H. Ishimura, I. Kobayashi, R. Kadoya, N. Kurita, K. Kawai, M. Takimoto-Kamimura,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  3. "Effect of cofactor-binding on the specific interactions between androgen receptor and its ligand: ab initio molecular simulations",
    I. Kobayashi, K. Shimamura, H. Ishimura, R. Kadoya, N. Kurita, K. Kawai, M. Takimoto-Kamimura,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  4. "Ab initio molecular simulations on the binding properties between mycobacterial FtsZ and its inhibitor",
    M. Fujimori, R. Kadoya, S. Ota, K. Pavel, Y. Blume, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  5. "Ab initio fragment molecular orbital calculations on the specific interactions between amyloid-β peptides in an in vivo amyloid-β fibril",
    H. Ishimura, R. Kadoya, K. Shimamura, S. Ota, M. Fujimori, A. Okamoto, S. Shulga, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  6. "Specific interactions between M. tuberculosis CYP130 and its inhibitors: molecular simulations using ab initio fragment molecular orbital method",
    R. Kadoya, M. Fujimori, R. Takeda, T. Mizushima, P. Kamsri, P. Meewong, P. Pungpo, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  7. "Ab initio molecular simulations on specific interactions between amyloid-β peptide and new curcumin derivatives",
    S. Ota, H. Ishimura, M. Fujimori, S. Shulga, N. Kurita N.
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  8. "Ab initio molecular simulations based on FMO method for proposing potent inhibitors to reverse transcriptase of HIV",
    R. Takeda, R. Kadoya, I. Kobayashi, P. Kamsri, P. Meewong, P. Pungpo, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  9. "Molecular simulations on specific interactions between β-Sectretase and its inhibitors for the treatment of Alzheimer’s disease",
    M. T. H. Khan, T. Murakawa, T. Okada, N. Kurita,
    Current Topics in Medicinal Chemistry, 2015, in press ???.
  10. "Influence of solvating water molecules on the attacking mechanisms of OH-radical to DNA base pairs: DFT calculations in explicit waters",
    K. Shimamura, N. Okutsu, E. Shimizu, S. Shulga, Y.B. Blume, V.I. Danilov, N. Kurita,
    Structural Chemistry, 2016, 27, 1793-1806, DOI 10.1007/s11224-016-0800-3.
  11. "DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water",
    N. Okutsu, K. Shimamura, E. Shimizu, S. Shulga, V.I. Danilov, N. Kurita,
    AIP Conference Proceedings 1709, 020006 (2016); doi: 10.1063/1.4941205.
  12. "Specific interactions between diarylpyrimidine derivatives and HIV-1 RT: Molecular docking and ab initio FMO calculations",
    R. Kadoya, T. Mizushima, T. Suzuki, P. Kamsri, P. Meewong, P. Pungpo and N. Kurita,
    PACCON 2015, 2015, 291-294.
  13. "Specific interactions between acetyl- and butyryl-cholinesterase and their inhibitors: ab initio molecular simulations",
    T. Suzuki, T. Murakawa, R. Kadoya, M.T.H.Khan, N. Kurita,
    PACCON 2015, 2015, 295-298.
  14. "Ab initio molecular simulations for model systems of metal organic frameworks and a proposal of novel organic ligands for MOFs",
    T. Sugimoto, T. Mizushima, A. Okamoto, N. Kurita,
    Materials Today Asia 2014, 2014, December 9-12, Hong Kong, Hong Kong.
  15. "Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations",
    H. Ishimura, R. Kadoya, T. Suzuki, T. Murakawa, S. Shulga, N. Kurita,
    Chemical Physics Letters, 2015, 633, 139-145.
  16. "Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation",
    Y. Matsushita, T. Murakawa, K. Shimamura, M. Oishi, T. Ohyama, N. Kurita,
    AIP conference proceedings, 2015, 1649, 121-129.
