Computation of the free-energy landscape of a protein involving α and β secondary-structure elements

• Project/Area Number: 19570156
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Osaka University
• Principal Investigator: HIGO Junichi Osaka University, 臨床医工学融合研究教育センター, 特任研究員 (80265719)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2008: ¥260,000 (Direct Cost: ¥200,000、Indirect Cost: ¥60,000); Fiscal Year 2007: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
• Keywords: フォールディング / 自由エネルギー地形 / マルチカノニカル / WWドメイン / ヒューマニン

Research Abstract

α/βの両方の二次構造を含む50残基のタンパク質Pina WW domain の自由エネルギー地形を求めるために、水をあらわに取り込んだ全原子タンパク質モデルでマルチカノニカル分子動力学計算を行った。天然構造から変性構造までを含む多様な立体構造集団を得て、自由エネルギー地形を求めた。シミュレーションは安価な小規模クラスターマシンを使用した。また、多数本のマルチカノニカルランを統合し、構造探索の効率を高める手法を開発した

Research Products

• [Journal Article] Verifying trivial parallelization of multicanonical molecular dynamics for conformational sampling of a polypeptide in explicit water (2009)
  • Author(s): J. Higo, N. Kamiya, T. Sugihara, Y.Yonezawa, H. Nakamur
  • Journal Title: Chem. Phys. Lett 473 Pages: 326-329
  • Peer Reviewed
• [Journal Article] Parallelization of Markov chain generation and its application to the multicanonical method (2009)
  • Author(s): T. Sugihara, J. Higo, H. Nakamura
  • Journal Title: J. Phys. Soc. Jpn. (in press)
  • NAID: 10025962130
  • Peer Reviewed
• [Journal Article] arXiv (2009)
  • Author(s): Takanori Sugihara, Junichi Higo, Haruki Nakamura
  • Journal Title: 0812 Pages: 2964-2964
  • Peer Reviewed
• [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling (2008)
  • Author(s): R. Yagisawa, N. Kamiya, J. Ikebe, K.Umezawa, J. Higo
  • Journal Title: Chem. Phys. Lett. 455 Pages: 293-296
  • Peer Reviewed
• [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling (2008)
  • Author(s): Ryosuke Yagisawa
  • Journal Title: Chemical Physics Letters 455 Pages: 293-296
  • Peer Reviewed
• [Journal Article] Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces (2008)
  • Author(s): Kazuyosi Ikeda
  • Journal Title: BMC Structural Biology 8 Pages: 37-37
  • Peer Reviewed
• [Journal Article] Structure dependency of a 24-residue peptide humanin on solvent and preferential solvation by trifluoroethanol studied by multicanonical sampling (2008)
  • Author(s): Ryosuke Yagisawa
  • Journal Title: Chemical Physics Letters (in press)
  • Peer Reviewed
• [Presentation] アルツハイマーβアミロイドペプチド構造の分子シミュレーション (2009)
  • Author(s): 肥後順一
  • Organizer: 物理学会年会(春)
  • Place of Presentation: 東京
  • Year and Date: 2009-03-29
• [Presentation] Fair current, vortex, and drying/wetting water flow around lysozyme investigated by molecular dynamics simulation (2008)
  • Author(s): K. Umezawa, R. Morikawa, H. Nakamura, J.Higo
  • Organizer: 生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-05
• [Presentation] Identification of essential variables for medium-size protein-segment and application to structural class assignment (2008)
  • Author(s): K. Ikeda, J. Higo, K. Tomii
  • Organizer: 生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-04
• [Presentation] Two types universality of a fold universe of 50-residue segment (2008)
  • Author(s): J. Ito, Y. Sonobe, K. Ikeda, K. Tomii, A.Yamagishi, J. Higo
  • Organizer: 生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-04
• [Presentation] Structure variation of a 24-residue peptide on solvent, and preferential solvation by trifluroethanol by multicanonical sampling (2008)
  • Author(s): R. Yagisawa, N. Kamiya, A. Yamagishi, J.Higo
  • Organizer: 生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-03
• [Presentation] Multicanonical molecular dynamics simulation of a protein with 57 residues in explicit water (2008)
  • Author(s): J, Ikebe, J. Higo, H. Nakamura
  • Organizer: 生物物理学会年会
  • Place of Presentation: 福岡
  • Year and Date: 2008-12-03
• [Presentation] Brownian dynamics simulation of hERG potassium ion channel and development of an accurate molecular docking method for protein and ligand (2008)
  • Author(s): N. Kamiya, J. Higo
  • Organizer: The 3rd MEI International Symposium
  • Place of Presentation: San Francisco, USA.
  • Year and Date: 2008-11-30
• [Presentation] アルファ/べータ両方の二次構造要素を含む40残基蛋白質のフォールディングシミュレーション (2008)
  • Author(s): 肥後順一、池部仁善、神谷成敏、中村春木
  • Organizer: 物理学会年会(秋)
  • Place of Presentation: 山形
  • Year and Date: 2008-09-22
• [Presentation] アルファ/ベーダ両方の二次構造要素を含む40残基蛋白質のフォールディングシミュレーション (2008)
