Atomistic mechanism of the oligomerization of p53 protein in DNA scanning

2020 年度 実績報告書

• 研究課題/領域番号: 19K23721
• 研究機関: 東京工業大学
• 研究代表者: TRAN PHUOC・DUY 東京工業大学, 生命理工学院, 助教 (50848546)
• 研究期間 (年度): 2019-08-30 – 2021-03-31
• キーワード: p53 protein / A2a receptor / eePaCS-MD

研究実績の概要

We have successfully performed the dissociation of the p53 core domain tetramers out of the complex with DNA. We found that the bending of DNA contributes largely to the dissociation of the core domain out of the tetramers. We have successfully carried out the C-terminal domain scanning of DNA and find key interaction that contributes to the binding. We developed the method to sample efficiently the slow domain motion of the protein using PCA analysis and Markov State Modeling. We successfully constructed the full length complex of A2a receptor bound to Gs protein. The structure is stable and we found the mechanism of signal transmission pathway in the A2a/Gs protein complex.

研究成果

• [雑誌論文] Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling (2021)
  • 著者名/発表者名: Huang Shuya Kate、Pandey Aditya、Tran Duy Phuoc、Villanueva Nicolas L.、Kitao Akio、Sunahara Roger K.、Sljoka Adnan、Prosser R. Scott
  • 雑誌名: Cell 巻: 184 ページ: 1884～1894.e14
  • DOI: 10.1016/j.cell.2021.02.041
  • 査読あり / 国際共著
• [雑誌論文] Edge expansion parallel cascade selection molecular dynamics simulation for investigating large-amplitude collective motions of proteins (2020)
  • 著者名/発表者名: Takaba Kenichiro、Tran Duy Phuoc、Kitao Akio
  • 雑誌名: The Journal of Chemical Physics 巻: 152 ページ: 225101～225101
  • DOI: 10.1063/5.0004654
  • 査読あり / 国際共著
• [雑誌論文] Generating Ampicillin-Level Antimicrobial Peptides with Activity-Aware Generative Adversarial Networks (2020)
  • 著者名/発表者名: Tucs Andrejs、Tran Duy Phuoc、Yumoto Akiko、Ito Yoshihiro、Uzawa Takanori、Tsuda Koji
  • 雑誌名: ACS Omega 巻: 5 ページ: 22847～22851
  • DOI: 10.1021/acsomega.0c02088
  • 査読あり / 国際共著
• [雑誌論文] PaCS-MD/MSM : Parallel Cascade Selection Molecular Dynamic Simulation in Combination with Markov State Model as an Efficient non-Bias Sampling Method (2020)
  • 著者名/発表者名: Duy Phuoc Tran, Hata Hiroaki, Ogawa Takumi, Taira Yuta, Kitao Akio
  • 雑誌名: アンサンブル : 分子シミュレーション研究会会誌 巻: 22 ページ: 151~156
  • 査読あり
• [学会発表] Biomolecular Functional Design: an Introduction to Recent Advances (2020)
  • 著者名/発表者名: Duy Tran
  • 学会等名: The 58th Annual Meeting of the Biophysical Society of Japan
  • 国際学会 / 招待講演
• [学会発表] DNA binding mechanisms of the p53 C-terminal domain elucidated by MD simulation (2020)
  • 著者名/発表者名: Yuta Taira, Duy Tran, Akio Kitao
  • 学会等名: The 58th Annual Meeting of the Biophysical Society of Japan
  • 国際学会
• [学会発表] Kinetic rate evaluation for protein complexes by PaCS-MD/MSM (2020)
  • 著者名/発表者名: Yoshiki Miyazawa, Phuoc Duy Tran, Kazuhiro Takemura, Akio Kitao
  • 学会等名: The 58th Annual Meeting of the Biophysical Society of Japan
  • 国際学会
• [学会発表] When computer simulations meet machine learning: unveiling the dynamics of biomolecular complexes (2020)
  • 著者名/発表者名: Duy Tran, Akio Kitao
  • 学会等名: The 9th Tokyo Tech International Symposium on Life Science and Technology
  • 招待講演