Characterizing the mechanism of chromatin remodeling by molecular dynamics simulations
| Project/Area Number |
20K06587
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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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| Review Section |
Basic Section 43040:Biophysics-related
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| Research Institution | Kyoto University |
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Principal Investigator |
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| Project Period (FY) |
2020-04-01 – 2023-03-31
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| Project Status |
Completed (Fiscal Year 2022)
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| Budget Amount *help |
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2022: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2020: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
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| Keywords | nucleosome sliding / all-atom MD simulation / string method / twist defects / nucleosome / molecular dynamics / chromatin remodeling / MD simulation / all-atom |
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| Outline of Research at the Start |
2020: 1. Setting up the supercomputing facilities needed during the project. 2. Performing all-atom simulation tests to identify the most suitable parameters for the production simulation runs.
2021: 3. Performing the production runs of nucleosome sliding. 4. Analyzing the data. 5. Presenting the preliminary results at an international conference in Japan.
2022: 6. Performing additional simulations and data analysis. 7. Submitting an article describing our findings to a peer-reviewed journal. 8. Presenting our work at an international conference outside Japan.
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| Outline of Final Research Achievements |
The DNA inside our nucleus is wrapped around proteins to form complexes called nucleosomes, whose structure and dynamics greatly affect the processing of genetic information. In this research, we performed computer simulations that allow us to visualize the molecular dynamics of nucleosomes at the level of individual atoms. Our simulations revealed the molecular mechanism of nucleosome motion along the genome, an important process that regulates the access to DNA, highlighting the high plasticity of protein-DNA interactions within nucleosomes. Importantly, we also showed that DNA sequence can affect the motion of nucleosomes, and therefore act as a new layer of information to regulate the genome on top of the one used to express proteins.
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| Academic Significance and Societal Importance of the Research Achievements |
Chromosomes inside our nucleus are not just a passive containers of genetic information: their structure and dynamics have great effect on many cellular processes. Our research used computer simulations to reveal how subtle molecular motions of chromosomes control the access to the genetic material.
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Report
(4 results)
Research Products
(6 results)
