Molecualr dynamics study on the molecuar permeability of membrane protein

• Project/Area Number: 23750008
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Physical chemistry
• Research Institution: Kanazawa University
• Principal Investigator: SAITO Hiroaki 金沢大学, 数物科学系, 助教 (40506820)
• Project Period (FY): 2011 – 2013
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2011: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
• Keywords: 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 / ペプチド / イオンチャネル / 溶媒和自由エネルギー / 分子動力学 / グラミシジン

Research Abstract

We have carried out molecular dynamics simulations to analysis the structure and dynamics of peptide and membrane protein in several lipid bilayer environments and have investigated the ion and molecular permeability through the channel of membrane protein. The thermal stability of membrane protein in the lipid bilayers has also been investigated by free energy calculation.

Research Products

• [Journal Article] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations (2014)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: Mol. Phys Volume: 112 Pages: 526-532
  • Peer Reviewed
• [Journal Article] Network of water molecules around guanine nucleotide in the Hras-GTP and-GDP complexes by MD simulations (2014)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Tomokazu Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: JPS Conf. Proc Volume: 016006
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer : Electrostatic Map and Ion Conduction (2014)
  • Author(s): Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
  • Journal Title: JPS Conf. Proc Volume: 012053
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Hsp90 and ADP : Hydrogen Bond Analysis for ADP Dissociation (2014)
  • Author(s): Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
  • Journal Title: JPS Conf. Proc Volume: 012056
  • Peer Reviewed
• [Journal Article] Protein--protein interactions of Azurin complex in liquid system (2014)
  • Author(s): Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
  • Journal Title: JPS Conf. Proc Volume: 012054
  • Peer Reviewed
• [Journal Article] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System (2014)
  • Author(s): Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
  • Journal Title: JPS Conf. Proc Volume: 012055
  • Peer Reviewed
• [Journal Article] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations (2014)
  • Author(s): T. Miyakawa
  • Journal Title: MOLECULAR PHYSICS Volume: 112 Issue: 3-4 Pages: 526-532
  • DOI: 10.1080/00268976.2013.852697
  • Peer Reviewed
• [Journal Article] Network of water molecules around guanine nucleotide in the Hras-GTP and -GDP complexes by MD simulations (2014)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Tomokazu Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: JPS Conf. Proc. Volume: volume 1 Pages: 16006-16006
  • DOI: 10.7566/jpscp.1.016006
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction (2014)
  • Author(s): Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
  • Journal Title: JPS Conf. Proc Volume: volume 1 Pages: 012053-012053
  • DOI: 10.7566/jpscp.1.012053
  • Peer Reviewed / Open Access
• [Journal Article] Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation (2014)
  • Author(s): Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
  • Journal Title: JPS Conf. Proc. Volume: volume 1 Pages: 012056-012056
  • DOI: 10.7566/jpscp.1.012056
  • Peer Reviewed
• [Journal Article] Protein--protein interactions of Azurin complex in liquid system (2014)
  • Author(s): Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
  • Journal Title: JPS Conf. Proc. Volume: volume 1
  • DOI: 10.7566/jpscp.1.012054
  • Peer Reviewed
• [Journal Article] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System (2014)
  • Author(s): Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
  • Journal Title: JPS Conf. Proc. Volume: volume 1
  • DOI: 10.7566/jpscp.1.012055
  • Peer Reviewed
• [Journal Article] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90 (2013)
  • Author(s): Kazutomo Kawaguchi, Hiroaki Saito, Susumu Okazaki, Hidemi Nagao
  • Journal Title: Chem. Phys. Lett Volume: 588 Pages: 226-230
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex (2013)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 113 Pages: 2333-2337
