Spectroscopy of Mixed-Valence CuA-Type Centers: Ligand-Field Control of Ground-State Properties Related to Electron Transfer

Capturing the Binuclear Copper State of Peptidylglycine Monooxygenase Using a Peptidyl-Homocysteine Lure

Peptidylglycine monooxygenase is a copper-dependent enzyme that catalyzes C-alpha hydroxylation of glycine extended pro-peptides, a critical post-translational step in peptide hormone processing. The canonical mechanism posits that dioxygen binds at the mononuclear M-center to generate a Cu(II)-superoxo species capable of H atom abstraction from the peptidyl substrate, followed by long-range electron tunneling from the CuH center. Recent crystallographic and biochemical data have challenged this mechanism, suggesting instead that an "open-to-closed" transition brings the copper centers closer, allowing reactivity within a binuclear intermediate. Here we present the first direct observation of an enzyme-bound binuclear copper species, captured by the use of an Ala-Ala-Phe-hCys inhibitor complex. This molecule reacts with the fully reduced enzyme to form a thiolate-bridged binuclear species characterized by EXAFS of the WT and its M314H variant and with the oxidized enzyme to form a novel mixed valence entity characterized by UV/vis and EPR. Mechanistic implications are discussed.

Fully Delocalized Mixed-Valent Cu1.5 Cu1.5 Complex: Strong Cu-Cu interaction and Fast Electron Self-Exchange Rate Despite Large Structural Changes

A flexible macrocyclic ligand with two tridentate {CNC} compartments can host two Cu ions in reversibly interconvertible states, Cu^I Cu^I (1) and mixed-valent Cu^1.5 Cu^1.5 (2). They were characterized by XRD and multiple spectroscopic methods, including EPR, UV/Vis absorption and MCD, in combination with TD-DFT and CASSCF calculations. 2 features a short Cu⋅⋅⋅Cu distance (≈2.5 Å; compared to ≈4.0 Å in 1) and a very high delocalization energy of 13 000 cm^-1 , comparable to the mixed-valent state of the biological Cu_A site. Electron self-exchange between 1 and 2 is rapid despite large structural reorganization, and is proposed to proceed via a sequential mechanism involving an active conformer of 1, viz. 1'; the latter has been characterized by XRD. Such electron transfer (ET) process is reminiscent of the conformationally gated ET proposed for biological systems. This redox couple is a unique pair of flexible dicopper complexes, achieving fast electron self-exchange closely related to the function of the Cu_A site.

The three-spin intermediate at the O-O cleavage and proton-pumping junction in heme-Cu oxidases

[Figure: see text].

Bis(μ-thiolato)-dicopper Containing Fully Spin Delocalized Mixed Valence Copper-Sulfur Clusters and Their Electronic Structural Properties with Relevance to the CuA Site

With aromatic and aliphatic thiol-S donor Schiff base ligands, the copper-sulfur clusters, [(L1)₈Cu^I₆Cu^II₂](ClO₄)₂·DMF·0.5CH₃OH (1) and [(L2)₁₂Cu^I₅Cu^II₁₁(μ₄-S)(μ₄-O)₆](ClO₄)·4H₂O, respectively, have been reported ( Chem. Commun. 2017, 53, 3334); HL1/HL2 are 2-(((3-methylthiophen-2-yl)methylene)amino)benzene/ethanethiol). Complex 1 comprises a wheel shaped Cu₈S₈ framework, made up of interlinked Cu₂{μ-S(R)}₂ units. To understand the properties with relevance to the Cu_A site and to check whether self-assembly generates similar type clusters to 1, three complexes, [(L3)₈Cu^I₆Cu^II₂](ClO₄)₂·(C₂H₅)₂O·2.5H₂O (2), [(L3^Cl)₈Cu^I₆Cu^II₂](ClO₄)₂·1.25(C₂H₅)₂O·1.25CH₃OH·2H₂O (3), and [(L3^CF3)₈Cu^I₆Cu^II₂](ClO₄)₂·2(C₂H₅)₂O·H₂O (4) have been synthesized with supporting ligands HL3^X (HL3 = 2-((furan-2-ylmethylene)amino)benzenethiol when X = -H; X = -Cl or -CF₃ para to thiol-S are HL3^Cl and HL3^CF3 ligands, respectively). The X-ray structures of 3 and 4 feature a similar Cu₈S₈ architecture to 1. The spectroscopic properties and the X-ray structures revealed that 2-4 are fully spin delocalized mixed valence (MV) of class-III type clusters. The structural parameters of the N₂Cu₂{μ-S(R)}₂ units of 3 and 4 closely resemble those of the MV binuclear Cu_A site. With the aid of UV-vis-NIR, EPR, and spectroelectrochemical studies, the electronic properties of these complexes have been described in comparison with the MV model complexes and Cu_A site.

