Simulation study on functions of an anti-microbial peptide

• Project/Area Number: 25330355
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Nagahama Institute of Bio-Science and Technology
• Principal Investigator: Yoda Takao 長浜バイオ大学, バイオサイエンス学部, 准教授 (50367900)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000); Fiscal Year 2013: ¥520,000 (Direct Cost: ¥400,000、Indirect Cost: ¥120,000)
• Keywords: 抗菌ペプチド / 分子シミュレーション / 分子動力学シミュレーション / 分子動力学法 / シミュレーション / 拡張アンサンブル法

Outline of Final Research Achievements

Here we performed simulation studies on conformations of a defensin-family peptide, Crp-4, and its interaction with membrane. Our replica-exchange molecular dynamics simulations have revealed effects of the evolutionally conserved disulfide bridges of Crp-4 on its conformations in an environment near negatively charged membrane. The spatial distribution of positively charged groups in the peptide has been shown to correlate with the number of disulfide bridges formed. The disulfide bridge between Cys11 and Cys28 seems to affect the hydrophobic cluster formation within the peptide molecule.

Research Products

• [Journal Article] Deciphering Supramolecular Structures with Protein-Protein Interaction Network Modeling (2015)
  • Author(s): Toshiyuki Tsuji, Takao Yoda, and Tsuyoshi Shirai
  • Journal Title: Sci. Rep. Volume: 5 Issue: 1 Pages: 16341-16341
  • DOI: 10.1038/srep16341
  • Peer Reviewed / Open Access
• [Journal Article] GENESIS: A hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations (2015)
  • Author(s): Jung, J., Mori, T., Kobayashi, C., Matsunaga, Y., Yoda, T., Feig, M., Sugita, Y.
  • Journal Title: WIREs; Comput. Mol. Sci. Volume: -
  • Peer Reviewed
• [Journal Article] Salt effects on hydrophobic-core formation in folding of a helical miniprotein studied by molecular dynamics simulations (2014)
  • Author(s): T. Yoda, Y. Sugita, and Y. Okamoto
  • Journal Title: Proteins: Structure, Function, and Bioinformatics Volume: 82 Issue: 6 Pages: 933-943
  • DOI: 10.1002/prot.24467
  • Peer Reviewed
• [Presentation] Simulation Study on Conformations of Antimicrobial Peptide Cryptdin 4 and its Mutants (2015)
  • Author(s): Takao Yoda
  • Organizer: 2nd International Symposium on Computational Materials and Biological Sciences
  • Place of Presentation: 名古屋大学
  • Year and Date: 2015-09-01
  • Int'l Joint Research / Invited
• [Presentation] Simulation Study on Conformations of Small Peptides. (2014)
  • Author(s): Takao Yoda
  • Organizer: Dushanbe Symposium on Computational Materials and Biological Sciences 2014
  • Place of Presentation: S.U. Umarov Physical-Technical Institute of the Academy of Sciences of the Republic of Tajikistan
  • Year and Date: 2014-09-24
  • Invited
• [Presentation] 抗菌ペプチド Cryptdin-4 ジスルフィド結合変異体の分子動力学シミュレーション (2014)
  • Author(s): 依田隆夫，辻敏之，杉田有治
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: ワークピア横浜／横浜産貿ホール マリネリア
  • Year and Date: 2014-06-27
• [Presentation] Salt effects on folding of a helical mini protein villin headpiece subdomain HP36 studied by generalized-ensemble simulations (2014)
  • Author(s): Takao Yoda, Yuji Sugita, and Yuko Okamoto
  • Organizer: Biophysical Society 58th Annual Meeting
  • Place of Presentation: Moscone Center, San Francisco CA.