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin?Cytochrome c551 Complex (2013)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Jiyoung Kang, Masaru Tateno, Hidemi Nagao
  • Journal Title: Chem. Phys. Lett Volume: 556 Pages: 297-302
  • Peer Reviewed
• [Journal Article] Computational Study of Oxidation Potential of Ketone Molecule (2013)
  • Author(s): Isman Kurniawan, Hiroaki Saito, Kazuto Kawaguchi, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 4 Pages: 45-52
  • Peer Reviewed
• [Journal Article] Structure and Hydration Free Energy of Ketone Compound in Neutral and Cationic State by Molecular Dynamics Simulation (2013)
  • Author(s): Masashi Iwayama, Kazutomo Kawaguchi, Hiroaki Saito and Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 4 Pages: 59-70
  • Peer Reviewed
• [Journal Article] Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation : A Comparison of Calculation Methods (2013)
  • Author(s): Meidy Triana Pakpahan, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 4 Pages: 71-78
  • Peer Reviewed
• [Journal Article] Coarse-grained Simulation of Azurin Crystal Complex System : Protein-protein Interactions (2013)
  • Author(s): Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 4 Pages: 79-86
  • Peer Reviewed
• [Journal Article] Theoretical study of a π-stacking interaction in carbonic anhydrase (2013)
  • Author(s): Muhamad Koyimatu, Hideto Shimahara, Kazutomo Kawaguchi, Hirosaki Saito, Kimikazu Sugimori, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 4 Pages: 87-94
  • Peer Reviewed
• [Journal Article] Analysis of water molecules in the Hras-GTP and GDP complexes with molecular dynamics simulations (2013)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 27 Pages: 351-360
  • Peer Reviewed
• [Journal Article] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp90 (2013)
  • Author(s): Kazutomo Kawaguchi, Hiroaki Saito, Susumu Okazaki, Hidemi Nagao
  • Journal Title: Chem. Phys. Lett. Volume: 588 Pages: 226-230
  • DOI: 10.1016/j.cplett.2013.10.015
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Simulations of the Hras-GTP complex and the Hras-GDP complex (2013)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem. Volume: 113 Issue: 21 Pages: 2333-2337
  • DOI: 10.1002/qua.24457
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A (2013)
  • Author(s): Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 633-636
  • DOI: 10.1063/1.4794649
  • Peer Reviewed
• [Journal Article] Evaluation of scoring functions for protein-ligand docking (2013)
  • Author(s): Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 645-648
  • DOI: 10.1063/1.4794652
  • Peer Reviewed
• [Journal Article] Transition State Analysis of Azurin via Go-like Model (2013)
  • Author(s): Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 641-644
  • DOI: 10.1063/1.4794651
  • Peer Reviewed
• [Journal Article] Theoretical Study on Entrainment Phenomenon in Model Molecular Systems (2013)
  • Author(s): H. Nagao, S. Kawamoto, M. Rusmerryani, A. Purqon, K. Kawaguchi, H. Saito
  • Journal Title: AIP Conference Proceedings Volume: 1518 Pages: 729-732
  • DOI: 10.1063/1.4794669
  • Peer Reviewed
• [Journal Article] Conformational Stability of Met20 Loop of DHFR:A molecular Dynamics Study (2013)
  • Author(s): Megumi Nishimura, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 654-657
  • DOI: 10.1063/1.4794654
  • Peer Reviewed
• [Journal Article] Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics (2013)
  • Author(s): Kazutomo Kawaguchi, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 637-640
  • DOI: 10.1063/1.4794650
  • Peer Reviewed
• [Journal Article] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein (2013)
  • Author(s): Muhamad Koyimatu, Hideto Shimahara, Masashi Iwayama, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 626-629
  • DOI: 10.1063/1.4794647
  • Peer Reviewed
• [Journal Article] A molecular dynamics study of Hras-GTP and GDP complexes: the properties of water molecules around guanine nucleotide (2013)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 594-597
  • DOI: 10.1063/1.4794639
  • Peer Reviewed
• [Journal Article] Molecular dynamics analyses of the dissociation process of ADP from Hsp90 (2012)
