分子シミュレーションによる膜タンパク質の分子透過性に関する理論的研究

2013 年度 研究成果報告書

• 研究課題/領域番号: 23750008
• 研究種目: 若手研究(B)
• 配分区分: 基金
• 研究分野: 物理化学
• 研究機関: 金沢大学
• 研究代表者: 齋藤 大明 金沢大学, 数物科学系, 助教 (40506820)
• 研究期間 (年度): 2011 – 2013
• キーワード: 分子動力学法 / 脂質二重層膜 / 膜タンパク質 / 自由エネルギー

研究概要

様々な脂質膜環境におけるペプチドおよび膜タンパク質の動的構造の解析，膜内安定性，イオン・分子透過性の評価を分子動力学シミュレーションと自由エネルギー計算により評価した．計算対象には代表的な抗菌性ペプチドであるグラミシジンAを用い，数種類の脂質膜における分子シミュレーションと自由エネルギー評価（膜内安定性）から，膜選択性機構に言及した．ペプチド－脂質膜間の相互作用特性の内訳（水和・静電・疎水性相互作用）を査察・解析・比較することにより，ペプチドの膜選択性に寄与する相互作用の詳細を解析した．

研究成果

• [雑誌論文] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations (2014)
  • 著者名/発表者名: Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: Mol. Phys 巻: 112 ページ: 526-532
  • 査読あり
• [雑誌論文] Network of water molecules around guanine nucleotide in the Hras-GTP and-GDP complexes by MD simulations (2014)
  • 著者名/発表者名: Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Tomokazu Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: JPS Conf. Proc 巻: 016006
  • 査読あり
• [雑誌論文] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer : Electrostatic Map and Ion Conduction (2014)
  • 著者名/発表者名: Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
  • 雑誌名: JPS Conf. Proc 巻: 012053
  • 査読あり
• [雑誌論文] Molecular Dynamics Study of Hsp90 and ADP : Hydrogen Bond Analysis for ADP Dissociation (2014)
  • 著者名/発表者名: Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
  • 雑誌名: JPS Conf. Proc 巻: 012056
  • 査読あり
• [雑誌論文] Protein--protein interactions of Azurin complex in liquid system (2014)
  • 著者名/発表者名: Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
  • 雑誌名: JPS Conf. Proc 巻: 012054
  • 査読あり
• [雑誌論文] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System (2014)
  • 著者名/発表者名: Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
  • 雑誌名: JPS Conf. Proc 巻: 012055
  • 査読あり
• [雑誌論文] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90 (2013)
  • 著者名/発表者名: Kazutomo Kawaguchi, Hiroaki Saito, Susumu Okazaki, Hidemi Nagao
  • 雑誌名: Chem. Phys. Lett 巻: 588 ページ: 226-230
  • 査読あり
• [雑誌論文] Molecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex (2013)
  • 著者名/発表者名: Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 113 ページ: 2333-2337
  • 査読あり
• [雑誌論文] Molecular Dynamics Study on Binding Free Energy of Azurin?Cytochrome c551 Complex (2013)
  • 著者名/発表者名: Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao
  • 雑誌名: Chem. Phys. Lett 巻: 556 ページ: 297-302
  • 査読あり
• [雑誌論文] Computational Study of Oxidation Potential of Ketone Molecule (2013)
  • 著者名/発表者名: Isman Kurniawan, Hiroaki Saito, Kazuto Kawaguchi, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 4 ページ: 45-52
  • 査読あり
• [雑誌論文] Structure and Hydration Free Energy of Ketone Compound in Neutral and Cationic State by Molecular Dynamics Simulation (2013)
  • 著者名/発表者名: Masashi Iwayama, Kazutomo Kawaguchi, Hiroaki Saito and Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 4 ページ: 59-70
  • 査読あり
• [雑誌論文] Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation : A Comparison of Calculation Methods (2013)
  • 著者名/発表者名: Meidy Triana Pakpahan, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 4 ページ: 71-78
  • 査読あり
• [雑誌論文] Coarse-grained Simulation of Azurin Crystal Complex System : Protein-protein Interactions (2013)
  • 著者名/発表者名: Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 4 ページ: 79-86
  • 査読あり
• [雑誌論文] Theoretical study of a π-stacking interaction in carbonic anhydrase (2013)
  • 著者名/発表者名: Muhamad Koyimatu, Hideto Shimahara, Kazutomo Kawaguchi, Hirosaki Saito, Kimikazu Sugimori, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 4 ページ: 87-94
  • 査読あり
• [雑誌論文] Analysis of water molecules in the Hras-GTP and GDP complexes with molecular dynamics simulations (2013)
  • 著者名/発表者名: T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
  • 雑誌名: Progress in Theoretical Chemistry and Physics 巻: 27 ページ: 351-360
  • 査読あり
• [雑誌論文] Molecular dynamics analyses of the dissociation process of ADP from Hsp90 (2012)
  • 著者名/発表者名: Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 112 ページ: 3791-3795
  • 査読あり
• [雑誌論文] Molecular dynamics study of gramicidin a in lipid bilayer : Structure and lateral pressure profile (2012)