A [3Cu:2S] cluster provides insight into the assembly and function of the CuZ site of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme reducing environmentally critical nitrous oxide (N₂O) to dinitrogen (N₂) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu_Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N₂OR in Escherichia coli. While no copper ion was found in the Cu_Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S_Z2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S_Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu_Z and is thus of high mechanistic interest.

Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.

A Binuclear CuA Center Designed in an All α-Helical Protein Scaffold

The primary and secondary coordination spheres of metal binding sites in metalloproteins have been investigated extensively, leading to the creation of high-performing functional metalloproteins; however, the impact of the overall structure of the protein scaffold on the unique properties of metalloproteins has rarely been studied. A primary example is the binuclear Cu_A center, an electron transfer cupredoxin domain of photosynthetic and respiratory complexes and, recently, a protein coregulated with particulate methane and ammonia monooxygenases. The redox potential, Cu-Cu spectroscopic features, and a valence delocalized state of Cu_A are difficult to reproduce in synthetic models, and every artificial protein Cu_A center to-date has used a modified cupredoxin. Here, we present a fully functional Cu_A center designed in a structurally nonhomologous protein, cytochrome c peroxidase (CcP), by only two mutations (Cu_ACcP). We demonstrate with UV-visible absorption, resonance Raman, and magnetic circular dichroism spectroscopy that Cu_ACcP is valence delocalized. Continuous wave and pulsed (HYSCORE) X-band EPR show it has a highly compact g_z area and small A_z hyperfine principal value with g and A tensors that resemble axially perturbed Cu_A. Stopped-flow kinetics found that Cu_A formation proceeds through a single T2Cu intermediate. The reduction potential of Cu_ACcP is comparable to native Cu_A and can transfer electrons to a physiological redox partner. We built a structural model of the designed Cu binding site from extended X-ray absorption fine structure spectroscopy and validated it by mutation of coordinating Cys and His residues, revealing that a triad of residues (R48C, W51C, and His52) rigidly arranged on one α-helix is responsible for chelating the first Cu(II) and that His175 stabilizes the binuclear complex by rearrangement of the CcP heme-coordinating helix. This design is a demonstration that a highly conserved protein fold is not uniquely necessary to induce certain characteristic physical and chemical properties in a metal redox center.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Arabidopsis thaliana Hcc1 is a Sco-like metallochaperone for CuA assembly in Cytochrome c Oxidase

The assembly of the Cu_A site in Cytochrome c Oxidase (COX) is a critical step for aerobic respiration in COX-dependent organisms. Several gene products have been associated with the assembly of this copper site, the most conserved of them belonging to the Sco family of proteins, which have been shown to perform different roles in different organisms. Plants express two orthologs of Sco proteins: Hcc1 and Hcc2. Hcc1 is known to be essential for plant development and for COX maturation, but its precise function has not been addressed until now. Here, we report the biochemical, structural and functional characterization of Arabidopsis thaliana Hcc1 protein (here renamed Sco1). We solved the crystal structure of the Cu⁺¹ -bound soluble domain of this protein, revealing a tri coordinated environment involving a CxxxCx_n H motif. We show that AtSco1 is able to work as a copper metallochaperone, inserting two Cu⁺¹ ions into the Cu_A site in a model of CoxII. We also show that AtSco1 does not act as a thiol-disulfide oxido-reductase. Overall, this information sheds new light on the biochemistry of Sco proteins, highlighting the diversity of functions among them despite their high structural similarities. DATABASE: PDB entry 6N5U (Crystal structure of Arabidopsis thaliana ScoI with copper bound).