  • Author(s): Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 112 Pages: 3791-3795
  • Peer Reviewed
• [Journal Article] Molecular dynamics study of gramicidin a in lipid bilayer : Structure and lateral pressure profile (2012)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Megumi Nishimura, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, Taku Mizukami, H. Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 112 Pages: 3834-3839
  • Peer Reviewed
• [Journal Article] Molecular dynamics studies of lipid bilayer with gramicidin A : effects of gramicidin A on membrane structure and hydrophobic match (2012)
  • Author(s): Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 112 Pages: 161-170
  • Peer Reviewed
• [Journal Article] Solvation effect on the structural change of globular protein : a molecular dynamics study (2012)
  • Author(s): Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 112 Pages: 344-350
  • Peer Reviewed
• [Journal Article] Cell penetrating peptide induces various deformations of lipid bilayer membrane : inverted micelle, double bilayer and trans-membrane (2012)
  • Author(s): Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki, Hidemi Nagao
  • Journal Title: Int. J. Quantum Chem Volume: 112 Pages: 178-183
  • Peer Reviewed
• [Journal Article] The potentials of the atoms around Mg2+ in the H-ras GTP complex and in the H-ras GDP complex (2012)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito and Hidemi Nagao
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 26 Pages: 525-543
  • Peer Reviewed
• [Journal Article] Free energy of cell-penetrating peptide through lipid bilayer membrane : coarse-grained model simulation (2012)
  • Author(s): S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 26 Pages: 503-511
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Glutathione S-transferase : Structure and Binding Character of Glutathione (2012)
  • Author(s): Y. Omae, H. Saito, H. Takagi, M. Nishimura, M. Iwayama, K. Kawaguchi, H. Nagao
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 26 Pages: 545-553
  • Peer Reviewed
• [Journal Article] Temperature Effects on Dynamics of Spherical Micelles : A Molecular Dynamics Study (2012)
  • Author(s): Gia Septiana Wulandari, Micke Rusmerryani, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 2 Pages: 59-68
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Studies on Structure and Dynamics of Spherical Micelles (2012)
  • Author(s): Micke Rusmerryani, Gia Septiana Wulandari, Shuhei Kawamoto, Hiroaki Saito, Kiyoshi Nishikawa, Hidemi Nagao
  • Journal Title: Recent Development in Computational Science Volume: 2 Pages: 69-77
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study on Binding Free Energy of Azurin-Cytochrome c551 Complex (2012)
  • Author(s): H. Saito, M. Iwayama, T. Mizukami, J. Kang, M.Tateno, H. Nagao
  • Journal Title: Chemical Physics Letters Volume: 556 Pages: 297-302
  • DOI: 10.1016/j.cplett.2012.12.016
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Analyses of the Dissociation Process of ADP from Hsp90 (2012)
  • Author(s): K. Kawaguchi, H. Takagi, M. Iwayama, M.Nishimura, T. Miyakawa, H. Saito, M. Takasu, H.Nagao
  • Journal Title: International Journal of Quantum Chemistry Volume: 112 Issue: 24 Pages: 3791-3795
  • DOI: 10.1002/qua.24229
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Structure and Lateral Pressure Profile (2012)
  • Author(s): H. Saito, M. Iwayama, H. Takagi, M. Nishimura, T. Miyakawa, K. Kawaguchi, M. Takasu, T. Mizukami, H. Nagao
  • Journal Title: International Journal of Quantum Chemistry Volume: 112 Issue: 24 Pages: 3834-3839
  • DOI: 10.1002/qua.24248
  • Peer Reviewed
• [Journal Article] Free energy of cell-penetrating peptide through lipid bilayer membrane: coarse-grained model simulation (2012)
  • Author(s): S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 26 Pages: 503-511
  • DOI: 10.1007/978-94-007-5297-9_29
  • ISBN: 9789400752962, 9789400752979
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Glutathione S-transferase: Structure and Binding Character of Glutathione (2012)
  • Author(s): Y. Omae, H. Saito, H. Takagi, M. Nishimura, M. Iwayama, K. Kawaguchi, H. Nagao
  • Journal Title: Progress in Theoretical Chemistry and Physics Volume: 26 Pages: 545-553
  • DOI: 10.1007/978-94-007-5297-9_32
