| Budget Amount *help |
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2017: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2016: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2015: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
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| Outline of Final Research Achievements |
I performed many runs of a coarse-grained molecular dynamics simulation for a protein-ligand system, where the ligand molecules were randomly placed around the protein. I constructed a Markov state model from the trajectories. Furthermore, I analyzed the model based on the transition path theory to find the transition state and ligand-binding pathways. As a result, it was shown that the transition state is located around the rim of the substrate-binding pocket and the ligand-binding pathways that have large contributions to the ligand binding tend to go along the grooves on the protein surface. This result supports the ligand-binding-pathway hypothesis we have proposed.
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