2014 Fiscal Year Final Research Report
Exploration of reactions and structural space in multi-degree-of-freedom and large-scale systems
Project Area | Materials Design through Computics: Complex Correlation and Non-equilibrium Dynamics |
Project/Area Number |
22104009
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Research Category |
Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
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Allocation Type | Single-year Grants |
Review Section |
Science and Engineering
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Research Institution | Nagoya University |
Principal Investigator |
YAMATO Takahisa 名古屋大学, 理学(系)研究科(研究院), 准教授 (90251587)
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Co-Investigator(Kenkyū-buntansha) |
MITSUTAKE Ayori 慶應義塾大学, 理工学部, 講師 (00338253)
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Co-Investigator(Renkei-kenkyūsha) |
OKAMOTO Yuko 名古屋大学, 大学院理学研究科, 教授 (70185487)
ADACHI Shinichi 大学共同利用機関法人高エネルギー加速器研究機構, 物質構造科学研究所, 教授 (60260220)
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Project Period (FY) |
2010-04-01 – 2015-03-31
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Keywords | 分子科学 / 計算物理 / 蛋白質 / 電子状態計算 / 分子シミュレーション |
Outline of Final Research Achievements |
Normal mode analysis was applied to lysozyme, calculated its compressibility and its change associated with the molecular evolution, while relaxation mode analysis was applied to chignolin and extracted reaction coordinates for folding/unfolding transitions. The ligand migration mechanism of myoglobin was studied by molecular dynamics simulation and time-resolved x-ray crystallography, and we obtained 3D maps of potential of mean force for placing carbon monoxide into the myoglobin molecule. A new method was proposed to analyze the residue-residue interactions, and the “crosstalk” among interacting residues was represented as a graph of energy exchange network. As an example, we analyzed the properties of a small globular domain, PDZ3, which is well known to exhibit single domain allostery. The active site formation mechanism of blue-light photoreceptor family proteins was investigated by in silico mutation and fragment molecular orbital calculations with electron correlations.
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Free Research Field |
生物物理学
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