  • ISBN: 9789400752962, 9789400752979
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Studies of Lipid Bilayer with Gramicidin A: Effects of Gramicidin A on Membrane Structure and Hydrophobic Match (2012)
  • Author(s): Hiroaki Saito, Taku Mizukami, Shuhei Kawamoto, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
  • Journal Title: International Journal of Quantum Chemistry Volume: 112 Issue: 1 Pages: 161-170
  • DOI: 10.1002/qua.23252
  • Peer Reviewed
• [Journal Article] Solvation Effect on the Structural Change of Globular Protein: A Molecular Dynamics Study (2012)
  • Author(s): Taku Mizukami, Hiroaki Saito, Shuhei Kawamoto,Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
  • Journal Title: International Journal of Quantum Chemistry Volume: 112 Issue: 1 Pages: 344-350
  • DOI: 10.1002/qua.23251
  • Peer Reviewed
• [Journal Article] Cell-Penetrating Peptide Induces Various Deformations of Lipid Bilayer Membrane: Inverted Micelle,Double Bilayer, and Transmembrane (2012)
  • Author(s): Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Shiroh Futaki, Hidemi Nagao
  • Journal Title: International Journal of Quantum Chemistry Volume: 112 Issue: 1 Pages: 178-183
  • DOI: 10.1002/qua.23177
  • Peer Reviewed
• [Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study (2011)
  • Author(s): Hiroaki Saito, Wataru Shinoda
  • Journal Title: J. Phys. Chem. B Volume: 115 Pages: 15241-15250
  • Peer Reviewed
• [Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study (2011)
  • Author(s): 斎藤大明、篠田渉
  • Journal Title: Journal of Physical Chemistry B Volume: 115 Issue: 51 Pages: 15241-15250
  • DOI: 10.1021/jp201611p
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study of Electrostatic Potential along Lipid Bilayer with Gramicidin A
  • Author(s): Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 633-636
  • Peer Reviewed
• [Journal Article] Evaluation of scoring functions for protein-ligand docking
  • Author(s): Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 645-648
  • Peer Reviewed
• [Journal Article] Transition State Analysis of Azurin via Go-like Model
  • Author(s): Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 641-644
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Study on Entrainment Phenomenon in Model Molecular Systems
  • Author(s): Hidemi Nagao, Michke Rusmerryani, Acep Purqon, Kazutomo Kawaguchi, Hiroaki Saito
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 729-732
  • Peer Reviewed
• [Journal Article] Conformational Stability of Met20 Loop of DHFR : A molecular Dynamics Study
  • Author(s): Megumi Nishimura, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 654-657
  • Peer Reviewed
• [Journal Article] Molecular dynamics studies of Hsp90 with ADP : protein-ligand binding dynamics
  • Author(s): Kazutomo Kawaguchi, Hiroyuki Takagi, Masako Takasu, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 637-640
  • Peer Reviewed
• [Journal Article] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein
  • Author(s): Muhamad Koyimatu, Hideto Shimahara, Masashi Iwayama, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 626-629
  • Peer Reviewed
• [Journal Article] A molecular dynamics study of Hras-GTP and GDP complexes : the properties of water molecules around guanine nucleotide
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 594-597
  • Peer Reviewed
• [Presentation] Thermal Stability of Gramicidin A in Lipid Bilayer: A Free Energy Analysis (2014)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Kazutomo Kawaguchi, Taku Mizukami, Takeshi Miyakawa, Masako Takasu, and Hidemi Nagao
  • Organizer: The 54th Sanibel Symposium
  • Place of Presentation: Florida, USA
• [Presentation] Analysis of the site-dipole fields around guanine nucleotides in the Hras-GTP and Hras-GDP complexes (2014)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: The 54th Sanibel Symposium
  • Place of Presentation: Florida, USA
• [Presentation] Hras-GTP/GDP の GTP/GDP周辺にある水分子水素結合場の分子動力学法による研究 (2014)
  • Author(s): 宮川毅, 森河良太, 高須昌子, 杉森公一,川口一朋, 齋藤大明, 長尾秀実
  • Organizer: 日本物理学会第69回年次大会
  • Place of Presentation: 神奈川
• [Presentation] 分子動力学法によるタンパク質－基質分子間の自由エネルギープロフィール (2014)
  • Author(s): 川口一朋、齋藤大明、長尾秀実
  • Organizer: 日本物理学会第69回年次大会
  • Place of Presentation: 神奈川
• [Presentation] 分子動力学法によるグラミシジンAの膜内安定性 (2014)
