Electronic Structures of Metal Sites in Proteins and Models: Contributions to Function in Blue Copper Proteins

Single-step purification and characterization of Pseudomonas aeruginosa azurin

Azurin is a small periplasmic blue copper protein found in bacterial strains such as Pseudomonas and Alcaligenes where it facilitates denitrification. Azurin is extensively studied for its ability to mediate electron-transfer processes, but it has also sparked interest of the pharmaceutical community as a potential antimicrobial or anticancer agent. Here we offer a novel approach for expression and single-step purification of azurin in Escherichia coli with high yields and optimal metalation. A fusion tag strategy using an N-terminal GST tag was employed to obtain pure protein without requiring any additional purification steps. After the on-column cleavage by HRV 3C Protease, azurin is collected and additionally incubated with copper sulphate to ensure sufficient metalation. UV-VIS absorption, mass spectroscopy, and circular dichroism analysis all validated the effective production of azurin, appropriate protein folding and the development of an active site with an associated cofactor. MD simulations verified that incorporation of the N-terminal GPLGS segment does not affect azurin structure. In addition, the biological activity of azurin was tested in HeLa cells.

Theoretical insights into the reduction of Azurin metal site with unnatural amino acid substitutions

Copper-containing proteins play crucial roles in biological systems. Azurin is a copper-containing protein which has a Type 1 copper site that facilitates electron transfer in the cytochrome chain. Previous research has highlighted the significant impact of mutations in the axial Met121 of the copper site on the reduction potential. However, the mechanism of this regulation has not been fully established. In this study, we employed theoretical modeling to investigate the reduction of the Type 1 copper site, focusing on how unnatural amino acid substitutions at Met121 influence its behavior. Our findings demonstrated a strong linear correlation between electrostatic interactions and the reduction potential of the copper site, which indicates that the perturbation of the reduction potential is primarily influenced by electrostatic interactions between the metal ion and the ligating atom. Furthermore, we found that CF/π and CF…H interactions could induce subtle changes in geometry and hence impact the electronic properties of the systems under study. In addition, our calculations suggest the coordination mode and ion-ligand distance could significantly impact the reduction potential of a copper site. Overall, this study offers valuable insights into the structural and electronic properties of the Type 1 copper site, which could potentially guide the design of future artificial catalysts.

Spectroscopic characterization and reactivity studies of a copper(II) iminoxyl radical complex

A CuII complex (1) of a bis-pyridine-dioxime ligand and its one-electron oxidized analog (1-ox) were thoroughly characterized by various spectroscopic techniques, including X-ray absorption spectroscopy. 1-ox was found to be a CuII complex of a ligand iminoxyl radical and represents the first example of such a type. Reorganization energy (λ) of 2.12 eV was determined for the 1-ox/1 couple, which is considerably higher than the type 1 protein and synthetic CuIII/II(OH) complexes.

A Bioinspired Copper-Pair Catalyst in Metal-Organic Frameworks for Molecular Dioxygen Activation and Aerobic Oxidative C-N Coupling

Open Cu sites were loaded to the UiO-67 metal-organic framework (MOF) skeleton by introduction of flexible Cu-binding pyridylmethylamine (pyma) side chains to the biphenyldicarboxylate linkers. Distance between Cu centers in the MOF pores was tuned by controlling the density of metal-binding side chains. "Interacted" Cu-pair or "isolated" monomeric Cu sites were achieved with high and low (pyma)Cu side chain loading, respectively. Spectroscopic and theoretical studies indicate that "interacted" Cu pairs can effectively bind and activate molecular dioxygen to form Cu2O2 clusters, which showed high catalytic activity for aerobic oxidative C-N coupling. On the contrary, MOF catalyst bearing isolated monomeric Cu sites only showed modest catalytic activity. Enhancement in catalytic performance for the Cu-pair catalyst is attributed to the remote synergistic effect of the paired Cu site, which binds molecular dioxygen and cleaves the O═O bond in a collaborative manner. This work demonstrates that noncovalently interacted metal-pair sites can effectively activate inert small molecules and promote heterogeneous catalytic processes.