Versatile coordination behaviour of the chloro-tetrazine-picolylamine ligand: mixed-valence binuclear Cu(i)/Cu(ii) complexes

The 3-Cl-6-amino-(2'-picolyl)-1,2,4,5-tetrazine ligand HL¹ has been synthesized and structurally characterized. Its versatile coordination behavior has been evidenced through reactions with Cu(Hfac)₂ and Cu(triflate)₂ precursors, which provided mixed-valence bimetallic Cu^1.5Cu^1.5 complexes [Cu₂(μ-Cl)(L¹)₂] 2 and [Cu₂(μ-triflate)(L¹)₂] 5. Changing the Cu(ii) precursor and the solvent leads to the formation of mononuclear octahedral Cu(ii) complexes [CuCl₂(HL¹)₂]·2CH₃CN 3 and [Cu(Hfac)₂(HL¹)] 4, in which only the amino-pyridine unit is involved in the coordination of the metal center. In contrast, in complexes 2 and 5, the ligands are deprotonated and bridge the metal centers as pyridine-amido-tetrazine fragments, while a bridging chloride or triflate ligand completes the coordination sphere of the metal ions. The Cu-Cu distances of 2.4313(4) Å in 2 and 2.5198(10) Å in 5 lie among the shorter values within mixed-valence bimetallic Cu complexes. Mixed-valence character is strongly supported by DFT calculations, showing the equal repartition of the unpaired electron between the two metal centers.

Fine Tuning of Functional Features of the CuA Site by Loop-Directed Mutagenesis

Here we report the spectroscopic and electrochemical characterization of three novel chimeric Cu_A proteins in which either one or the three loops surrounding the metal ions in the Thermus thermophilus protein have been replaced by homologous human and plant sequences while preserving the set of coordinating amino acids. These conservative modifications mimic basic differences between Cu_A sites from different organisms and allow for fine tuning the energy gap between alternative electronic ground states of Cu_A.. This results in a systematic modulation of thermodynamic and kinetic electron transfer (ET) parameters and in the selection of one of two possible redox-active molecular orbitals, which differ in the ET reorganization energy by a factor of 2. Moreover, the ET mechanism is found to be frictionally controlled, and the modifications introduced into the different chimeras do not affect the frictional activation parameter.

Dramatic Electronic Perturbations of CuA Centers via Subtle Geometric Changes

Cu_A is a binuclear copper site acting as electron entry port in terminal heme-copper oxidases. In the oxidized form, Cu_A is a mixed valence pair whose electronic structure can be described using a potential energy surface with two minima, σ_u* and π_u, that are variably populated at room temperature. We report that mutations in the first and second coordination spheres of the binuclear metallocofactor can be combined in an additive manner to tune the energy gap and, thus, the relative populations of the two lowest-lying states. A series of designed mutants span σ_u*/π_u energy gaps ranging from 900 to 13 cm^-1. The smallest gap corresponds to a variant with an effectively degenerate ground state. All engineered sites preserve the mixed-valence character of this metal center and the electron transfer functionality. An increase of the Cu-Cu distance less than 0.06 Å modifies the σ_u*/π_u energy gap by almost 2 orders of magnitude, with longer distances eliciting a larger population of the π_u state. This scenario offers a stark contrast to synthetic systems, as model compounds require a lengthening of 0.5 Å in the Cu-Cu distance to stabilize the π_u state. These findings show that the tight control of the protein environment allows drastic perturbations in the electronic structure of Cu_A sites with minor geometric changes.

Characterization of a long overlooked copper protein from methane- and ammonia-oxidizing bacteria

Methane-oxidizing microbes catalyze the oxidation of the greenhouse gas methane using the copper-dependent enzyme particulate methane monooxygenase (pMMO). Isolated pMMO exhibits lower activity than whole cells, however, suggesting that additional components may be required. A pMMO homolog, ammonia monooxygenase (AMO), converts ammonia to hydroxylamine in ammonia-oxidizing bacteria (AOB) which produce another potent greenhouse gas, nitrous oxide. Here we show that PmoD, a protein encoded within many pmo operons that is homologous to the AmoD proteins encoded within AOB amo operons, forms a copper center that exhibits the features of a well-defined Cu_A site using a previously unobserved ligand set derived from a cupredoxin homodimer. PmoD is critical for copper-dependent growth on methane, and genetic analyses strongly support a role directly related to pMMO and AMO. These findings identify a copper-binding protein that may represent a missing link in the function of enzymes critical to the global carbon and nitrogen cycles.