  • Author(s): 齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 日本化学会第94春季年会
  • Place of Presentation: 名古屋
• [Presentation] Molecular dynamics study on mean force and free energy difference between Hsp90 and ADP (2014)
  • Author(s): Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
  • Organizer: Nagoya Symposium on Depletion Forces: Celebrating the 60th Anniversary of the Asakura-Oosawa Theory
  • Place of Presentation: 名古屋
• [Presentation] Molecular Dynamics Study of Gramicidin A in Lipid Bilayer: Electrostatic Map and Ion Conduction (2013)
  • Author(s): Hiroaki SAITO, Masashi IWAYAMA, Kazutomo KAWAGUCHI, Taku MIZUKAMI, Takeshi MIYAKAWA, Masako TAKASU, and Hidemi NAGAO
  • Organizer: The 12th Asia Pacific Physics Conference (APPC12)
  • Place of Presentation: 千葉
• [Presentation] Molecular Dynamics Study of Hsp90 and ADP: Hydrogen Bond Analysis for ADP Dissociation (2013)
  • Author(s): Kazutomo KAWAGUCHI, Hiroaki SAITO, Hidemi NAGAO
  • Organizer: The 12th Asia Pacific Physics Conference (APPC12)
  • Place of Presentation: 千葉
• [Presentation] Protein--protein interactions of Azurin complex in liquid system (2013)
  • Author(s): Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and Hidemi Nagao
  • Organizer: The 12th Asia Pacific Physics Conference (APPC12)
  • Place of Presentation: 千葉
• [Presentation] Π-stacking Interaction between Heterocyclic Rings in a Reaction Field of Biological System (2013)
  • Author(s): Muhamad KOYIMATU, Hideto SHIMAHARA, Kimikazu SUGIMORI, Kazutomo KAWAGUCHI, Hiroaki SAITO, and Hidemi NAGAO
  • Organizer: The 12th Asia Pacific Physics Conference (APPC12)
  • Place of Presentation: 千葉
• [Presentation] MD法とQM/MM計算によるブルー銅タンパク質の酸化還元電位に関する理論的研究 (2013)
  • Author(s): 岩山 将士，齋藤 大明，杉森 公一，川口 一朋，長尾 秀実
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] Theoretical studies on effects of protein--protein interactions on azurin complex stability by coarse-grained model (2013)
  • Author(s): Rusmerryani Micke，Takasu Masako，Kawaguchi Kazutomo，Saito Hiroaki，Nagao Hidemi
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] Theoretical Study of a π-stacking Interaction Effect to the Orientation of His64 of Carbonic Anhydrase (2013)
  • Author(s): Koyimatu Muhamad，Shimahara Hideto，Sugimori Kimikazu，Sugimori Tetsuya，Saito Hirosaki，Kawaguchi Kazutomo，Nagao Hidemi
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] Structure and stability of the binding of HNP-1 with DPPC lipid bilayer: a molecular dynamics study (2013)
  • Author(s): Primasari Nandia，Saito Hiroaki，Nurbaiti Santi，Kawaguchi Kazutomo，Nagao Hidemi
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] Hsp90とADPの解離過程における自由エネルギープロフィールと相互作用解析 (2013)
  • Author(s): 川口 一朋，齋藤 大明，長尾 秀実
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] 脂質二重層膜におけるグラミシジンAの静電ポテンシャル特性と電場応答 (2013)
  • Author(s): 齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 第7回分子科学討論会
  • Place of Presentation: 京都
• [Presentation] Electrostatic potential and lateral pressure profile of lipid bilayer containing gramicidin A in effective electrostatic field (2013)
  • Author(s): 齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Analysis of network of water molecules in molecular dynamics simulations of Hras-GTP and GDP complexes (2013)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Free energy profile and dissociation pathway in the dissociation process of ADP from Hsp90 (2013)
  • Author(s): Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Development of new algolithm for calculation of the energy distribution function by GPGPU (2013)
  • Author(s): Takuhito Shiogama, Tsuhito Yoshida, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Theoretical study on the structural stability of the vesicle by parallelized coarse-grained simulation (2013)
  • Author(s): Tsuhito Yoshida, Kazuma Tamura, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Theoretical study on the self-assembly of satellite tobacco mosaic virus using coarse grained simulation (2013)
  • Author(s): Masato Teranishi, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: 第51回生物物理年会
  • Place of Presentation: 京都
• [Presentation] Theoretical studies of redox potential for metalloprotein by combining MD and QM/MM simulations (2013)
  • Author(s): Masashi Iwayama, Hiroaki Saito, Kimikazu Sugimori, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: 3rd International Conference on Molecular Simulatio