In Situ UV-Vis-NIR Absorption Spectroscopy and Catalysis

This review highlights in situ UV-vis-NIR range absorption spectroscopy in catalysis. A variety of experimental techniques identifying reaction mechanisms, kinetics, and structural properties are discussed. Stopped flow techniques, use of laser pulses, and use of experimental perturbations are demonstrated for in situ studies of enzymatic, homogeneous, heterogeneous, and photocatalysis. They access different time scales and are applicable to different reaction systems and catalyst types. In photocatalysis, femto- and nanosecond resolved measurements through transient absorption are discussed for tracking excited states. UV-vis-NIR absorption spectroscopies for structural characterization are demonstrated especially for Cu and Fe exchanged zeolites and metalloenzymes. This requires combining different spectroscopies. Combining magnetic circular dichroism and resonance Raman spectroscopy is especially powerful. A multitude of phenomena can be tracked on transition metal catalysts on various supports, including changes in oxidation state, adsorptions, reactions, support interactions, surface plasmon resonances, and band gaps. Measurements of oxidation states, oxygen vacancies, and band gaps are shown on heterogeneous catalysts, especially for electrocatalysis. UV-vis-NIR absorption is burdened by broad absorption bands. Advanced analysis techniques enable the tracking of coking reactions on acid zeolites despite convoluted spectra. The value of UV-vis-NIR absorption spectroscopy to catalyst characterization and mechanistic investigation is clear but could be expanded.

Overlooked Hydrogen Bond in a Blue Copper Protein Uncovered by Neutron and Sub-Ångström Resolution X-ray Crystallography

Metalloproteins play fundamental roles in organisms and are utilized as starting points for the directed evolution of artificial enzymes. Knowing the strategies of metalloproteins, by which they exquisitely tune their activities, will not only lead to an understanding of biochemical phenomena but also contribute to various applications. The blue copper protein (BCP) has been a renowned model system to understand the biology, chemistry, and physics of metalloproteins. Pseudoazurin (Paz), a blue copper protein, mediates electron transfer in the bacterial anaerobic respiratory chain. Its redox potential is finely tuned by hydrogen (H) bond networks; however, difficulty in visualizing H atom positions in the protein hinders the detailed understanding of the protein's structure-function relationship. We here used neutron and sub-ångström resolution X-ray crystallography to directly observe H atoms in Paz. The 0.86-Å-resolution X-ray structure shows that the peptide bond between Pro80 and the His81 Cu ligand deviates from the ideal planar structure. The 1.9-Å-resolution neutron structure confirms a long-overlooked H bond formed by the amide of His81 and the S atom of another Cu ligand Cys78. Quantum mechanics/molecular mechanics calculations show that this H bond increases the redox potential of the Cu site and explains the experimental results well. Our study demonstrates the potential of neutron and sub-ångström resolution X-ray crystallography to understand the chemistry of metalloproteins at atomic and quantum levels.

Synthesis, Characterization, and Reactivity of High-Valent Carbene Dicarboxamide-Based Nickel Pincer Complexes