  • Author(s): 肥後順一
  • Organizer: 日本物理学会2008年秋期大会
  • Place of Presentation: 岩手大学上田キャンパス
  • Year and Date: 2008-09-22
• [Presentation] マルチカノニカル分子動力学法によるアミロイドペプチドの会合シミュレーション (2008)
  • Author(s): 神谷成敏,米澤康滋、中村春木、肥後順一
  • Organizer: 物理学会年会(秋)
  • Place of Presentation: 山形
  • Year and Date: 2008-09-20
• [Presentation] 蛋白質周辺における水分子の協調的挙動の分子動力学シミュレーションによる解析 (2008)
  • Author(s): 梅澤公二、肥後順一、中村春木、田代櫻子、神藤平三郎
  • Organizer: 物理学会年会(秋)
  • Place of Presentation: 山形
  • Year and Date: 2008-09-20
• [Presentation] マルチカノニカル分子動力学シミュレーションによって描かれるdisordered protein (水中アミロイドβ 12-36 残基断片)の自由エネルギー地形 (2008)
  • Author(s): 池部仁善、神谷成敏、伊東純一,神藤平三郎、中村春木、肥後順一
  • Organizer: 物理学会年会(秋)
  • Place of Presentation: 山形
  • Year and Date: 2008-09-20
• [Presentation] An enhanced conformational sampling of a 40-residue protein consisting of alpha and beta secondary structures in explicit solvent (2008)
  • Author(s): J. Higo, N. Kamiya
  • Organizer: The Joint 2nd Pacific Rim International Conference on Protein Science and 4th Asian-Oceania Human Proteome Organization
  • Place of Presentation: ケアンズ、オーストラリア
  • Year and Date: 2008-06-24
• [Presentation] Assembly simulation of four peptide chains in explicit water by multicanonical molecular dynamics (2008)
  • Author(s): N. Kamiya, Y. Yonezawa, H. Nakamura, J.Higo
  • Organizer: The Joint 2nd Pacific Rim International Conference on Protein Science and 4th Asian-Oceania Human Proteome Organization
  • Place of Presentation: ケアンズ、オーストラリア
  • Year and Date: 2008-06-24
• [Presentation] アルファ/ベータ両二次構造を含む40残基蛋白質の立体構造サンプリング (2008)
  • Author(s): 肥後順一、池部仁善、神谷成敏、中村春木
  • Organizer: 蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-11
• [Presentation] 蛋白質周辺における水の協調的な流れの分子動力学シミュレーションによる解析 (2008)
  • Author(s): 梅澤公二、肥後順一、山岸明彦、中村春木、田代櫻子、神藤平三郎
  • Organizer: 蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-11
• [Presentation] マルチカノニカル分子動力学法によるアミロイドペプチド4本鎖の会合シミュレーション (2008)
  • Author(s): 神谷成敏、米澤康滋、中村春木、肥後順一
  • Organizer: 蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-10
• [Presentation] Disordered proteinである水中アルツハイマーβアミロイドペプチドAβ(12-36)の自由エネルギー地形 (2008)
  • Author(s): 池部仁善、神谷成敏、伊東純一、神藤平三郎、肥後順一
  • Organizer: 蛋白質科学会年会
  • Place of Presentation: 東京
  • Year and Date: 2008-06-10
• [Presentation] マルチカノニカル分子動力学法による水中および30%TFE溶液中でのhumaninの自由エネルギー地形 (2007)
  • Author(s): 八木沢良介
  • Organizer: 第45回生物物理学会年会
  • Place of Presentation: パシフィコ横浜(神奈川)
  • Year and Date: 2007-12-21
• [Presentation] Prediction of protein structure from the free-energy landscapes (2007)
  • Author(s): J. Higo, N. Kamiya
  • Organizer: The 2nd MEI International Symposium
  • Place of Presentation: Osaka
  • Year and Date: 2007-12-08
• [Presentation] Structure universe of 50-residue protein segments constructed by residue-residue native contacts (2007)
  • Author(s): Y. Sonobe, J. Ito, A. Yamagishi, K. Tomii, J.Higo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-05
• [Presentation] Free-energy landscapes of humanin in water and in TFE/water using multicanonical molecular dynamics (2007)
  • Author(s): R. Yagisawa, N. Kamiya, A. Yamagishi, J.Higo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-05
• [Presentation] A process of protein-ligand approach mediated by solvent-dipole field (2007)
  • Author(s): N. Takano, N. Hamasaki, H. Miyagawa, A.Yamagishi, J. Higo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-05
• [Presentation] Conformational sampling of a 40-residue protein consisting of alpha and beta secondary-structure elements in explicit solvent (2007)
  • Author(s): J. Higo, J. Ikebe, N. Kamiya, H. Nakamura,H. Shindo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-04
• [Presentation] Free-energy landscape of the disordered state of an Altzheimer's beta amyloid peptide in water studied by multicanonical molecular dynamics (2007)
  • Author(s): J. Ikebe, N. Kamiya, J. Ito, H. Shindo, A.Yamagishi, J, Higo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-04
• [Presentation] Collective water flows around a protein : a novel insight into explicit solvent characteristics (2007)
  • Author(s): K. Umezawa, J. Higo, A. Yamagishi, S.Tashiro, H. Shindo
  • Organizer: 情報計算化学生物学会2007年大会
  • Place of Presentation: 広島
  • Year and Date: 2007-10-04
• [Book] 蛋白質の水和とフォールディング (2008)
  • Author(s): 肥後順一
  • Publisher: 「物性研究」(物性研究刊行会)
• [Book] 物性研究 (2008)
  • Author(s): 肥後順一
  • Total Pages: 4
  • Publisher: 京都大学物性研究刊行会