Methane- and ammonia-oxidizing bacteria use the integral membrane, copper-dependent enzymes particulate methane monooxygenase (pMMO) and ammonia monooxygenase (AMO) to oxidize methane and ammonia. Here the authors structurally characterize the copper-binding protein PmoD, which contains an unusual CuA site and their genetic analyses strongly support a pMMO and AMO related function of PmoD.

Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase

The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N₂O to N₂ in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O₂ to H₂O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu^1.5+(CyS)₂Cu^1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.

Mechanistic Aspects of Redox-Induced Assembly and Disassembly of S-Bridged [2M-2S] Structures

Sulfur-bridged binuclear structures [2M-2S] play a pivotal role in a variety of chemical processes such as bond breaking and formation and electron transfer. In general, structural persistence is deemed essential to the respective function but owing to the lack of a suitable molecular model system, the current understanding of the factors that control the thermodynamic and kinetic stability of [2M-2S] cores clearly is limited. This work reports a series of binuclear complexes of nickel derived from a 1,4-terphenyldithiophenol ligand platform that is ideally suited for mechanistic work to overcome this limitation. Redox-induced assembly and disassembly of S-bridged [2M-2S] fragments have been investigated at the molecular level. As part of an extended square scheme, metastable binuclear structures that are significant mechanistically have been identified, characterized, and their reactivity studied quantitatively. Electronic properties that are inherent to [2M-2S] structures and determine thermodynamic and kinetic stability are differentiated from steric effects imposed by co-ligands.

The catalytic cycle of nitrous oxide reductase - The enzyme that catalyzes the last step of denitrification

The reduction of the potent greenhouse gas nitrous oxide requires a catalyst to overcome the large activation energy barrier of this reaction. Its biological decomposition to the inert dinitrogen can be accomplished by denitrifiers through nitrous oxide reductase, the enzyme that catalyzes the last step of the denitrification, a pathway of the biogeochemical nitrogen cycle. Nitrous oxide reductase is a multicopper enzyme containing a mixed valence CuA center that can accept electrons from small electron shuttle proteins, triggering electron flow to the catalytic sulfide-bridged tetranuclear copper "CuZ center". This enzyme has been isolated with its catalytic center in two forms, CuZ*(4Cu1S) and CuZ(4Cu2S), proven to be spectroscopic and structurally different. In the last decades, it has been a challenge to characterize the properties of this complex enzyme, due to the different oxidation states observed for each of its centers and the heterogeneity of its preparations. The substrate binding site in those two "CuZ center" forms and which is the active form of the enzyme is still a matter of debate. However, in the last years the application of different spectroscopies, together with theoretical calculations have been useful in answering these questions and in identifying intermediate species of the catalytic cycle. An overview of the spectroscopic, kinetics and structural properties of the two forms of the catalytic "CuZ center" is given here, together with the current knowledge on nitrous oxide reduction mechanism by nitrous oxide reductase and its intermediate species.

[Cu6 (NGuaS)6 ]2+ and its oxidized and reduced derivatives: Confining electrons on a torus

The hexanuclear thioguanidine mixed-valent copper complex cation [Cu₆ (NGuaS)₆ ]⁺² (NGuaS = o-SC₆ H₄ NC(NMe₂ )₂ ) and its oxidized/reduced states are theoretically analyzed by means of density functional theory (DFT) (TPSSh + D3BJ/def2-TZV (p)). A detailed bonding analysis using overlap populations is performed. We find that a delocalized Cu-based ring orbital serves as an acceptor for donated S p electrons. The formed fully delocalized orbitals give rise to a confined electron cloud within the Cu₆ S₆ cage which becomes larger on reduction. The resulting strong electrostatic repulsion might prevent the fully reduced state. Experimental UV/Vis spectra are explained using time-dependent density functional theory (TD-DFT) and analyzed with a natural transition orbital analysis. The spectra are dominated by MLCTs within the Cu₆ S₆ core over a wide range but LMCTs are also found. The experimental redshift of the reduced low energy absorption band can be explained by the clustering of the frontier orbitals. © 2017 Wiley Periodicals, Inc.