High-valent metal-fluoride complexes are currently being explored for concerted proton-electron transfer (CPET) reactions, the driving force being the high bond dissociation energy of H-F (BDEH-F = 135 kcal/mol) that is formed after the reaction. Ni(III)-fluoride-based complexes on the pyridine dicarboxamide pincer ligand framework have been utilized for CPET reactions toward phenols and hydrocarbons. We have replaced the central pyridine ligand with an N-heterocyclic carbene carbene to probe its effect in both stabilizing the high-valent Ni(III) state and its ability to initiate CPET reactions. We report a monomeric carbene-diamide-based Ni(II)-fluoride pincer complex that was characterized through 1H/19F NMR, mass spectrometry, UV-vis, and X-ray crystallography analysis. Although carbenes and deprotonated carboxamides in the Ni(II)-fluoride complex are expected to stabilize the Ni(III) state upon oxidation, the Ni(III)/Ni(II) redox process occurred at very high potential (0.87 V vs Fc+/Fc, dichloromethane) and was irreversible. Structural studies indicate significant distortion in the imidazolium "NCN" carbene plane of Ni(II)-fluoride caused by the formation of six-membered metallacycles. The high-valent NiIII-fluoride analogue was synthesized by the addition of 1.0 equiv CTAN (ceric tetrabutylammonium nitrate) in dichloromethane at -20 °C which was characterized by UV-vis, mass spectrometry, and EPR spectroscopy. Density functional theory studies indicate that the Ni-carbene bond elongated, while the Ni-F bond shortened upon oxidation to the Ni(III) species. The high-valent Ni(III)-fluoride was found to react with the substituted phenols. Analysis of the KIE and linear free energy relationship correlates well with the CPET nature of the reaction. Preliminary analysis indicates that the CPET is asynchronous and is primarily driven by the E0' of the Ni(III)-fluoride complex.

Probing conformational kinetics of catalase with and without magnetic field by single-entity collision electrochemistry

The conformational motions of enzymes are crucial for their catalytic activities, but these fluctuations are usually spontaneous and unsynchronized and thus difficult to obtain from ensemble-averaged measurements. Here, we employ label-free single-entity electrochemical measurements to monitor in real time the fluctuating enzymatic behavior of single catalase molecules toward the degradation of hydrogen peroxide. By probing the electrochemical signals of single catalase molecules at a carbon nanoelectrode, we were able to observe three distinct current traces that could be attributed to conformational changes on the sub-millisecond timescale. Whereas, nearly uniform single long peaks were observed for single catalase molecules under a moderate magnetic field due to the restricted conformational changes of catalase. By combining high-resolution current signals with a multiphysics simulation model, we studied the catalytic kinetics of catalase with and without a magnetic field, and further estimated the maximum catalytic rate and conformational transition rate. This work introduces a new complementary approach to existing single-molecule enzymology, giving further insight into the enzymatic reaction mechanism.

Deciphering the effect of amine versus imine ligands of copper(II) complexes in 2-aminophenol oxidation

A series of amine (1-6) and imine (5',6') based copper(II) complexes with tridentate (NNO) ligand donors were synthesized and characterized using modern analytical techniques. All the complexes were subjected to 2-aminophenol (OAP) oxidation to form 2-aminophenoxazin-3-one, as a functional analogue of an enzyme, phenoxazinone synthase. In addition, a critical comparison of the reactivity using the amine-based complexes with their respective imine counterparts was achieved in both experimental as well as theoretical studies. For instance, the kinetic measurement revealed that the imine-based copper(II) complexes (kcat, 2.4 × 105-6.2 × 106 h-1) are better than amine-based (kcat, 6.3 × 104-3.9 × 105 h-1) complexes. The complex-substrate adducts [Cu(L3)(OAP)] (7) and [Cu(L3')(OAP)] (7') were characterized for both systems by mass spectrometry. Further, the DFT study was performed with amine- (3) and imine- (3') based copper(II) complexes, to compare their efficacy in the oxidation of OAP. The mechanistic investigations reveal that the key elementary step to determine the reactivity of 3 and 3' is the proton-coupled electron transfer (PCET) step occurring from the intermediates 7/7'. Further, the computed HOMO-LUMO energy gap of 7' was smaller than 7 by 0.8 eV, which indicates the facile PCET compared to that of 7. Moreover, the coupling of the OAP moiety using imine-complexes (ΔGR.E = -5.8 kcal/mol) was found to be thermodynamically more favorable than amine complexes (ΔGR.E = +3.3 kcal/mol). Overall, the theoretical findings are in good agreement with the experimental results.

