Multi-scale simulation of protein-ligand binding process
| Project/Area Number |
24570179
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | The University of Tokyo |
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Principal Investigator |
TERADA Tohru 東京大学, 農学生命科学研究科, 准教授 (40359641)
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| Research Collaborator |
NEGAMI Tatsuki
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| Project Period (FY) |
2012-04-01 – 2015-03-31
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| Project Status |
Completed (Fiscal Year 2014)
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| Budget Amount *help |
¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
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)
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| Keywords | 分子動力学シミュレーション / タンパク質 / リガンド / パスウェイ / マルチコピー・マルチスケール法 / 粗視化モデル / 自由エネルギー計算 / MARTINI / マルチスケールシミュレーション |
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| Outline of Final Research Achievements |
I established a method to reproduce the protein-ligand binding process in a coarse-grained molecular dynamics (MD) simulations. This method was applied to many protein-ligand pairs that differ in terms of the shape of the ligand-binding pocket and the physicochemical properties of the pocket and the ligand. The comparison of the results suggested that the ligands enter the ligand-binding pockets through specific pathways. Furthermore, I also established a method to refine the ligand-binding pathway with all-atom MD simulations and to calculate free-energy profile along the pathway.
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Report
(4 results)
Research Products
(6 results)
