Statistical Properties of Peptide and Gel

• Project/Area Number: 24540442
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Biophysics/Chemical physics
• Research Institution: Tokyo University of Pharmacy and Life Science
• Principal Investigator: TAKASU Masako 東京薬科大学, 生命科学部, 教授 (50202148)
• Co-Investigator(Kenkyū-buntansha): MORIKAWA Ryota 東京薬科大学, 生命科学部, 講師 (70266899) ; MIYAKAWA Takeshi 東京薬科大学, 情報教育研究センター(生命科学部), 助教 (40287462)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2013: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2012: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: ペプチド / ゲル / シミュレーション / 分子動力学 / タンパク質 / 繊維化

Outline of Final Research Achievements

We study the statistical properties of peptides and gel. Peptides consist of amino acids and take particular conformation in solvent. Polymers and gels are usually made from monomers and can take different conformations and are useful material for industrial purposes. Peptides related to cell attachment, and the peptides related to diabetics are studied using molecular dynamics simulation. We use all-atom model or coarse grained model for our study.

Research Products

• [Journal Article] Molecular Dynamics Simulation of γS-WT and γS-G18V (2015)
  • Author(s): Ozawa, A., Yamada, H., Mori, S., Noguchi, Y., Miyakawa, T., Morikawa, R., Takasu, M.
  • Journal Title: JPS Conf. Proc. Volume: 5 Pages: 011003-011003
  • DOI: 10.7566/jpscp.5.011003
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Itoga, H., Morikawa, R., Miyakawa, T., Yamada, H., Natsume, Y., Ueta, T., Takasu, M. (2015)
  • Author(s): Itoga, H., Morikawa, R., Miyakawa, T., Yamada, H., Natsume, Y., Ueta, T., Takasu, M.
  • Journal Title: JPS Conf. Proc. Volume: 5 Pages: 011002-011002
  • DOI: 10.7566/jpscp.5.011002
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Molecular Dynamics Simulation of a Coarse Grained Model of Tetra-PEG Gel with Monomers of 5 and 9 particles (2015)
  • Author(s): Ogawa, S., Waide, S., Takasu, M., Miyakawa, T., R. Morikawa, R., Sakai, T., Chung, U.
  • Journal Title: JPS Conf. Proc. Volume: 5 Pages: 011006-011006
  • DOI: 10.7566/jpscp.5.011006
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structure Analysis of GLP-1 in DPC Micelle (2015)
  • Author(s): Mori, S., Yamada, H., Noguchi, Y., Miyakawa, T., Morikawa, R., Watanabe, T. Takasu, M.
  • Journal Title: Pep. Sci. Volume: 2014 Pages: 213-216
  • Peer Reviewed
• [Journal Article] Quantum Chemical Calculations of Structure of Antitumor Cyclic Hexapeptide RA-VII (2015)
  • Author(s): Noguchi, Y., Yamada, H., Mori, S., Miyakawa, T., Morikawa, R., Yokojima, S., Hitotsuyanagi, Y., Takeya, K., Takasu, M.
  • Journal Title: Pep. Sci. Volume: 2014 Pages: 165-168
  • Peer Reviewed
• [Journal Article] Solvent Site-dipole Fields around Guanine Nucleotides in the Hras-GTP Complex and in the Hras-GDP Complex (2014)
  • Author(s): Miyakawa, T., Morikawa, R., Takasu, M., Sugimori, K., Kawaguchi, K., Saito, H., Nagao, H.
