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.