Adsorption and Electron Transfer of Bacterial Decaheme Cytochrome Mtrf on Gold Surface Studied with Atomistic Molecular Dynamics Simulation, Free Energy Computation and Kinetic Monte Carlo Simulation

The study of electron transfer (ET) of the decaheme cytoheme (MtrF) from the metal-respiring bacteria, Shewanella oneidensis MR-1, on substrate surface has important applications for bio-technologies and bio-energy. The orientations and structures of the adsorbed protein on the substrate surface play a key role in ET transfer efficiency. In this work, a hybrid simulation scheme of atomistic molecular dynamics and free energy computations was developed to predict the orientations of MtrF on Au (111) surface. Our simulations demonstrate that protein’s adsorption kinetics and orientation are regulated by the fine balance between protein-surface interactions and dehydration of both protein and gold surfaces. The dehydration of gold surface serves as the crucial driving force for the adsorption. The orientation with the heme ring close and perpendicular to the surfaces is one of the most possible configurations. We also predicted ET transfer with Kinetic Monte Carlo simulation by using the most likely equilibrated structures.