  • Journal Title: AIP Conf. Proc. Volume: 1599 Pages: 322-325
  • DOI: 10.1063/1.4876843
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation (2014)
  • Author(s): Fukuda, M., Komatsu, Y., Yamada, H., Morikawa, R., Miyakawa, T., Takasu, M., Akanuma, S., Yamagishi, A
  • Journal Title: Molecular Simulation Volume: 40 Issue: 6 Pages: 498-503
  • DOI: 10.1080/08927022.2013.824571
  • 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] Numerical Simulation of the Twitching Motility of Bacterium Crawling on a Solid Surface (2014)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, T. Kawaguchi, H. Saito, H. Nagao
  • Journal Title: JPS Conf. Proc. Volume: 1 Pages: 16019-16019
  • DOI: 10.7566/jpscp.1.016019
  • Peer Reviewed
• [Journal Article] Coarse-Grained Molecular Dynamics Simulation of IPMDH Proteins (2014)
  • Author(s): Y. Hirata, Y. Komatsu, M. Fukuda, H. Yamada, T. Miyakawa, R. Morikawa, S. Akanuma, A. Yamagishi, M. Takasu
  • Journal Title: JPS Conf. Proc. Volume: 1 Pages: 16010-16010
  • DOI: 10.7566/jpscp.1.016010
  • Peer Reviewed
• [Journal Article] Conformation Analysis of Peptides Derived from Laminin Alpha 1–2 Chain Using Molecular Dynamics Simulation (2014)
  • Author(s): H. Yamada, M. Fukuda, T. Miyakawa, R. Morikawa, M. Takasu
  • Journal Title: JPS Conf. Proc. Volume: 1 Pages: 16016-16016
  • DOI: 10.7566/jpscp.1.016016
  • Peer Reviewed
• [Journal Article] Computer Simulation Analysis of the Protein Binding Interfaces that Form a 4-Helix Bundle Motif (2014)
  • Author(s): M. Fukuda, H. Yamada, R. Morikawa, T. Miyakawa, M. Takasu, S. Akanuma, A. Yamagishi
  • Journal Title: JPS Conf. Proc. Volume: 1 Pages: 16020-16020
  • DOI: 10.7566/jpscp.1.016020
  • 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] Conformation Analysis of the A2G80 Peptide Derived from Laminin α2 Chain by Molecular Dynamics Simulation (2014)
  • Author(s): Y. Fukasawa, J. Kumai, F. Katagiri, Y. Kikkawa, K. Hozumi, M. Nomizu, S. Mori, H. Yamada, M. Fukuda, T. Miyakawa, R. Morikawa and M. Takasu
  • Journal Title: Peptide Science Volume: 2013 Pages: 289-292
  • Peer Reviewed
• [Journal Article] Structure Analysis of GLP-1 by Molecular Dynamics Simulation (2014)
  • Author(s): S. Mori, H. Yamada, M. Fukuda, Y. Fukasawa, T. Miyakawa, R. Morikawa, M. Takasu, T. Watanabe
  • Journal Title: Peptide Science Volume: 2013 Pages: 285-288
  • 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, A. Dobashi, K. Sugimori, K. Kawaguchi, H. Saito, H. Nagao
  • Journal Title: Prog. Theor. Chem. Phys. Volume: 27, Pages: 351-360
  • DOI: 10.1007/978-3-319-01529-3_19
  • ISBN: 9783319015286, 9783319015293
  • Peer Reviewed
• [Journal Article] Simulation study of bacterial colonies formed by the twitching motility: the effect of slingshot-like motions of bacteria on the colony edge (2013)
  • Author(s): R. Morikawa, T. Miyakawa, M. Tamakoshi and M. Takasu,
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 590-593
  • 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 and H. Nagao,
  • Journal Title: AIP Conf. Proc. Volume: 1518 Pages: 594-597
  • Peer Reviewed
• [Journal Article] Simulation Study of Protein-protein Interfaces Based on the 4-helix Bundle Structure (2013)
  • Author(s): M. Fukuda, Y. Komatsu, R. Morikawa, T. Miyakawa1, M. Takasu1, S. Akanuma1, and A. Yamagishi
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 606-609
  • Peer Reviewed
• [Journal Article] Analysis of the Histone Protein Tail and DNA in Nucleosome Using Molecular Dynamics Simulation (2013)