  • Place of Presentation: 神戸
• [Presentation] Thermal Statibilty of Gramicidin A in Lipid Bilayer: A Molecular Dynamics Study (2013)
  • Author(s): Hiroaki Saito, Kawaguchi Kazutomo, Hidemi Nagao
  • Organizer: 3rd International Conference on Molecular Simulation
  • Place of Presentation: 神戸
• [Presentation] Molecular dynamics study on mean force between Hsp90 and ADP (2013)
  • Author(s): Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: 3rd International Conference on Molecular Simulation
  • Place of Presentation: 神戸
• [Presentation] Theoretical studies on oxidation of molecules by combining MD and QM/MM calculations (2013)
  • Author(s): Masashi Iwayama, Isman Kurniawan, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: The 53rd Sanibel Symposium
  • Place of Presentation: Florida, USA
• [Presentation] Hras-GTP内におけるGTP周辺にある水分子の分子動力学法による研究 (2013)
  • Author(s): 宮川毅, 森河良太, 高須昌子, 杉森公一, 川口一朋, 齋藤大明, 長尾秀実
  • Organizer: 第６８回 日本物理学会 春季大会
  • Place of Presentation: 広島
• [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and lateral pressure profile (2012)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Kazutomo Kawaguchi, and Hidemi Nagao
  • Organizer: The 5th International Symposium on Computational Sciences (ISCS) 2012
  • Place of Presentation: Yogyakarta, Indonesia
  • Invited
• [Presentation] Free energy profile for binding of ADP to Hsp90 by molecular dynamics simulation (2012)
  • Author(s): Kazutomo Kawaguchi, Hiroyuki Takagi, Masashi Iwayama, Hiroaki Saito, and Hidemi Nagao
  • Organizer: The 5th International Symposium on Computational Sciences (ISCS) 2012
  • Place of Presentation: Yogyakarta, Indonesia
  • Invited
• [Presentation] 脂質二重層膜におけるグラミシジンAの構造と圧力特性 (2012)
  • Author(s): 齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 第６回分子化学討論会
  • Place of Presentation: 東京
• [Presentation] Dual Go-Modelを用いたジヒドロ葉酸還元酵素の構造遷移解析 (2012)
  • Author(s): 寺西 壯登，川口 一朋，齋藤 大明，長尾 秀実
  • Organizer: 第６回分子化学討論会
  • Place of Presentation: 東京
• [Presentation] 炭酸脱水酵素の水素結合ネットワークとHis64 (2012)
  • Author(s): 島原 秀登，杉森 公一，岩山 将士，杉森 哲也，川口 一朋，齊藤 大明，吉田 卓也，中沢 隆，大久保 忠恭，小林 祐次，長尾 秀実
  • Organizer: 第６回分子化学討論会
  • Place of Presentation: 東京
• [Presentation] GPGPUによるエネルギー分布関数計算の高速化 (2012)
  • Author(s): 塩釜 拓仁，齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 第６回分子化学討論会
  • Place of Presentation: 東京
• [Presentation] 分子動力学計算における相互作用計算の高速化手法の評価 (2012)
  • Author(s): 吉田 津日門，齋藤 大明，川口 一朋，長尾 秀実
  • Organizer: 第６回分子化学討論会
  • Place of Presentation: 東京
• [Presentation] Free energy profile for binding of ADP to Hsp90 with molecular dynamics simulation (2012)
  • Author(s): K. Kawaguchi, H. Takagi, M. Iwayama, M. Nishimura, H. Saito, Hidemi Nagao
  • Organizer: 第５０回日本生物物理学会年会
  • Place of Presentation: 名古屋
• [Presentation] Structure and lateral pressure profile of lipid bilayer containing gramicidin A by molecular dynamics simulation (2012)
  • Author(s): H. Saito, M. Iwayama, M. Nishimura, H. Takagi, K. Kawaguchi, H. Nagao
  • Organizer: 第５０回日本生物物理学会年会
  • Place of Presentation: 名古屋
• [Presentation] Analysis of water molecules in molecular dynamics simulations of H-ras GTP and GDP complexes (2012)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, Hidemi Nagao
  • Organizer: 第５０回日本生物物理学会年会
  • Place of Presentation: 名古屋
• [Presentation] Solvation free energy in protein docking process (2012)
  • Author(s): Taku Mizukami, Hiroaki Siato, Hidemi Nagao
  • Organizer: 第５０回日本生物物理学会年会
  • Place of Presentation: 名古屋
• [Presentation] Binding Free Energy of Azurin–Cytochrome c551 Complex by all-atom Molecular Dynamics Simulation (2012)
  • Author(s): H. Saito, M. Iwayama, T. Mizukami, K. Kawaguchi, Hidemi Nagao
  • Organizer: Conference on Computational Physics (CCP2012)
  • Place of Presentation: Kobe, Japan
• [Presentation] Free energy profile of Hsp90-ADP binding by molecular dynamics simulations (2012)
  • Author(s): K. Kawaguchi, H. Saito, Hidemi Nagao
  • Organizer: Conference on Computational Physics (CCP2012)
  • Place of Presentation: Kobe, Japan
• [Presentation] Hsp90 との結合・解離における ADP の解析 (2012)
  • Author(s): 川口一朋, 齋藤大明, 長尾秀実
  • Organizer: 第26回分子シミュレーション討論会
  • Place of Presentation: Kobe, Japan
• [Presentation] 脂質二重層膜におけるグラミシジン A の構造と圧力特性 (2012)
  • Author(s): 齋藤大明, 川口一朋 , 長尾秀実
