Contribution of Electrostatics to the Kinetics of Electron Transfer from NADH-Cytochrome b₅ Reductase to Fe(III)-Cytochrome b₅

Brownian dynamics (BD) simulations provide here a theoretical atomic-level treatment of the reduction of human ferric cytochrome b₅ (cyt b₅) by NADH-cytochrome b₅ reductaste (cyt b₅r) and several of its mutants. BD is used to calculate the second-order rate constant of electron transfer (ET) between the proteins for direct correlation with experiments. Interestingly, the inclusion of electrostatic forces dramatically increases the reaction rate of the native proteins despite the overall negative charge of both proteins. The role played by electrostatic charge distribution in stabilizing the ET complexes and the role of mutations of several amino acid residues in stabilizing or destabilizing the complexes are analyzed. The complex with the shortest ET reaction distance (<i>d</i> = 6.58 Å) from rigid body BD is further subjected to 1 ns of molecular dynamics (MD) in a periodic box of TIP3P water to produce a more stable complex allowed by flexibility and with a shorter average reaction distance <i>d</i> = 6.02 Å. We predict a docking model in which the following ion–ion interactions are dominant (cyt b₅r/cyt b₅): Lys162-Heme O1D/Lys163-Asp64/Arg91-Heme O1A/Lys125-Asp70