  • Author(s): R. Fujimori, Y. Komatsu, M. Fukuda, T. Miyakawa, R. Morikawa and M. Takasu
  • Journal Title: AIP Conf. Proc Volume: 1518 Pages: 602-605
  • Peer Reviewed
• [Journal Article] The Potentials of the Atoms around Mg2+ in the H-ras GTP and GDP Complexes (2012)
  • Author(s): T. Miyakawa, R. Morikawa, M. Takasu, K. Sugimori, T. Mizukami, K. Kawaguchi, H. Saito and H. Nagao
  • Journal Title: Prog. Theor. Chem. Phys. Volume: 26 Pages: 525-543
  • Peer Reviewed
• [Journal Article] Designing the Binding Surface of Proteins to Construct Nano-Fibers (2012)
  • Author(s): Y. Komatsu, H. Yamada, S. Kawamoto, M. Fukuda, T. Miyakawa, R. Morikawa, M. Takasu, S. Akanuma, A. Yamagishi
  • Journal Title: Prog. Theor. Chem. Phys Volume: 26 Pages: 555-567
  • 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, R. Morikawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda
  • Journal Title: Prog. Theor. Chem. Phys. Volume: 26 Pages: 503-511
  • Peer Reviewed
• [Journal Article] Constructing Protein Nano-Fiber and Estimation of the Electronic State Around Metal Ions (2012)
  • Author(s): Y. Komatsu, M. Fukuda, H. Yamada, S. Kawamoto, T. Miyakawa, R. Morikawa, M. Takasu, S. Yokojima S. Akanuma, A. Yamagishi
  • Journal Title: Int. J. Quant. Chem. Volume: 112 Pages: 3750-3755
  • Peer Reviewed
• [Presentation] Molecular Dynamics Simulation of Coarse Grained Models of Gel and Proteins (2015)
  • Author(s): Takasu, M., Sugiyama, H., Hirata, Y., Yamada, H., Miyakawa, T., Morikawa, R.
  • Organizer: Computational Chemistry Symposium in 11th International Conference of Computational Methods in Sciences and Engineering 2015
  • Place of Presentation: Athens, Greece
  • Year and Date: 2015-03-20 – 2015-03-23
  • Invited
• [Presentation] Molecular Dynamics Simulation of γS-WT and γS-G18V (2014)
  • Author(s): Ozawa, A., Yamada, H., Mori, S., Noguchi, Y., Miyakawa, T., Morikawa, R., Takasu, M.
  • Organizer: Computational Science Workshop 2014
  • Place of Presentation: Tsukuba, Japan
  • Year and Date: 2014-08-20 – 2014-08-22
• [Presentation] Shape Deformation of Vesicles Containing Hard Spheres (2014)
  • Author(s): Itoga, H., Morikawa, R., Miyakawa, T., Yamada, H., Natsume, Y., Ueta, T., Takasu, M.
  • Organizer: Computational Science Workshop 2014
  • Place of Presentation: Tsukuba, Japan
  • Year and Date: 2014-08-20 – 2014-08-22
• [Presentation] Molecular Dynamics Simulation of a Coarse Grained Model of Tetra-PEG Gel with Monomers of 5 and 9 particles (2014)
  • Author(s): Ogawa, S., Waide, S., Takasu, M., Miyakawa, T., Morikawa, R., Sakai, T., Chung, U., Molecular Dynamics Simulation of a Coarse Grained Model of Tetra-PEG Gel with Monomers of 5 and 9 particles
  • Organizer: Computational Science Workshop 2014
  • Place of Presentation: Tsukuba, Japan
  • Year and Date: 2014-08-20 – 2014-08-22
• [Presentation] Solvent Site-dipole Fields around Guanine Nucleotides in the Hras-GTP Complex and in the Hras-GDP Complex (2014)
  • Author(s): Computational Chemistry Symposium in 11th International Conference of Computational Methods in Sciences and Engineering 2015
  • Organizer: 7th International Conference on Times of Polymers Composites
  • Place of Presentation: Ischia, Italy
  • Year and Date: 2014-06-22 – 2014-06-26
• [Presentation] Molecular Dynamics Simulation of A2G80 Peptide Derived from Laminin α2 Chain (2014)
  • Author(s): Fukasawa, Y., Kumai, J., Katagiri, F., Hozumi, K., Kikkawa, Y., Nomizu, M., Yamada, H., Fukuda, M., Mori, S., Miyakawa, T., Morikawa, R., and Takasu, M.
