Free Energy Landscape Analysis of Prion Protein

2008 Fiscal Year Final Research Report

• Project/Area Number: 19700279
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: National Institute of Advanced Industrial Science and Technology
• Principal Investigator: SEKIJIMA Masakazu National Institute of Advanced Industrial Science and Technology, 生命情報工学研究センター, 研究員 (80371053)
• Project Period (FY): 2007 – 2008
• Keywords: コンピュータシミュレーション

Research Abstract

大規模シミュレーションを実行することで、慣性半径(Rg, Radius of gyration)と初期構造からのRMSD (Root Mean Square Deviation)に対しての自由エネルギー地形を求め、マウスとウシのプリオンタンパク質に自由エネルギー最小な状態の他に、構造転換の中間状態となり得る準安定状態が存在することを示した。

Research Products

• [Journal Article] State transition probability analysis of protein folding based on large scale molecular dynamics simulation (2008)
  • Author(s): S. Tokunaga, K.Ikeda, S. Honda, Y. Sawada, Y. Muraoka,T. Noguchi, M. Sekijima
  • Journal Title: In Proceedingsof the 17th IASTED International Conference on Applied Simulation and Modelling (ASM2008) Pages: 164-169
• [Journal Article] Free Energy Landscape Analysis System based on Parallel Molecular Dynamics Simulation (2007)
  • Author(s): M. Sekijima, J. Doi, S. Honda, T. Noguchi, and S. Shimizu, and Y. Akiyama
  • Journal Title: IPSJ Transaction on Bioinformatics, Vol.48 No.SIG17(TBIO3) Pages: 30-39
• [Journal Article] Development of Molecular Dynamics Simulation based Flexible Docking System (2007)
  • Author(s): S. Kimura, M. Sekijima, M. Takata, T. Noguchi, and K. Joe
  • Journal Title: In Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007) Pages: 739-745
• [Journal Article] Optimization of Molecular Dynamics Simulation on Cell Processor (2007)
  • Author(s): M. Sasaki, M. Sekijima, M. Takata, and K. Joe
  • Journal Title: In Proceedings of the 2007 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007) Pages: 780-786
• [Journal Article] Dvelopment of SVM based Prediction System for Metalbinding Sites in Protein (2007)
  • Author(s): M. Nakazawa, M. Takata, K. Yokota, T. Noguchi, M. Sekijima, and K. Joe
  • Journal Title: In Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2007) Pages: 972-978
• [Journal Article] High-Density Surface Reconstruction of Fine Arts and Documents for Complete Reproduction and Counterfeit Detection (2007)
  • Author(s): J. Doi, K. Shimizu, and M. Sekijima
  • Journal Title: In Proceedings of the 2007 IEEE International Conference on Networking, Sensing and Control (ICNSC2007) Pages: 392-397
• [Journal Article] Optimization and Evaluation of Parallel Molecular Dynamics Simulation on Blue Gene/L (2007)
  • Author(s): M. Sekijima, J. Doi, T. Noguchi, and S. Shimizu
  • Journal Title: In Proceedingsof the IASTED International Conference on Parallel and Distributed Computer and Networks (PDCN2007) Pages: 257-262
• [Journal Article] Crystal Structure of a Ten-Amino Acid Protein
  • Author(s): S. Honda, T. Akiba, Y. Kato, Y. Sawada, M. Sekijima, M. Ishimura, A. Ooishi, H. Watanabe, T. Odahara, H. Kazuaki
  • Journal Title: Journal of the American Chemical Society (accepted)
• [Journal Article] Large Scale Computing for Protein-Protein Binding Free Energy Calculation
  • Author(s): J. Ikeda, K. Ohno, S. Akioka, M. Orita, Y. Muraoka, T. Noguchi, M. Sekijima
  • Journal Title: In Proceedings of the 2008 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA 2008) Pages: 771-775
• [Presentation] 超並列計算機を用いた生体分子解析 -疾病関連蛋白質解析と世界最小蛋白質設計への応用- (2007)
  • Author(s): 関嶋政和、本田真也、野口保
  • Organizer: 次世代スーパーコンピューティング・シンポジウム2007
  • Place of Presentation: 東京
  • Year and Date: 20070000
• [Presentation] Free Energy Landscape Analysis of Prion Protein (2007)
  • Author(s): M. Sekijima, C. Motono, Y. Akiyama, and T.Noguchi
  • Organizer: 51th Biophysical Society Annual Meeting
  • Place of Presentation: Baltimore
  • Year and Date: 20070000
• [Remarks] 招待講演 M. Sekijima,"Application of HPC to the analysis of disease related protein and the design of novel proteins",Hardware and software for large-scale biological computing in the next decade, 2007, Okinawa
• [Remarks] 研究会報告 木村紗知、戸田幹人、関嶋政和、高田雅美、野口保、城和貴「タンパク質立体構造における時系列特徴抽出」情報処理学会研究会報告, 2009-MPS-73,pp.97-100,2009, 沖縄
• [Remarks] 研究会報告 中澤昌美、高田雅美、横田恭宣、野口保、関嶋政和、城和貴「SVM を用いた生体分子への金属結合部位予測手法の提案」2009-MPS-73,pp.213-216, 2009, 沖縄
• [Remarks] 研究会報告 徳永慎一、関嶋政和、村岡洋一、野口保「確率的情報処理による生体分子の熱揺らぎ解析に関する研究」情報処理学会研究会報告, 2007-BIO-11,pp.275-280,2007, 東京
• [Remarks] 研究会報告 池田潤一、関嶋政和、村岡洋一、野口保「分子動力学法を用いたタンパク質・リガンドの相互作用解析」 情報処理学会研究会報告, 2007-MPS-67,pp.143-146,2007, 東京