Statistical analysis of conformational changes of proteins
| Project/Area Number |
24770159
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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 | Institute of Physical and Chemical Research |
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Principal Investigator |
MATSUNAGA YASUHIRO 独立行政法人理化学研究所, 計算科学研究機構, 基礎科学特別研究員 (60464525)
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| Project Period (FY) |
2012-04-01 – 2014-03-31
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| Project Status |
Completed (Fiscal Year 2013)
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| Budget Amount *help |
¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2012: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
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| Keywords | 統計数理 / タンパク質 / 分子動力学シミュレーション / アデニル酸キナーゼ / 多剤排出トランスポーター / シミュレーション / 分子動力学 / 機械学習 |
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| Research Abstract |
With the help of recent advances in computer hardware and software, it is becoming possible to simulate functionally relevant conformational changes of biomolecules. On the other hand, however, the amount of simulation data is rapidly increasing and it is becoming difficult to treat such large amount of data without statistical analysis. In this study, we have developed a framework for the statistical analysis of molecular dynamics simulation data. The developed framework was successfully applied to conformational change data of two cases: (i) The most slowest degrees of freedom (involving the P-loop and a hinge region) in Adenylate Kinase was identified from 9 microseconds simulation data. (ii) Free energy differences along the conformational change pathways of multidrug transporter AcrB was successfully evaluated.
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Report
(3 results)
Research Products
(17 results)
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[Journal Article] PLoS One2012
Author(s)
Matsunaga, Y., Koike, R., Ota, M., Tame, J. R. H. & Kidera, A.
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Journal Title
Influence of structural symmetry on protein dynamics.
Volume: 7
Issue: 11
Pages: 11-11
DOI
Related Report
Peer Reviewed
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