Seminars2012 – 2016


  • Aug 4, 2016 (10:00~13:00)

    "Generalized-ensemble quantum simulations of molecular systems"

    Prof. Yuko Okamoto (Nagoya University)
  • "Evolving developments in multi-site lambda dynamics free energy methods"

    Prof. Charles L. Brooks III (University of Michigan, USA)
  • "Role of membrane and cholesterol in genesis of Aβ protein"

    Prof. John Straub (Boston University, USA)


  • Jun 18, 2015 (10:30~13:00)

    "Molecular dynamics simulations of ribosomes: integrating theory and experiment"

    Dr. Karissa Sanbonmatsu (Los Alamos National Laboratory, USA)

    Using an integrated approach, we combine data from X-ray crystallography, cryo-EM and biochemical data. Over the past decade, we have developed a pipeline that begins with X-ray crystallographic structures and uses molecular simulation to produce all-atom models consistent with cryo-EM reconstructions. Theses models are then used as beginning and end points for simulations of large-scale conformational changes. Our strategy has been highly successful in the case of the accommodation conformational change during tRNA selection in bacteria. Here, we predicted the universally conserved accommodation corridor, the importance of which has been verified in several independent experimental studies. We have also recently identified the hybrid corridor, responsible for tRNA hybrid state formation during translocation. Our latest addition to our pipeline is the incorporation of chemical probing data describing the mobility of the RNA backbone in solution. We have developed a novel algorithm to generate molecular dynamics simulations highly consistent with chemical probing data. We have applied these techniques to ribosomes to investigate their dynamics and conformational changes.


  • January 9, 2014 (10:30~13:00)

    "Can the protein structure explain the biological function -a case study in kinesin-microtubule system"

    Dr. Yasushi Okada (RIKEN QBiC)
  • January 8, 2014 (10:00~12:00)

    "Recent research on lipid raft"

    Prof. Akihiro Kusumi (Institute for Frontier Medical Sciences, Kyoto University)


  • September 5, 2013 (10:30~12:00)

    "Peptide Chemistry Based Structural Biology for Receptor Tyrosine Kinase"

    Dr. Takeshi Sato (Institute for Protein Research, Osaka University)


  • May 31, 2012 (13:00~15:00)

    " “In situ” protein structure and dynamics observation by NMR"

    Dr. Kohsuke Inomata (RIKEN Quantitative Biology Center)

    In-cell NMRとは細胞内蛋白質に対する選択的な高分解能異種核多次元NMR測定のことで、蛋白質の構造・動的挙動を原子レベルで解析することが可能である。我々は、HIV-1ウイルスのTat1蛋白質由来のCell Penetrating Peptide(CPP)を利用して、高効率に安定同位体標識された蛋白質を細胞質に導入することで、ヒト等高等哺乳動物体細胞におけるin-cell NMR測定に成功した。またその過程で、pyrenebutyrateによる細胞処理、細胞質におけるCPPの切断が、目的蛋白質の細胞質・核質への均一な導入に必須であることを見出した。更に、上記手法を用いて、細胞内における蛋白質の、細胞内在性の蛋白質との相互作用と、外部投与した低分子薬剤との相互作用を検出する試みを行い、一定の成果を得た。また、細胞内での蛋白質の構造安定性を重水素/軽水素交換実験によって解析したところ、in vitroに比べて不安定であることを示唆する結果を得た。上記に示すように、in-cell NMRという手法を用いることによって、高等哺乳動物体細胞内のような複雑な環境下において、特定の蛋白質の構造・動態を原子レベルで解析することが可能となった。本発表では、これまでの成果を概観するとともに、現在進行中のプロジェクト、特に細胞内蛋白質の構造安定性解析に関する進捗と今後の展望について述べる。

  • April 5, 2012 (13:00~15:00)

    "Free energy analysis of solvent effect on biomolecules using the method of energy representation"

    Dr. Yasuhito Karino (Institute for Chemical Research, Kyoto University)

    Solvation free energy is one of the most important physical quantities to elucidate the hydration effect on protein in solution phase. In this study, the solvation free energy of horse heart cytochrome c immersed in water was calculated using the molecular dynamics simulation coupled with the energy-representation method. The protein intramolecular energy and the solvation free energy are found to compensate each other in the course of equilibrium structural fluctuation, and the roles of the attractive and repulsive components in the protein-water interaction are examined for the solvation free energy.