Rapid Electron Transfer Self-Exchange in Conformationally Dynamic Copper Coordination Complexes

We report the electron transfer (ET) self-exchange rate constants (k11) for a pair of CuII/I complexes utilizing dpaR (dpa = dipicolylaniline, R = OMe, SMe) ligands assessed by NMR line broadening experiments. These ligands afford copper complexes that are conformationally dynamic in one oxidation state. With R = OMe, the CuI complex is dynamic, while with R = SMe, the CuII complex is dynamic. Both complexes exhibit unexpectedly large k11 values of 2.48(6) × 105 and 2.21(9) × 106 M-1 s-1 for [CuCl(dpaOMe)]+/0 and [CuCl(dpaSMe)]+/0, respectively. Among the fastest reported molecular copper coordination complexes to date, that of [CuCl(dpaSMe)]+/0 exceeds all others by an order of magnitude and compares only with those observed in type 1 blue copper proteins. The dynamicity of these complexes establishes pre-steady-state conformational equilibria that minimize the inner-sphere reorganization energies to 0.71 and 0.62 eV for R = OMe and SMe, respectively. In contrast to the emphasis on rigidity in the formulation of entatic states applied to blue copper proteins, the success of these two systems highlights the relevance of conformational dynamicity in mediating rapid ET.

Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks

Though thiols are exceptionally versatile, their high reactivity has also hindered the synthesis and characterization of well-defined thiol-containing porous materials. Leveraging the mild conditions of the noncovalent peptide assembly, we readily synthesized and characterized a number of frameworks with thiols displayed at many unique positions and in several permutations. Importantly, nearly all assemblies were structurally determined using single-crystal X-ray diffraction to reveal their rich sequence-structure landscape and the cooperative noncovalent interactions underlying their assembly. These observations and supporting molecular dynamics calculations enabled rational engineering by the positive and negative design of noncovalent interactions. Furthermore, the thiol-containing frameworks undergo diverse single-crystal-to-single-crystal reactions, including toxic metal ion coordination (e.g., Cd2+, Pb2+, and Hg2+), selective uptake of Hg2+ ions, and redox transformations. Notably, we find a framework that supports thiol-nitrosothiol interconversion, which is applicable for biocompatible nitric oxide delivery. The modularity, ease of synthesis, functionality, and well-defined nature of these peptide-based thiol frameworks are expected to accelerate the design of complex materials with reactive active sites.

The structure of plastocyanin tunes the midpoint potential by restricting axial ligation of the reduced copper ion

Blue copper proteins are models for illustrating how proteins tune metal properties. Nevertheless, the mechanisms by which the protein controls the metal site remain to be fully elucidated. A hindrance is that the closed shell Cu(I) site is inaccessible to most spectroscopic analyses. Carbon deuterium (C-D) bonds used as vibrational probes afford nonperturbative, selective characterization of the key cysteine and methionine copper ligands in both redox states. The structural integrity of Nostoc plastocyanin was perturbed by disrupting potential hydrogen bonds between loops of the cupredoxin fold via mutagenesis (S9A, N33A, N34A), variably raising the midpoint potential. The C-D vibrations show little change to suggest substantial alteration to the Cu(II) coordination in the oxidized state or in the Cu(I) interaction with the cysteine ligand. They rather indicate, along with visible and NMR spectroscopy, that the methionine ligand distinctly interacts more strongly with the Cu(I) ion, in line with the increases in midpoint potential. Here we show that the protein structure determines the redox properties by restricting the interaction between the methionine ligand and Cu(I) in the reduced state.

