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2013 Fiscal Year Final Research Report

Molecualr dynamics study on the molecuar permeability of membrane protein

Research Project

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Project/Area Number 23750008
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Physical chemistry
Research InstitutionKanazawa University

Principal Investigator

SAITO Hiroaki  金沢大学, 数物科学系, 助教 (40506820)

Project Period (FY) 2011 – 2013
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
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

(34 results)

All 2014 2013 2012 2011 Other

All Journal Article (34 results) (of which Peer Reviewed: 34 results)

  • [Journal Article] Analysis of water molecules around GTP in Hras-GTP complex and GDP in Hras-GDP complex by molecular dynamics simulations2014

    • 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 simulations2014

    • 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 Conduction2014

    • 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 Dissociation2014

    • 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 system2014

    • 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 System2014

    • 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] Molecular dynamics study on the free energy profile for dissociation of ADP from N-terminal domain of Hsp902013

    • 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 complex2013

    • 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 Complex2013

    • 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 Molecule2013

    • 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 Simulation2013

    • 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 Methods2013

    • 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 Interactions2013

    • 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 anhydrase2013

    • 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 simulations2013

    • 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 analyses of the dissociation process of ADP from Hsp902012

    • 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 profile2012

    • 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 match2012

    • 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 study2012

    • 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-membrane2012

    • 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 complex2012

    • 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 simulation2012

    • 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 Glutathione2012

    • 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 Study2012

    • 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 Micelles2012

    • 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] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study2011

    • Author(s)
      Hiroaki Saito, Wataru Shinoda
    • Journal Title

      J. Phys. Chem. B

      Volume: 115 Pages: 15241-15250

    • 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

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Published: 2015-06-25  

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