Taku Mizukami

Molecular Dynamics Study of Hydration Water Behavior in Blue Copper Protein

We carry out the molecular dynamics(MD) simulation of type 1 blue copper protein azurin in room and some lower temperatures to investigate the behavior of hydration water molecules in the protein surface. In this study, we find the anomalous behavior of the water molecules , which depend on the system temperatures. These water molecules have hydrogen bond to the protein surface residues. We specify the residues type, being classified as the hydration donor and the hydration acceptor of water molecules. We analyze the residue type, and the bond length and bond strength between solvent water molecules in each temperature. Moreover, we estimate the B‐factor of these residues which indicates the fluctuation of hydration residues in each temperature. B‐factor values depend on the system temperatue althought the number of hydration residue do not depend on the temperature.

Free Energy Calculation of Docking Structure of Azurin(I)‐Cytochrome c551(III) Complex Systems by Using the Energetic Representation

We investigate the docking stability of Azurin(I)—Cytochrome C551(III) complex by molecular dynamic simulations. The charge distribution around the active sites for Azurin(I) and Cytochrome C551(III) is estimated by quantum chemical calculation to simulate the complex system by molecular dynamic simulations. We estimete some physical properties such as the root square mean deviation, distance between iron ion in active site of Cytochrome C551(III) and copper ion in active site of Azurin(I), the dynamical cross‐correlation map and free energy in the energetic representation. We discuss the stability of the complex system of Azurin(I)—Cytochrome C551(III) from these properties.

Theoretical Study of Free Energy in Docking Stability of Azurin(II)‐Cytochrome c551(II) Complex System

The docking structure of the Azurin‐Cytochrome C551 is presented. We investigate a complex system of Azurin(II)‐Cytochrome C551(II) by using molecular dynamics simulation. We estimate some physical properties, such as root‐mean‐square deviation (RMSD), binding energy between Azurin and Cytochrome C551, distance between Azurin(II) and Cytochrome C551(II) through center of mass and each active site. We also discuss docking stability in relation to the configuration by free energy between Azurin(II)‐Cytochrome C551(II) and Azurin(I)‐Cytochrome C551(III).