In situ characterization of cofacial Co(IV) centers in Co4O4 cubane: Modeling the high-valent active site in oxygen-evolving catalysts

The Co₄O₄ cubane is a representative structural model of oxidic cobalt oxygen-evolving catalysts (Co-OECs). The Co-OECs are active when residing at two oxidation levels above an all-Co(III) resting state. This doubly oxidized Co(IV)₂ state may be captured in a Co(III)₂(IV)₂ cubane. We demonstrate that the Co(III)₂(IV)₂ cubane may be electrochemically generated and the electronic properties of this unique high-valent state may be probed by in situ spectroscopy. Intervalence charge-transfer (IVCT) bands in the near-IR are observed for the Co(III)₂(IV)₂ cubane, and spectroscopic analysis together with electrochemical kinetics measurements reveal a larger reorganization energy and a smaller electron transfer rate constant for the doubly versus singly oxidized cubane. Spectroelectrochemical X-ray absorption data further reveal systematic spectral changes with successive oxidations from the cubane resting state. Electronic structure calculations correlated to experimental data suggest that this state is best represented as a localized, antiferromagnetically coupled Co(IV)₂ dimer. The exchange coupling in the cofacial Co(IV)₂ site allows for parallels to be drawn between the electronic structure of the Co₄O₄ cubane model system and the high-valent active site of the Co-OEC, with specific emphasis on the manifestation of a doubly oxidized Co(IV)₂ center on O-O bond formation.

Magnetic Circular Dichroism Evidence for an Unusual Electronic Structure of a Tetracarbene-Oxoiron(IV) Complex

In biology, high valent oxo-iron(IV) species have been shown to be pivotal intermediates for functionalization of C-H bonds in the catalytic cycles of a range of O₂-activating iron enzymes. This work details an electronic-structure investigation of [Fe^IV(O)(L^NHC)(NCMe)]²⁺ (L^NHC = 3,9,14,20-tetraaza-1,6,12,17-tetraazoniapenta-cyclohexacosane-1(23),4,6(26),10,12(25),15,17(24),21-octaene, complex 1) using helium tagging infrared photodissociation (IRPD), absorption, and magnetic circular dichroism (MCD) spectroscopy, coupled with DFT and highly correlated wave function based multireference calculations. The IRPD spectrum of complex 1 reveals the Fe-O stretching vibration at 832 ± 3 cm^-1. By analyzing the Franck-Condon progression, we can determine the same vibration occurring at 616 ± 10 cm^-1 in the E(d_xy → d_xz,yz) excited state. Both values are similar to those measured for [Fe^IV(O)(TMC)(NCMe)]²⁺ (TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane). The low-temperature MCD spectra of complex 1 exhibit three pseudo A-term signals around 12 500, 17 000, and 24 300 cm^-1. We can unequivocally assign them to the ligand field transitions of d_xy → d_xz,yz, d_xz,yz → d_z2, and d_xz,yz → d_x2-y2, respectively, through direct calculations of MCD spectra and independent determination of the MCD C-term signs from the corresponding electron donating and accepting orbitals. In comparison with the corresponding transitions observed for [Fe^IV(O) (SR-TPA)(NCMe)]²⁺ (SR-TPA = tris(3,5-dimethyl-4-methoxypyridyl-2-methy)amine), the excitations within the (FeO)²⁺ core of complex 1 have similar transition energies, whereas the excitation energy for d_xz,yz → d_x2-y2 is significantly higher (∼12 000 cm^-1 for [Fe^IV(O)(SR-TPA)(NCMe)]²⁺). Our results thus substantiate that the tetracarbene ligand (L^NHC) of complex 1 does not significantly affect the bonding in the (FeO)²⁺ unit but strongly destabilizes the d_x2-y2 orbital to eventually lift it above d_z2. As a consequence, this unusual electron configuration leads to an unprecedentedly larger quintet-triplet energy separation for complex 1, which largely rules out the possibility that the H atom transfer reaction may take place on the quintet surface and hence quenches two-state reactivity. The resulting mechanistic implications are discussed.

