Theoretical studies of conformation transition dynamics and functions of biomolecules
Project/Area Number |
25288011
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Research Category |
Grant-in-Aid for Scientific Research (B)
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Allocation Type | Partial Multi-year Fund |
Section | 一般 |
Research Field |
Physical chemistry
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Research Institution | Institute for Molecular Science |
Principal Investigator |
SAITO Shinji 分子科学研究所, 理論・計算分子科学研究領域, 教授 (70262847)
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Co-Investigator(Renkei-kenkyūsha) |
TAKADA Shoji 京都大学, 大学院理学研究科, 教授 (60304086)
AKIYAMA Shuji 分子科学研究所, 協奏分子システム研究センター, 教授 (50391842)
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Research Collaborator |
ONO Jun-ichi
MORI Toshifumi
KODA Shin-ichi
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Project Period (FY) |
2013-04-01 – 2016-03-31
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Project Status |
Completed (Fiscal Year 2016)
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Budget Amount *help |
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2015: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
Fiscal Year 2014: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
Fiscal Year 2013: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
|
Keywords | 階層的動力学 / 構造変化 / 概日リズム / 時計タンパク質KaiC / 二次元寿命スペクトル / 三時間相関関数 / 分子動力学 / 時計タンパク質 / タンパク質 / 構造変化動力学 / 階層ダイナミクス / 動的構造 / 反応座標 / 分子シミュレーション / 多時間相関関数 / 生体分子 / 構造遍歴 |
Outline of Final Research Achievements |
In this research project, we have developed two new analytical methods to reveal conformational fluctuations and changes of biomolecular systems. One is the method to extract slow modes in a dynamic quantity, for example a time-correlation matrix, calculated from the trajectories of molecular dynamics simulations. We applied the present method to examine the folding/unfolding processes of FiP35 WW domain and villin headpiece subdomain. The other is a development of time-dependent two-dimensional lifetime spectra to reveal the time evolution of coupling of motions between different time scales. We applied the method to the structural fluctuations of Adenylate kinase calculated with a coarse grained model. In addition to the development of the above methods, we have investigated the local structure of KaiC, which is the main protein of circadian rhythm of cyanobacteria.
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Report
(4 results)
Research Products
(36 results)
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[Journal Article] Atomic-scale origins of slowness in the cyanobacterial circadian clock2015
Author(s)
J. Abe, T. B. Hiyama, A. Mukaiyama, S. Son, T. Mori, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, S. Akiyama
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Journal Title
Science
Volume: 349
Issue: 6245
Pages: 312-316
DOI
Related Report
Peer Reviewed / Int'l Joint Research
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