Exploring Electron Transfer Between Heme Proteins of Cytochrome c Super Family in Biosensors: A Molecular Mechanics Study

Abstract

Electron transfer between heme proteins with mediators plays an important role in the fabrication of sensitive bio-nano sensors. Heme protein Cytochrome c (pdb code—1HRC) was chosen as the mediator with Cytochrome c′ (pdb code—1A7V) as the probe protein for our investigation on the electron transfer process. We used the software GRAMM, HEX, and MACRODOX to build the protein complex with further evaluation by GROMACS potential. After molecular mechanics refinement by GROMACS the protein complexes were evaluated in terms of the following criteria: Hydrophobic packing, proximity of the hemes, hydrogen bonds, enthalpy and entropy of binding. The free energy was calculated for each complex to derive the feasible stable models. The combined electron transport of the chosen geometric models was evaluated to choose the possible models. Electrostatic potential was calculated using the program APBS around the heme in the presence and absence of other proteins. From our studies, we derived multiple feasible models and possible electronic path. These studies helped us to understand the relay mechanism between the two proteins and to design mutant proteins by rational site directed mutagenesis to enhance the redox potential and thereby improving the signal to noise ratio in amperometric bionano sensors.