Optical response of the Cu2 S2 diamond core in Cu2II(NGuaS)2 Cl2

Density functional theory (DFT) and time-dependent DFT calculations are presented for the dicopper thiolate complex Cu2 (NGuaS)2 Cl2 [NGuaS=2-(1,1,3,3-tetramethylguanidino) benzenethiolate] with a special focus on the bonding mechanism of the Cu2 S2 Cl2 core and the spectroscopic response. This complex is relevant for the understanding of dicopper redox centers, for example, the CuA center. Its UV/Vis absorption is theoretically studied and found to be similar to other structural CuA models. The spectrum can be roughly divided in the known regions of metal d-d absorptions and metal to ligand charge transfer regions. Nevertheless the chloride ions play an important role as electron donors, with the thiolate groups as electron acceptors. The bonding mechanism is dissected by means of charge decomposition analysis which reveals the large covalency of the Cu2 S2 diamond core mediated between Cu dz2 and S-S π and π* orbitals forming Cu-S σ bonds. Measured resonant Raman spectra are shown for 360- and 720-nm excitation wavelength and interpreted using the calculated vibrational eigenmodes and frequencies. The calculations help to rationalize the varying resonant behavior at different optical excitations. Especially the phenylene rings are only resonant for 720 nm. © 2016 Wiley Periodicals, Inc.

Role of Calcium in Secondary Structure Stabilization during Maturation of Nitrous Oxide Reductase

The copper enzyme nitrous oxide reductase catalyzes the two-electron reduction of nitrous oxide N₂O to dinitrogen N₂. Its maturation largely occurs in the periplasm and includes the insertion of at least one Ca²⁺ ion per monomer. Here we have investigated the role of this structural cation in recombinantly produced apo-N₂OR from Shewanella denitrificans and have determined the three-dimensional structure of the protein by X-ray crystallography. In the absence of Ca²⁺, substantial parts of the enzyme surrounding the binding sites for the copper ions show structural disorder. Reconstitution of the binuclear CuA site was possible in vitro but required the presence of Ca²⁺ ions for a stable insertion of the center. In contrast, an excess of Ca²⁺ prevented copper insertion, and the structural analysis of the Ca²⁺apo form revealed that the cation is sufficient to structure the disordered regions of the protein even in the absence of Cu ions, indicating that the geometry of the two noncanonical copper centers is largely predetermined by the protein structure.

Binuclear Cu(A) Formation in Biosynthetic Models of Cu(A) in Azurin Proceeds via a Novel Cu(Cys)2His Mononuclear Copper Intermediate

Cu(A) is a binuclear electron transfer (ET) center found in cytochrome c oxidases (CcOs), nitrous oxide reductases (N₂ORs), and nitric oxide reductase (NOR). In these proteins, the Cu(A) centers facilitate efficient ET (kET > 10⁴s⁻¹) under low thermodynamic driving forces (10-90 mV). While the structure and functional properties of Cu(A) are well understood, a detailed mechanism of the incorporation of copper into the protein and the identity of the intermediates formed during the Cu(A) maturation process are still lacking. Previous studies of the Cu(A) assembly mechanism in vitro using a biosynthetic model Cu(A) center in azurin (Cu(A)Az) identified a novel intermediate X (Ix) during reconstitution of the binuclear site. However, because of the instability of Ix and the coexistence of other Cu centers, such as Cu(A)' and type 1 copper centers, the identity of this intermediate could not be established. Here, we report the mechanism of Cu(A) assembly using variants of Glu114XCuAAz (X = Gly, Ala, Leu, or Gln), the backbone carbonyl of which acts as a ligand to the Cu(A) site, with a major focus on characterization of the novel intermediate Ix. We show that Cu(A) assembly in these variants proceeds through several types of Cu centers, such as mononuclear red type 2 Cu, the novel intermediate Ix, and blue type 1 Cu. Our results show that the backbone flexibility of the Glu114 residue is an important factor in determining the rates of T2Cu → Ix formation, suggesting that Cu(A) formation is facilitated by swinging of the ligand loop, which internalizes the T2Cu capture complex to the protein interior. The kinetic data further suggest that the nature of the Glu114 side chain influences the time scales on which these intermediates are formed, the wavelengths of the absorption peaks, and how cleanly one intermediate is converted to another. Through careful understanding of these mechanisms and optimization of the conditions, we have obtained Ix in ∼80-85% population in these variants, which allowed us to employ ultraviolet-visible, electron paramagnetic resonance, and extended X-ray absorption fine structure spectroscopic techniques to identify the Ix as a mononuclear Cu(Cys)(2)(His) complex. Because some of the intermediates have been proposed to be involved in the assembly of native Cu(A), these results shed light on the structural features of the important intermediates and mechanism of Cu(A) formation.