  • 著者名/発表者名: Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Megumi Nishimura, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, Taku Mizukami, H. Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 112 ページ: 3834-3839
  • 査読あり
• [雑誌論文] Molecular dynamics studies of lipid bilayer with gramicidin A : effects of gramicidin A on membrane structure and hydrophobic match (2012)
  • 著者名/発表者名: Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 112 ページ: 161-170
  • 査読あり
• [雑誌論文] Solvation effect on the structural change of globular protein : a molecular dynamics study (2012)
  • 著者名/発表者名: Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Hidemi Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 112 ページ: 344-350
  • 査読あり
• [雑誌論文] Cell penetrating peptide induces various deformations of lipid bilayer membrane : inverted micelle, double bilayer and trans-membrane (2012)
  • 著者名/発表者名: Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki, Hidemi Nagao
  • 雑誌名: Int. J. Quantum Chem 巻: 112 ページ: 178-183
  • 査読あり
• [雑誌論文] The potentials of the atoms around Mg2+ in the H-ras GTP complex and in the H-ras GDP complex (2012)
  • 著者名/発表者名: T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
  • 雑誌名: Progress in Theoretical Chemistry and Physics 巻: 26 ページ: 525-543
  • 査読あり
• [雑誌論文] Free energy of cell-penetrating peptide through lipid bilayer membrane : coarse-grained model simulation (2012)
  • 著者名/発表者名: S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
  • 雑誌名: Progress in Theoretical Chemistry and Physics 巻: 26 ページ: 503-511
  • 査読あり
• [雑誌論文] Molecular Dynamics Study of Glutathione S-transferase : Structure and Binding Character of Glutathione (2012)
  • 著者名/発表者名: Y. Omae, H. Saito, H. Takagi, M. Nishimura, M. Iwayama, K. Kawaguchi, H. Nagao
  • 雑誌名: Progress in Theoretical Chemistry and Physics 巻: 26 ページ: 545-553
  • 査読あり
• [雑誌論文] Temperature Effects on Dynamics of Spherical Micelles : A Molecular Dynamics Study (2012)
  • 著者名/発表者名: Gia Septiana Wulandari, Micke Rusmerryani, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 2 ページ: 59-68
  • 査読あり
• [雑誌論文] Molecular Dynamics Studies on Structure and Dynamics of Spherical Micelles (2012)
  • 著者名/発表者名: Micke Rusmerryani, Gia Septiana Wulandari, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
  • 雑誌名: Recent Development in Computational Science 巻: 2 ページ: 69-77
  • 査読あり
• [雑誌論文] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study (2011)
  • 著者名/発表者名: Hiroaki Saito, Wataru Shinoda
  • 雑誌名: J. Phys. Chem. B 巻: 115 ページ: 15241-15250
  • 査読あり
• [雑誌論文] Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A
  • 著者名/発表者名: Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 633-636
  • 査読あり
• [雑誌論文] Evaluation of scoring functions for protein-ligand docking
  • 著者名/発表者名: Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 645-648
  • 査読あり
• [雑誌論文] Transition State Analysis of Azurin via Go-like Model
  • 著者名/発表者名: Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 641-644
  • 査読あり
• [雑誌論文] Molecular Dynamics Study on Entrainment Phenomenon in Model Molecular Systems
  • 著者名/発表者名: Hidemi Nagao, Michke Rusmerryani, Acep Purqon, Kazutomo Kawaguchi, Hiroaki Saito
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 729-732
  • 査読あり
• [雑誌論文] Conformational Stability of Met20 Loop of DHFR : A molecular Dynamics Study
  • 著者名/発表者名: Megumi Nishimura, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 654-657
  • 査読あり
• [雑誌論文] Molecular dynamics studies of Hsp90 with ADP : protein-ligand binding dynamics
  • 著者名/発表者名: Kazutomo Kawaguchi, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 637-640
  • 査読あり
• [雑誌論文] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein
  • 著者名/発表者名: Muhamad Koyimatu, Hideto Shimahara, Masashi Iwayama, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 626-629
  • 査読あり
• [雑誌論文] A molecular dynamics study of Hras-GTP and GDP complexes : the properties of water molecules around guanine nucleotide
  • 著者名/発表者名: T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • 雑誌名: AIP Conf. Proc 巻: 1518 ページ: 594-597
  • 査読あり