  • Organizer: The 54th Sanibel Symposium
  • Place of Presentation: St. Simons Island, GA USA
• [Presentation] nalysis of the site-dipole fields around guanine nucleotides in the Hras-GTP and Hras-GDP complexes (2014)
  • Author(s): Miyakawa, T., Morikawa, R., Takasu, M., Sugimori, K., Kawaguchi, K., Saito, H., Nagao, H.
  • Organizer: The 54th Sanibel Symposium
  • Place of Presentation: St. Simons Island, GA USA
• [Presentation] Gelation of tetrahedral monomers studied by molecular dynamics simulation (2013)
  • Author(s): Ogawa, S., Miyakawa, T., Morikawa, R., Takasu, M., Sakai, T., Chung, U.
  • Organizer: 3rd International Conference on Molecular Simulation
  • Place of Presentation: Kobe, Japan
• [Presentation] Molecular Dynamics Simulation of EF1 and EF2 Peptides Derived from Laminin (2013)
  • Author(s): Yamada, H., Fukuda, M., Fukasawa, Y., Miyakawa, T., Morikawa, R. and Takasu, M.
  • Organizer: 4th Asia Pacific International Peptide Symposium
  • Place of Presentation: Osaka, Japan
• [Presentation] Conformation Analysis of the A2G80 Peptide Derived from Laminin α2 chain by Molecular Dynamics Simulation (2013)
  • Author(s): Fukasawa, Y., Kumai, J., Katagiri, F., Kikkawa, Y., Hozumi, K., Nomizu, M., Yamada, H., Fukuda, M., Miyakawa, T., Morikawa, R., and Takasu, M.
  • Organizer: 4th Asia Pacific International Peptide Symposium
  • Place of Presentation: Osaka, Japan
• [Presentation] Structure Analysis of GLP-1 by Molecular Dynamics Simulation (2013)
  • Author(s): 9. Mori, S., Yamada, H., Fukuda, M., Miyakawa, T., Morikawa, R., Takasu, M., Watanabe, T.
  • Organizer: 4th Asia Pacific International Peptide Symposium
  • Place of Presentation: Osaka, Japan
• [Presentation] Analysis of water molecules in the Hras-GTP and GDP complexes with molecular dynamics simulations, (2012)
  • Author(s): Miyakawa, T., Morikawa, R., Takasu, M., Sugimori, K., Kawaguchi, K., Saito, H., Nagao, H.,
  • Organizer: 17th International Workshop on Quantum Systems in Chemistry and Physics QSCP-XVII
  • Place of Presentation: Turku, Finland
• [Presentation] Simulation study of bacterial colonies formed by the twitching motility: the effect of slingshot-like motions of bacteria on the colony edge (2012)
  • Author(s): Morikawa, R., Miyakawa, T., Tamakoshi, M.. and Takasu, M
  • Organizer: 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: Sendai, Japan
• [Presentation] A Molecular Dynamics Study of Hras-GTP and GDP Complexes: the Properties of Water Molecules around Guanine Nucleotide (2012)
  • Author(s): Miyakawa, T., Morikawa, R., Takasu, M., Sugimori, K., Kawaguchi, K., Saito, H., and Nagao, H
  • Organizer: 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: Sendai, Japan
• [Presentation] Simulation Study of Protein-protein Interfaces Based on the 4-helix Bundle Structure (2012)
  • Author(s): Fukuda, M., Komatsu, Y., Morikawa, R., Miyakawa, T., Takasu, M., Akanuma, S., and Yamagishi, A.,
  • Organizer: 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: Sendai, Japan
• [Presentation] Analysis of the Histone Protein Tail and DNA in Nucleosome Using Molecular Dynamics Simulation (2012)
  • Author(s): Fujimori, R., Komatsu, Y., Fukuda, M., Miyakawa, T., Morikawa, R., Takasu, M
  • Organizer: 4th International Symposium on Slow Dynamics in Complex Systems
  • Place of Presentation: Sendai, Japan