Di- and Trinuclear Mixed-Valence Copper Amidinate Complexes from Reduction of Iodine

Molecular examples of mixed-valence copper complexes through chemical oxidation are rare but invoked in the mechanism of substrate activation, especially oxygen, in copper-containing enzymes. To examine the cooperative chemistry between two metals in close proximity to each other we began studying the reactivity of a dinuclear Cu(I) amidinate complex. The reaction of [(2,6-Me2C6H3N)2C(H)]2Cu2, 1, with I2 in tetrahydrofuran (THF), CH3CN, and toluene affords three new mixed-valence copper complexes [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I3)(THF)2, 2, [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I) (NCMe)2, 3, and [(2,6-Me2C6H3N)2C(H)]3Cu3(μ3-I)2, 4, respectively. The first two compounds were characterized by UV-vis and electron paramagnetic resonance spectroscopies, and their molecular structure was determined by X-ray crystallography. Both di- and trinuclear mixed-valence intermediates were characterized for the reaction of compound 1 to compound 4, and the molecular structure of 4 was determined by X-ray crystallography. The electronic structure of each of these complexes was also investigated using density functional theory.

Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase

The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics.

Magnetic circular dichroism and computational study of mononuclear and dinuclear iron(IV) complexes

High-valent iron(IV)-oxo species are key intermediates in the catalytic cycles of a range of O2-activating iron enzymes. This work presents a detailed study of the electronic structures of mononuclear ([FeIV(O)(L)(NCMe)]2+, 1, L = tris(3,5-dimethyl-4-methoxylpyridyl-2-methyl)amine) and dinuclear ([(L)FeIV(O)(μ-O)FeIV(OH)(L)]3+, 2) iron(IV) complexes using absorption (ABS), magnetic circular dichroism (MCD) spectroscopy and wave-function-based quantum chemical calculations. For complex 1, the experimental MCD spectra at 2-10 K are dominated by a broad positive C-term band between 12000 and 18000 cm-1. As the temperature increases up to ~20 K, this feature is gradually replaced by a derivative-shaped signal. The computed MCD spectra are in excellent agreement with experiment, which reproduce not only the excitation energies and the MCD signs of key transitions but also their temperature-dependent intensity variations. To further corroborate the assignments suggested by the calculations, the individual MCD sign for each transition is independently determined from the corresponding electron donating and accepting orbitals. Thus, unambiguous assignments can be made for the observed transitions in 1. The ABS/MCD data of complex 2 exhibit ten features that are assigned as ligand-field transitions or oxo- or hydroxo-to-metal charge transfer bands, based on MCD/ABS intensity ratios, calculated excitation energies, polarizations, and MCD signs. In comparison with complex 1, the electronic structure of the FeIV=O site is not significantly perturbed by the binding to another iron(IV) center. This may explain the experimental finding that complexes 1 and 2 have similar reactivities toward C-H bond activation and O-atom transfer.

Theoretically exploring the key role of the Lys412 residue in the conversion of N2O to N2by nitrous oxide reductase from Achromobacter cycloclastes

The active Cu_Zcluster of NOR provides strong back-donation to coordinated N₂O and activates the O atom of the N₂O group facilitating H-bonding and protonationviathe Lys412 residue.

The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer

In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the CuA site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

N2O reduction at a dissymmetric {Cu2S}-containing mixed-valent center

Through a bio-inspired approach of the active site of the metalloenzyme nitrous oxide reductase, we isolated and characterized a dinuclear mixed-valent dicopper complex capable of N₂O reduction at room temperature.

