Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis

Molecular basis of H2O2/O2.-/.OH discrimination during electrochemical activation of DyP peroxidases: The critical role of the distal residues

Here, we show that the replacement of the distal residues Asp and/or Arg of the DyP peroxidases from Bacillus subtilis and Pseudomonas putida results in functional enzymes, albeit with spectroscopically perturbed active sites. All the enzymes can be activated either by the addition of exogenous H2O2 or by in situ electrochemical generation of the reactive oxygen species (ROS) •OH, O2•- and H2O2. The latter method leads to broader and upshifted pH-activity profiles. Both WT enzymes exhibit a differential predominance of ROS involved in their electrochemical activation, which follows the order •OH > O2•- > H2O2 for BsDyP and O2•- > H2O2 > •OH for PpDyP. This ROS selectivity is preserved in mutants with unperturbed sites but is blurred out for distorted sites. The underlying molecular basis of the selectivity mechanisms is analysed through molecular dynamics simulations, which reveal distorted hydrogen bonding networks and higher throughput of the access tunnels in the variants exhibiting no selectivity. The electrochemical activation method provides superior performance for protein variants with a high prevalence of the alternative •OH and O2•- species. These results constitute a promising advance towards engineering DyPs for electrocatalytic applications.

Beyond the coupled distortion model: structural analysis of the single domain cupredoxin AcoP, a green mononuclear copper centre with original features

Cupredoxins are widely occurring copper-binding proteins with a typical Greek-key beta barrel fold. They are generally described as electron carriers that rely on a T1 copper centre coordinated by four ligands provided by the folded polypeptide. The discovery of novel cupredoxins demonstrates the high diversity of this family, with variations in terms of copper-binding ligands, copper centre geometry, redox potential, as well as biological function. AcoP is a periplasmic cupredoxin belonging to the iron respiratory chain of the acidophilic bacterium Acidithiobacillus ferrooxidans. AcoP presents original features, including high resistance to acidic pH and a constrained green-type copper centre of high redox potential. To understand the unique properties of AcoP, we undertook structural and biophysical characterization of wild-type AcoP and of two Cu-ligand mutants (H166A and M171A). The crystallographic structures, including native reduced AcoP at 1.65 Å resolution, unveil a typical cupredoxin fold. The presence of extended loops, never observed in previously characterized cupredoxins, might account for the interaction of AcoP with physiological partners. The Cu-ligand distances, determined by both X-ray diffraction and EXAFS, show that the AcoP metal centre seems to present both T1 and T1.5 features, in turn suggesting that AcoP might not fit well to the coupled distortion model. The crystal structures of two AcoP mutants confirm that the active centre of AcoP is highly constrained. Comparative analysis with other cupredoxins of known structures, suggests that in AcoP the second coordination sphere might be an important determinant of active centre rigidity due to the presence of an extensive hydrogen bond network. Finally, we show that other cupredoxins do not perfectly follow the coupled distortion model as well, raising the suspicion that further alternative models to describe copper centre geometries need to be developed, while the importance of rack-induced contributions should not be underestimated.

Stepwise nitrosylation of the nonheme iron site in an engineered azurin and a molecular basis for nitric oxide signaling mediated by nonheme iron proteins

Mononitrosyl and dinitrosyl iron species, such as {FeNO}⁷, {FeNO}⁸ and {Fe(NO)₂}⁹, have been proposed to play pivotal roles in the nitrosylation processes of nonheme iron centers in biological systems. Despite their importance, it has been difficult to capture and characterize them in the same scaffold of either native enzymes or their synthetic analogs due to the distinct structural requirements of the three species, using redox reagents compatible with biomolecules under physiological conditions. Here, we report the realization of stepwise nitrosylation of a mononuclear nonheme iron site in an engineered azurin under such conditions. Through tuning the number of nitric oxide equivalents and reaction time, controlled formation of {FeNO}⁷ and {Fe(NO)₂}⁹ species was achieved, and the elusive {FeNO}⁸ species was inferred by EPR spectroscopy and observed by Mössbauer spectroscopy, with complemental evidence for the conversion of {FeNO}⁷ to {Fe(NO)₂}⁹ species by UV-Vis, resonance Raman and FT-IR spectroscopies. The entire pathway of the nitrosylation process, Fe(ii) → {FeNO}⁷ → {FeNO}⁸ → {Fe(NO)₂}⁹, has been elucidated within the same protein scaffold based on spectroscopic characterization and DFT calculations. These results not only enhance the understanding of the dinitrosyl iron complex formation process, but also shed light on the physiological roles of nitric oxide signaling mediated by nonheme iron proteins.

Stepwise nitrosylation from Fe(ii) to {FeNO}⁷, {FeNO}⁸ and then to {Fe(NO)₂}⁹ is reported for the first time in the same protein scaffold, providing deeper understanding of the detailed mechanism of dinitrosyl iron complex formation.

CuA-based chimeric T1 copper sites allow for independent modulation of reorganization energy and reduction potential

Attaining rational modulation of thermodynamic and kinetic redox parameters of metalloproteins is a key milestone towards the (re)design of proteins with new or improved redox functions. Here we report that implantation of ligand loops from natural T1 proteins into the scaffold of a CuA protein leads to a series of distorted T1-like sites that allow for independent modulation of reduction potentials (E°') and electron transfer reorganization energies (λ). On the one hand E°' values could be fine-tuned over 120 mV without affecting λ. On the other, λ values could be modulated by more than a factor of two while affecting E°' only by a few millivolts. These results are in sharp contrast to previous studies that used T1 cupredoxin folds, thus highlighting the importance of the protein scaffold in determining such parameters.

HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered CuA Site in Azurin and Its His120Gly Variant

A comparative study of the ¹H and ¹⁴N hyperfine interactions between the Cu_A site in an engineered Cu_A center in azurin (WT-Cu_AAz) and its His120Gly variant (H120G-Cu_AAz) using the two-dimensional ESEEM technique, HYSCORE, is reported. HYSCORE spectroscopy has clarified conflicting results in previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies and found clear differences between the two Cu_A azurins. Specifically, a hyperfine coupling A_N⊥ of 15.3 MHz was determined for the first time from the frequencies of double-quantum transitions of ¹⁴N histidine nitrogens coordinated to Cu_A in WT-Cu_AAz. In contrast, such coupling was not observed in the spectra of H120G-Cu_AAz, indicating at least a several megahertz increase in A_N⊥ for the coordinated nitrogen in this variant. In addition, ¹⁴N HYSCORE spectra of WT-Cu_AAz show interaction with only one type of weakly coupled nitrogen assigned to the remote N_ε atom of coordinated imidazole residues based on the quadrupole coupling constant ( e² Qq/4 h) of ∼0.4 MHz. The spectrum of H120G-Cu_AAz resolves additional features typical for backbone peptide nitrogens with larger e² Qq/4 h values of ∼0.7 MHz. Hyperfine couplings with these nitrogens vary between ∼0.4 and 0.7 MHz. In addition, the two resolved cross-peaks from C_β protons in H120G-Cu_AAz display only ∼1 MHz shifts relative to the corresponding peaks in WT-Cu_AAz. These new findings have provided the first experimental evidence of the previous density functional theory analysis that predicted changes in the delocalized electron spin population of ∼0.02-0.03 (i.e., ∼10%) on copper and sulfur atoms of the Cu_A center in H120 variants relative to WT-Cu_AAz and resolved contradicting results between EPR and ENDOR studies of the valence distribution in Cu_AAz and its variants.