Artificial Cytochrome b:  Computer Modeling and Evaluation of Redox Potentials

Abstract

We generated atomic coordinates of an artificial protein that was recently synthesized to model the central part of the native cytochrome b (Cb) subunit consisting of a four-helix bundle with two hemes. Since no X-ray structure is available, the structural elements of the artificial Cb were assembled from scratch using all known chemical and structural information available and avoiding strain as much as possible. Molecular dynamics (MD) simulations applied to this model protein exhibited root-mean-square deviations as small as those obtained from MD simulations starting with the crystal structure of the native Cb subunit. This demonstrates that the modeled structure of the artificial Cb is relatively rigid and strain-free. The model structure of the artificial Cb was used to determine the redox potentials of the two hemes by calculating the electrostatic energies from the solution of the linearized Poisson-Boltzmann equation (LPBE). The calculated redox potentials agree within 20 meV with the experimentally measured values. The dependence of the redox potentials of the hemes on the protein environment was analyzed. 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 groups 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 bridges 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.

Identification of Residues Crucially Involved in the Binding of the Heme Moiety of Soluble Guanylate Cyclase

“…The sGC prosthetic heme is embedded in a hydrophobic binding pocket between the histidine 105, tyrosine 135, and the arginine 139. Comparable interactions were described for various other heme binding proteins such as cytochrome P-450, cytochrome b, or FixL (37)(38)(39).…”

Tuning Heme Redox Potentials in the Cytochrome c Subunit of Photosynthetic Reaction Centers

“…Atomic Partial Charges-Amino acid partial charges were taken from the CHARMM22 parameter set (21); non-standard charge states for some titratable groups (Arg, Cys, Lys, Tyr, C-ter, N-ter) not available there were used as calculated before (16). Fractional degrees of protonation needed for the optimization of hydrogen positions after a first titration procedure were accounted for by using atomic partial charges that were obtained by linear interpolation between the charges for the fully protonated and fully deprotonated state of the corresponding molecular groups.…”

“…The respective experimental pK a values of the model compounds in aqueous solution were used as reported before (16). The only redox active groups treated as such were the hemes considered together with their axial and cysteine ligands but without the PR, which were treated separately as independent titratable groups.…”

“…Theoretical work on heme proteins was performed before by several groups (see for example Refs. [15][16][17]. Gunner and Honig (15) calculated the redox potentials of the hemes in the R. viridis RC.…”

Redox Potential of Quinones in Both Electron Transfer Branches of Photosystem I

“…Potentials-To characterize factors that influence A 1 redox potentials, we discriminate between "direct" and "indirect" contributions on A 1 redox potentials, which are because of a specific residue/cofactor as was done in similar investigations before (17). The former is because of the charges of the considered residue/cofactor that interact with A 1 and thus lead to a shift in the redox potential.…”