Department   Undergraduate School  , School of Science and Technology
   Position   Associate Professor
Research Period 2010/04~2015/03
Research Topic Exploration of reactions and structural space in multi-degree-of-freedom and large-scale systems
Research Type KAKENHI Research
Consignor Japan Society for the Promotion of Science
Research Program Type Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
KAKENHI Grant No. 22104009
Responsibility Research Contributor
Representative Person YAMATO Takahisa
Collaborative Researcher OKAMOTO Yuko, ADACHI Shinichi
Details 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.