  • Organizer: 第26回分子シミュレーション討論会
  • Place of Presentation: 福岡
• [Presentation] Molecular dynamics studies of Hsp90 with ADP: protein-ligand binding dynamics (2012)
  • Author(s): K. Kawaguchi, H. Takagi, M. Takasu, H. Saito, H. Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Theoretical Model for Assessing Properties of Local Structures in Metalloprotein (2012)
  • Author(s): M. Koyimatu, H. Shimahara, M. Iwayama, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Oxidation Potential of Ketone Molecule: Structural Fluctuation Dependence (2012)
  • Author(s): Isman Kurniawan, Muhamad Koyimatu, Masashi Iwayama, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] A molecular dynamics study of Hras-GTP and GDP complexes: the properties of water molecules around guanine nucleotide (2012)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Conformational Stability of Met20 Loop of DHFR: A molecular Dynamics Study (2012)
  • Author(s): M. Nishimura, H. Saito, K. Kawaguchi, H. Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Evaluation of scoring functions for protein-ligand docking (2012)
  • Author(s): Meidy T. Pakpahan, Micke Rusmerryani, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Transition State Analysis of Azurin via Go-like Model (2012)
  • Author(s): Micke Rusmerryani, Meidy T. Pakpahan, Megumi Nishimura, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Molecular dynamics study of electrostatic potential along lipid bilayer with gramicidin A (2012)
  • Author(s): Hiroaki Saito, Megumi Nishimura, Hiroyuki Takagi, Takeshi, Miyakawa, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Theoretical study on entrainment phenomenon in model molecular systems (2012)
  • Author(s): Hidemi Nagao, Michke Rusmerryani, Acep Pruqon, Kazutomo Kawaguchi, Hiroaki Saito
  • Organizer: The 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: 仙台
• [Presentation] Molecular dynamics analyses of dissociation process of ADP from Hsp90 (2012)
  • Author(s): K. Kawaguchi, H. Takagi, M. Iwayama, H. Saito, H. Nagao
  • Organizer: International Symposium On Computational Science 2013
  • Place of Presentation: Kanazawa, Japan
  • Invited
• [Presentation] Theoretical Study of π-stacking Interaction in Carbonic Anhydrase (2012)
  • Author(s): M. Koyimatu, H. Shimahara, K. Kawaguchi, H. Saito, and H. Nagao
  • Organizer: International Symposium On Computational Science 2013
  • Place of Presentation: Kanazawa, Japan
• [Presentation] Binding Free Energy of Protein-Ligand by combining Docking and MD Simulation: A Comparison of Calculation Methods (2012)
  • Author(s): M. T. Pakpahan, H. Saito, K. Kawaguchi, and H. Nagao
  • Organizer: International Symposium On Computational Science 2013
  • Place of Presentation: Kanazawa, Japan
• [Presentation] Computational Study of Oxidation Potential Fluctuation of Ketone Molecule (2012)
  • Author(s): Isman Kurniawan, H. Saito, K. Kawaguchi, H. Nagao
  • Organizer: International Symposium On Computational Science 2013
  • Place of Presentation: Kanazawa, Japan
• [Presentation] Molecular dynamics study of gramicidin A in lipid bilayer: structure and energetics" (2012)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Hiroyuki Takagi, Takeshi Miyakawa, Kazutomo Kawaguchi, Masako Takasu, and Hidemi Nagao
  • Organizer: The 52nd Sanibel Symposium
  • Place of Presentation: The King and prince beach & golf resort , アメリカ
• [Presentation] Molecular dynamics simulaitoins of the N-terminal domain of Hsp90 with nucleotides (2012)
  • Author(s): Kazutomo Kawaguchi Massashi Iwayama, Hiroyuki Takagi, Takeshi Miyakawa, Hiroaki Saito, Masako Takasu, Hidemi Nagao
  • Organizer: The 52nd Sanibel Symposium
  • Place of Presentation: The King and prince beach & golf resort , アメリカ
• [Presentation] Molecular dynamics simulations of the Hras-GTP complex and the Hras-GDP complex (2012)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Msako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: The 52nd Sanibel Symposium
  • Place of Presentation: The King and prince beach & golf resort , アメリカ
• [Presentation] Solvation effect on the protein docking process: a molecular dynamics study (2012)
  • Author(s): Taku Mizukami, Hiroaki Saito, Takeshi Miyakawa, Masashi Iwayama, Masako Takasu, Hidemi Nagao
  • Organizer: The 52nd Sanibel Symposium
