Artificial cytochrome b: Computer modeling and evaluation of redox potentials

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subun it consisting of a four-helix bundle with two hemes. Since no X-ray structu re is available, the structural elements of the artificial Cb were assemble d from scratch using all known chemical and structural information availabl e and avoiding strain as much as possible. Molecular dynamics (MD) simulati ons applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal struc ture of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model struct ure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of th e linearized Poisson-Boltzmann equation (LPBE). The calculated redox potent ials agree within 20 meV with the experimentally measured values. The depen dence of the redox potentials of the hemes on the protein environment was a nalyzed. Accordingly, the total shift in the redox potentials is mainly due to the low dielectric medium of the protein, the protein backbone charges, and the salt bridges formed between the arginines and the propionic acid g roups of the hemes. The difference in the shift of the redox potentials is due to the interactions with the hydrophilic side chains and the salt bridg es formed with the propionic acids of the hemes. For comparison and to test the computational procedure, the redox potentials of the two hemes in the native Cb from the cytochrome bc(1) (Cbc(1)) complex were also calculated. Also in this case the computed redox potentials agree well with experiments .