Redox properties of cytochrome b5: a mutagenesis and DPV study of the pH and ionic strength dependence of redox potentials and interactions with myoglobin by DPV

Iron-Histidine Coordination in Cytochrome b5: A Local Vibrational Mode Study

For a series of cytochrome b5 proteins isolated from various species, including bacteria, animals, and humans, we analyzed the intrinsic strength of their distal/proximal FeN bonds and the intrinsic stiffness of their axial NFeN bond angles. To assess intrinsic bond strength and bond angle stiffness, we employed local vibrational stretching force constants ka(FeN) and bending force constants ka(NFeN) derived from the local mode theory developed by our group; the ferric and ferrous oxidation states of the heme Fe were considered. All calculations were conducted with the QM/MM methodology. We found that the reduction of the heme Fe from the ferric to the ferrous state makes the FeN axial bonds weaker, longer, less covalent, and less polar. Additionally, the axial NFeN bond angle becomes stiffer and less flexible. Local mode force constants turned out to be far more sensitive to the protein environment than geometries; evaluating force constant trends across diverse protein groups and monitoring changes in the axial heme-framework revealed redox-induced changes to the primary coordination sphere of the protein. These results indicate that local mode force constants can serve as useful feature data for training machine learning models that predict cytochrome b5 redox potentials, which currently rely more on geometric data and qualitative descriptors of the protein environment. The insights gained through our investigation also offer valuable guidance for strategically fine-tuning artificial cytochrome b5 proteins and designing new, versatile variants.

What Are We Missing by Not Measuring the Net Charge of Proteins?

The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pK_a . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pK_a values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔG_z ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔG_z contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.

High-resolution crystal structures of the solubilized domain of porcine cytochrome b5

Mammalian microsomal cytochrome b5 has multiple electron-transfer partners that function in various electron-transfer reactions. Four crystal structures of the solubilized haem-binding domain of cytochrome b5 from porcine liver were determined at sub-angstrom resolution (0.76-0.95 Å) in two crystal forms for both the oxidized and reduced states. The high-resolution structures clearly displayed the electron density of H atoms in some amino-acid residues. Unrestrained refinement of bond lengths revealed that the protonation states of the haem propionate group may be involved in regulation of the haem redox properties. The haem Fe coordination geometry did not show significant differences between the oxidized and reduced structures. However, structural differences between the oxidized and reduced states were observed in the hydrogen-bond network around the axial ligand His68. The hydrogen-bond network could be involved in regulating the redox states of the haem group.