  • Place of Presentation: The King and prince beach & golf resort , アメリカ
• [Presentation] Binding free energy of oxidized Azurin - reduced Cytochrome c551 Complex (2011)
  • Author(s): Hiroaki Saito, Masashi Iwayama, Taku Mizukami, Hidemi Nagao
  • Organizer: The Seventh Congress of the International Society for Theoretical Chemical Physics (ISTCP-VII)
  • Place of Presentation: 早稲田大学, 東京
• [Presentation] Theoretical Study on the Redox Reaction of Azurin in Water Solvent (2011)
  • Author(s): Masashi Iwayama, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] Structural analysis of ligand binding mechanism of Hsp90 (2011)
  • Author(s): Kazutomo Kawaguchi, Acep Purqon, Hiroaki Saito, Hidemi Nagao
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] Free energy of cell-penetrating peptide in lipid bilayer membrane: coarse-grained simulation (2011)
  • Author(s): Shuhei Kawamoto, Takeshi Miyakawa, Masako Takasu, Ryota Morikawa, Tatsuki Oda, Hiroaki Saito, Shiroh Futaki
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] The potentials of the atoms around Mg2+ in the H-ras GTP complex and in the H-ras GDP complex (2011)
  • Author(s): Takeshi Miyakawa, Ryota Morikawa, Masako Takasu, Kimikazu Sugimori, Kazutomo Kawaguchi, Hiroaki Saito, Hidemi Nagao
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] Structure and dynamics of glutathione and glutathione-transferaseT2-2: a molecular dynamics study (2011)
  • Author(s): Yuriko Omae, Hiroaki Saito, Kazutomo Kawaguchi, Hidemi Nagao
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] Free energy profile of water across cholesterol containing lipid bilayer (2011)
  • Author(s): Hiroaki Saito, Wataru Shinoda
  • Organizer: XVIth International Workshop on Quantum Systems in Chemistry and Physics (QSCP-XVI)
  • Place of Presentation: 石川県立美術館, 石川県
• [Presentation] グラミシジンAを添加した脂質二重層膜の分子動力学シミュレーション (2011)
  • Author(s): 齋藤大明，アチェププルコン，川口一朋，長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 分子動力学法によるＤＨＦＲの構造変位に対する自由エネルギー変化 (2011)
  • Author(s): 西村めぐみ, 齋藤大明, 川口一朋, AcepPurqon, 長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 分子動力学法によるHsp90と基質分子の自由エネルギー解析 (2011)
  • Author(s): 川口一朋、Acep Purqon、齋藤大明、長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] ドパミン受容体－リガンド分子間の結合自由エネルギー解析 (2011)
  • Author(s): 高木 啓行，川口 一朋，齋藤 大明，Acep Purqon，長尾 秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 溶液中における鉄イオンFe2+/Fe3+の酸化還元電位に関する理論的研究 (2011)
  • Author(s): 岩山将士, 齋藤大明, 川口一朋, 長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 分子動力学シミュレーションによるグルタチオンとグルタチオン転移酵素T2-2の結合エネルギー計算 (2011)
  • Author(s): 大前裕莉子，齋藤大明，川口一朋，長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 量子化学計算によるアスコルビン酸の酸化還元電位 (2011)
  • Author(s): 杉森哲也，齋藤大明，川口一朋，西川清，長尾秀実
  • Organizer: 第５回分子科学討論会
  • Place of Presentation: 札幌コンベンションセンター, 北海道
• [Presentation] 膜透過ペプチドによる脂質二重膜の構造変化の膜曲げ弾性依存 (2011)
  • Author(s): 川本周平, 高須昌子, 宮川毅, 森河良太, 小田竜樹, 齋藤大明, 二木史朗, 長尾秀実
  • Organizer: 第４９回生物物理学会年会
  • Place of Presentation: 兵庫県立大学, 兵庫県
• [Presentation] H-ras GTP複合体とH-ras GDP複合体の分子動力学シミュレーション (2011)
  • Author(s): 宮川毅, 森河良太, 高須昌子, 齋藤大明, 長尾秀実
  • Organizer: 第４９回生物物理学会年会
  • Place of Presentation: 兵庫県立大学, 兵庫県
• [Presentation] C型肝炎ウイルスにおけるNS3セリンプロテアーゼ阻害剤cVH種に関する分子動力学シミュレーション (2011)
  • Author(s): 岩山将士, 川口一朋, 齋藤大明, 長尾秀実
  • Organizer: 第４９回生物物理学会年会
  • Place of Presentation: 兵庫県立大学, 兵庫県
• [Presentation] PYP構造変化に伴う溶媒和自由エネルギーの変化 (2011)
  • Author(s): 水上卓, 齋藤大明, 長尾秀実
  • Organizer: 第４９回生物物理学会年会
  • Place of Presentation: 兵庫県立大学, 兵庫県
• [Presentation] Azurin-Cytochrome c551 複合体の結合自由エネルギー (2011)
  • Author(s): 齋藤大明, 岩山将士, 水上卓, 西川清
  • Organizer: 第２回計算統計物理学研究会
  • Place of Presentation: 金沢大学, 石川県
• [Presentation] コレステロールを含んだ脂質二重膜の水分子透過性 (2011)
  • Author(s): 齋藤大明，篠田渉
  • Organizer: 第25回分子シミュレーション討論会
  • Place of Presentation: 東京工業大学, 東京
• [Presentation] 熱力学的積分法を用いた Hsp90 と基質分子の結合自由エネルギープロフィール (2011)
  • Author(s): 川口一朋，A. Purqon，齋藤大明，長尾秀実
  • Organizer: 第25回分子シミュレーション討論会
  • Place of Presentation: 東京工業大学, 東京
• [Presentation] Hras-GTP 結合系ならびに Hras-GDP 結合系の分子動力学シミュレーション (2011)
  • Author(s): 宮川毅，森河良太，高須昌子，杉森公一， 川口一朋，齋藤大明，長尾秀実
  • Organizer: 第25回分子シミュレーション討論会
  • Place of Presentation: 東京工業大学, 東京
• [Presentation] 膜透過ペプチドの脂質二重膜内における自由エネルギー (2011)
  • Author(s): 川本周平，高須昌子，宮川毅，森河良太，小田竜樹，齋藤大明，二木史朗，長尾秀実
  • Organizer: 第25回分子シミュレーション討論会
  • Place of Presentation: 東京工業大学, 東京