Native Cu(A) redox sites are largely resilient to pH variations within a physiological range

Previous studies on engineered CuA centres have shown that one of the histidine ligands is protonated and dissociated from the metal site at physiological pH values, thus suggesting a role in regulating proton-coupled electron transfer of cytochrome c oxidases in vivo. Here we report that for native CuA such protonation does not take place at physiologically relevant pH values and, furthermore, no significant changes in the spectroscopic and redox properties of the metal site occur at low pH.

Redox-state sensing by hydrogen bonds in the CuA center of cytochrome c oxidase

Cytochrome c oxidases (CcO) couple electron transfer to active proton translocation through a gated mechanism that minimizes energy losses by preventing protons from flowing backwards or leaking. Such a complex mechanism requires that information about the redox and protonation states of the different centers be transmitted between different parts of the oxidase. Here we report a network of residues located around the electron entry point of CcO, the CuA site in subunit II, that experience collective pH equilibria around neutral pH. This network starts at the occluded side of the CuA site and extends to the interface between subunits I and II of the CcO, where the proton exit is located and through which electrons flow into subunit I. One of the residues in this network is directly involved in a hydrogen bond to one of the CuA ligands, whose strength is highly sensitive to the redox state of the metal center. We propose that this interaction mediates the transmission of redox changes from ET centers to other functional regions of the oxidase, and possibly also in other similar machineries, as part of their gating and regulatory mechanisms.

Axial interactions in the mixed-valent CuA active site and role of the axial methionine in electron transfer

Within Cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent CuA sites is less clear. Recently, the mutation of the axial Met to Leu in a CuA site engineered into azurin (CuA Az) was found to have a limited effect on E(0) relative to this mutation in blue copper (BC). Detailed low-temperature absorption and magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance studies on CuA Az (WT) and its M123X (X = Q, L, H) axial ligand variants indicated stronger axial ligation in M123L/H. Spectroscopically validated density functional theory calculations show that the smaller ΔE(0) is attributed to H2O coordination to the Cu center in the M123L mutant in CuA but not in the equivalent BC variant. The comparable stabilization energy of the oxidized over the reduced state in CuA and BC (CuA ∼ 180 mV; BC ∼ 250 mV) indicates that the S(Met) influences E(0) similarly in both. Electron delocalization over two Cu centers in CuA was found to minimize the Jahn-Teller distortion induced by the axial Met ligand and lower the inner-sphere reorganization energy. The Cu-S(Met) bond in oxidized CuA is weak (5.2 kcal/mol) but energetically similar to that of BC, which demonstrates that the protein matrix also serves an entatic role in keeping the Met bound to the active site to tune down E(0) while maintaining a low reorganization energy required for rapid electron transfer under physiological conditions.

Mechanism of copper incorporation in subunit II of cytochrome C oxidase from Thermus thermophilus: identification of intermediate species

Detailed spectroscopic and kinetic studies of incorporation of copper ion in the wild type (WT) and the D111AA (AA = K, N, or E) mutants of the metal ion binding site of the soluble fragment of subunit II of cytochrome c oxidase from Thermus thermophilus (TtCuA) showed the formation of at least two distinct intermediates. The global analyses of the multiwavelength kinetic results suggested a four-step reaction scheme involving two distinct intermediates in the pathway of incorporation of copper ions into the apoprotein forming the purple dinuclear CuA. An early intermediate similar to the red copper binding proteins was detected in the WT as well as in all the mutants. The second intermediate was a green copper species in the case of WT TtCuA. Mutation of Asp111, however, formed a second intermediate that is distinctly different from that formed in the case of the WT protein, suggesting that mutants follow pathways of copper ion incorporation different from that in the WT protein. The electrostatic interaction between Asp111 and the coordinating His114 possibly plays a subtle role in the mechanism of incorporation of metal ion into the protein. The overall Kd for WT TtCuA was found to be ~8 nM, which changed with mutation of the Asp111 residue. The activation and thermodynamic parameters were also determined from the temperature- and pH-dependent multiwavelength kinetics, and the results are discussed to unravel the role of Asp111 in the mechanism of formation of the dinuclear CuA center in cytochrome c oxidase.

Alternative ground states enable pathway switching in biological electron transfer

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant Cu(A) redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronic wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. These findings suggest a unique role for alternative or "invisible" electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein-protein interactions and membrane potential may optimize and regulate electron-proton energy transduction.