Effect of protein flexibility in docking of electron-transfer proteins cytochrome b<sub>5</sub> and cytochrome b<sub>5</sub> reductase
The process of efficient electron transport is one of the primary regulation mechanisms in biology. Human cytochrome b5 reductase is an enzyme that catalyzes the rapid reduction of cytochrome b5 by cytoplasmic NADH to initiate the function of the heme protein as a central electron donor for several specific reactions that occur in the cytoplasmic surface of liver endoplasmic reticulum (Oshino et al., 1971; Keyes & Cinti, 1980). The electrostatic potential is an essential factor when a protein molecule docks with another protein molecule to perform efficient electron transfer, and plays a crucial role in stabilizing protein-protein complexes. It was found in a previous study at TTU (Kollipara, 2008) that short-range specific attractive ion-ion interactions steer proteins into favorable orientations for electron transfer. However, Brownian dynamics (BD) docking simulations showed results with only partial agreement with kinetics experiments. A possible shortcoming of the BD approach is that the proteins are treated as rigid bodies. For obtaining better results molecular dynamics (MD) methodology is brought into play here by applying the AMBER94 molecular mechanics force field and including solvent, allowing atomic motions and flexibility within and between the proteins in the study of protein-protein complexes. We present results showing the short time (150 ps and 1 ns MD) dynamic nature of the electron transfer complex. For the explicit solvent model we found that introduction of flexibility produced modest and subtle changes in the complex conformation in which a number of key ion-ion contacts are shortened. The reaction distance changed very little, indicating that gross conformational changes were not observed in simulations. The proteins retained the configuration close to what they have in the crystal. More dramatic changes were observed in implicit solvent simulations, where the solvent is treated as a dielectric continuum. Solvent thus plays a key role in mediating the electron transfer complex interactions.
0494: Physical chemistry