Multiscale enhanced sampling for ligand binding
| Project/Area Number |
15K18520
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Multi-year Fund |
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| Research Field |
Biophysics
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| Research Institution | Yokohama City University |
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Principal Investigator |
Moritsugu Kei 横浜市立大学, 生命医科学研究科, 特任准教授 (80599506)
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| Project Period (FY) |
2015-04-01 – 2018-03-31
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| Project Status |
Completed (Fiscal Year 2017)
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| Budget Amount *help |
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2017: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2015: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
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| Keywords | リガンド結合 / グルタミン結合タンパク質 / グルタミン酸受容体 / 分子動力学シミュレーション / MSES法 / 全原子空間探索 / 全原子構造探索 |
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| Outline of Final Research Achievements |
Biomacromolecules such as proteins realize the molecular functions such as signal transduction and transcriptional regulation through the structural changes which are highly regulated by the specific interactions with other proteins or ligand molecules. In this study, computer simulations of protein-ligand complexes were performed by applying our newly developed Multi-scale Enhanced Sampling, allowing all-atom structural sampling of the protein-ligand interaction processes in solution to be successfully achieved. The free-energy landscape was calculated using the derived structural ensemble and revealed the most probable pathway of the protein-ligand binding coupled with the protein structural change by way of the native side-chain interaction formations and the desolvation at atomistic resolution.
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Report
(4 results)
Research Products
(16 results)
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[Journal Article] Structure of the Dnmt1 reader module complexed with a unique two-mono-ubiquitin mark on histone H3 reveals the basis for DNA methylation maintenance.2017
Author(s)
Ishiyama S, Nishiyama A, Saeki Y, Moritsugu K Morimoto D, Yamaguchi L, Arai N, Matsumura R, Kawakami T, Mishima Y, Hojo H, Shimamura S, Ishikawa F, Tajima S, Tanaka K, Ariyoshi M, Shirakawa M, Ikeguchi M, Kidera A, Suetake I, Arita K, Nakanishi M
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Journal Title
Mol Cell
Volume: 68
Issue: 2
Pages: 350-360
DOI
Related Report
Peer Reviewed / Open Access
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