Katsuhiko Nishiyama

Analysis of interactions between green fluorescent protein and silicon substrates using molecular dynamics simulations

We have performed a series of molecular dynamics (MD) simulations on interactions between green fluorescent protein (GFP) and Si substrates. The results show that GFP adsorbs directly on the hydrophobic substrate, and via water molecules on the hydrophilic substrate. The adsorption-induced changes in the conformation of GFP are smaller on the hydrophilic substrate than on the hydrophobic substrate. On the other hand, the dynamic atom motions in GFP are larger on the hydrophobic substrate than on the hydrophilic substrate. In order to prevent the denaturation of proteins caused by immobilization on a substrate, the Si surface should be prepared from the viewpoints of both conformation and dynamic atom motions.

Analysis of binding behavior between dynamic structures of a papain and the peptide consisting of 10 GLY residues

The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural changes in the highly flexible residues in papain were larger. Binding stability and sites would be significantly influenced by the highly flexible residues. Analysis of such residues would provide an important guideline for clarification of enzymatic activities and modification of structural dynamics of such residues would allow us to control enzymatic activities.

Analysis of Interactions between Luciferase and Si Substrates Using Molecular Dynamics Simulations

A series of molecular dynamics (MD) simulations have been performed to investigate the interactions between luciferase and Si substrates. The results show that luciferase adsorbs directly on the hydrophobic Si substrate, and via water molecules on the hydrophilic one. The adsorption-induced changes in conformation of luciferase are smaller on the hydrophilic Si substrate than on the hydrophobic one. The dynamic atom motions in luciferase are larger on the hydrophilic Si substrate than on the hydrophobic one. Inside the active site, the adsorption-induced changes in distances between the atoms forming hydrogen bonds to substrate luciferin are smaller on the hydrophilic Si substrate than the hydrophobic one. In order to prevent the denaturation of luciferase caused by immobilization, the solid surface should be hydrophilic. For higher thermostability, after immobilization, however, a hydrophobic surface is preferable since the dynamic atom motions in luciferase are smaller on a hydrophobic surface. The solid surface should be prepared delicately both from the viewpoint of preventing the denaturation caused by immobilization and improving the thermostability.

Behavior of peptides combining 1 alanine residue and 8 glycine residues on papain associated with structural fluctuations

I investigated the behavior of the peptides combining 1 ALA residue and 8 GLY residues on papain associated with structural fluctuations via molecular dynamics and docking simulations. Although the chance of binding to sites near the active center of papain was reduced by replacing the GLY residue in 9GLY with ALA residue, binding stability was improved by the replacement. Furthermore, both the chance and binding stability were greatly affected by positioning of ALA residue in the peptides. Residue in peptides should be replaced in view of the balance between chance of binding to sites near active center and binding stability.

Heat shock structure of luciferase on wet-treated Si surface

Heat shock structure of luciferase on a wet-treated Si surface was estimated by molecular dynamics simulations. The structural changes in the active site of luciferase were smaller on the hydrophobic Si surface than on the hydrophilic Si surface at high temperature, although the structural changes in the active site of luciferase were smaller on the hydrophilic Si surface than on the hydrophobic Si surface at room temperature. The fine wet-treatment could improve the heat shock resistance of luciferase on the Si surface.

Thermal behavior of luciferase on nanofabricated hydrophobic Si surface

The thermal behavior of luciferase on the nanofabricated hydrophobic Si surface was investigated using molecular dynamics simulations. The structural changes in the active site of luciferase were smaller on the nanofabricated hydrophobic Si surface than on the non-nanofabricated and wet-treated Si surface at high temperature. These nanofabrication techniques would prevent the decrease in activity of luciferase on the Si surface at high temperature. Thus, it would be possible to use biomedical applications for diagnosing tropical diseases by these techniques.