  17. "Ab initio fragment molecular orbital calculations on specific interactions between acetylcholinesterase and its carbamate inhibitors",
    T. Okada, T. Murakawa, M. T. H. Khan, K. Komers, M. Kovářová, N. Kurita,
    Current Topics in Medicinal Chemistry, 2014, in press.
  18. "Molecular simulations on specific interactions between β-Secretase and its inhibitors for the treatment of Alzheimer’s disease",
    M.T.H.Khan, T. Okada, T. Murakawa, N. Kurita,
    Current Topics in Medicinal Chemistry, 2014, in press.
  19. "ab initio molecular simulations for proposing potent inhibitors to butyrylcholinesterases",
    T. Murakawa, Y. Matsushita, T. Suzuki, M.T.H.Khan, N. Kurita,
    Journal of Molecular Graphics and Modeling, 2014, 54, 54-61.
  20. "Structures and electronic properties of metal organic frameworks: DFT and ab initio FMO calculations for model systems",
    T. Sugimoto, T. Mizushima, A. Okamoto, N. Kurita,
    Chemical physical Letters, 2014, 612, 295-301.

国際学会における発表(最新の10件)

  1. "Molecular dynamics and ab initio FMO calculations on the effect of water molecules on the interactions between androgen receptor and its ligand and cofactor",
    K. Shimamura, H. Ishimura, I. Kobayashi, R. Kadoya, N. Kurita, K. Kawai, M. Takimoto-Kamimura,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  2. "Effect of cofactor-binding on the specific interactions between androgen receptor and its ligand: ab initio molecular simulations",
    I. Kobayashi, K. Shimamura, H. Ishimura, R. Kadoya, N. Kurita, K. Kawai, M. Takimoto-Kamimura,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  3. "Ab initio molecular simulations on the binding properties between mycobacterial FtsZ and its inhibitor",
    M. Fujimori, R. Kadoya, S. Ota, K. Pavel, Y. Blume, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  4. "Ab initio fragment molecular orbital calculations on the specific interactions between amyloid-β peptides in an in vivo amyloid-β fibril",
    H. Ishimura, R. Kadoya, K. Shimamura, S. Ota, M. Fujimori, A. Okamoto, S. Shulga, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  5. "Specific interactions between M. tuberculosis CYP130 and its inhibitors: molecular simulations using ab initio fragment molecular orbital method",
    R. Kadoya, M. Fujimori, R. Takeda, T. Mizushima, P. Kamsri, P. Meewong, P. Pungpo, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  6. "Ab initio molecular simulations on specific interactions between amyloid-β peptide and new curcumin derivatives",
    S. Ota, H. Ishimura, M. Fujimori, S. Shulga, N. Kurita N.
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  7. "Ab initio molecular simulations based on FMO method for proposing potent inhibitors to reverse transcriptase of HIV",
    R. Takeda, R. Kadoya, I. Kobayashi, P. Kamsri, P. Meewong, P. Pungpo, N. Kurita,
    Proceedings of The 2016 International Conference On Advanced Informatics, 2016, Penang, Malaysia, accepted.
  8. "Specific interactions between amyloid-β peptides in three-fold symmetric hexamer: ab initio molecular simulations",
    H. Ishimura, S. Ota, R. Kadoya, and N. Kurita
    CBI Annual Meeting 2015, 2015, October 27-29, Tokyo, Japan.
  9. "Specific interactions between M.tuberculosis CYP130 and econazole derivatives: Molecular docking and ab initio FMO calculations",
    R. Kadoya, R. Takeda, M. Fujimori, H. Ishimura, P. Kamsri, P. Meewong, P. Pungpo and N. Kurita
    CBI Annual Meeting 2015, 2015, October 27-29, Tokyo, Japan.
  10. "Specific Interactions between M. tuberculosis CYP130 and Novel Inhibitors: ab initio Molecular Simulations",
    T. Mizushima, R. Kadoya, P. Kamsri, P. Meewong, P. Pungpo, and N. Kurita
    PACCON 2015(Pure and Applied Chemistry International Conference 2015), 2015, January 21-23, Bangkok, Thailand.
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