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.