Kinetic and mechanistic investigations of dioxygen reduction by a molecular Cu(II) catalyst bearing a pentadentate amidate ligand

A pentadentate Cu(II) complex, [CuII(dpaq)](ClO4) (1), featuring a redox active ligand, H-dpaq (H-dpaq = 2-[bis(pyridine-2-ylmethyl)]amino-N-quinolin-8-yl-acetamidate), catalyses four-electron reduction of dioxygen by decamethylferrocene (Fc*) in the presence of trifluoroacetic acid (CF3COOH) in acetone at 298 K. No catalytic oxygen reduction was observed in the presence of stronger Brønsted acids than CF3COOH, such as perchloric acid (HClO4) or trifluoromethanesulphonic acid (HOTf). In contrast, facile catalytic reduction of O2 occurs by Fc* with 1 and HClO4 or HOTf in dimethylformamide (DMF). The use of CF3COOH as the proton source in DMF results in the suppression of O2 reduction under otherwise identical reaction conditions. While the O2 reduction reactions in DMF are linearly dependent on the pKa of Brønsted acids, the acid dependence on catalytic O2-reduction reactivity by 1 in acetone showed complete reversal. Cyclic voltammetry studies using p-chloranil as the probe substrates in the presence of acids in the solvents reveal that the strengths of the protonic acids increase significantly in acetone compared to that in DMF. The amidate-N in [CuII(dpaq)](ClO4) (1) undergoes protonation in the presence of HClO4 or HOTf in DMF to form [CuII(H-dpaq)]2+ (1-H+), but not in the presence of CF3COOH. Enhanced acid strength of CF3COOH in acetone, however, effectively protonates 1 and triggers O2 reduction. Protonation of 1 with HClO4 or HOTf in acetone results in the change of its coordination environment, and this protonated species does not trigger O2 reduction. Detailed kinetic studies indicate that 1-H+ undergoes reduction by two-electrons and the reduced species binds O2 to form a Cu(II)-superoxo intermediate. This is followed by a rate-determining proton-coupled electron-transfer (PCET) reduction to generate the Cu(II)-hydroperoxo intermediate. While catalytic O2 reduction in acetone occurs predominantly via a 4e-/4H+ pathway, product selectivity (H2O vs. H2O2) in DMF depends upon the concentration of the reductant (Fc*). While dioxygen reduction to H2O2 is favoured at low [Fc*], mechanistic studies suggest that O2 reduction with high [Fc*] proceeds via a [2e- + 2e-] mechanism, where the released H2O2 during catalysis is further reduced to water.

Reparameterization of Non-Bonded Parameters for Copper Ions in Plastocyanin: An Adaptive Force Matching Study

Molecular mechanics rely on existing experimental and theoretical inputs to confidently calculate the trajectories of molecular systems. These calculations, however, are often hindered by missing force field parameters. A notable subject of this problem is metal centers of proteins. This study parameterized, through an adaptive force matching (AFM) workflow, the copper cofactor of plastocyanin in its two oxidation states. New 12-6 Lennard-Jones (LJ) parameters and atomic partial charges were generated to complete the non-bonded description of the copper site. Our models show uniform distorted tetrahedral structures for reduced plastocyanin, Cu(I), and oxidized plastocyanin, Cu(II). These structures align with the QM/MM MD results and existing crystallography studies. TD-DFT calculations, meanwhile, showed that conformations with elongated axial Cu-SMet and shortened equatorial Cu-SCys bonds retain the experimental UV-Vis profile of blue copper (BC) proteins, thus signifying the importance of Cu-S interactions on BC proteins' unique spectroscopic properties.

Biochemical Characterization of the Copper Nitrite Reductase from Neisseria gonorrhoeae

The copper-containing nitrite reductase from Neisseria gonorrhoeae has been shown to play a critical role in the infection mechanism of this microorganism by producing NO and abolishing epithelial exfoliation. This enzyme is a trimer with a type 1 copper center per subunit and a type 2 copper center in the subunits interface, with the latter being the catalytic site. The two centers were characterized for the first time by EPR and CD spectroscopy, showing that the type 1 copper center has a high rhombicity due to its lower symmetry and more tetragonal structure, while the type 2 copper center has the usual properties, but with a smaller hyperfine coupling constant (A// = 10.5 mT). The thermostability of the enzyme was analyzed by differential scanning calorimetry, which shows a single endothermic transition in the thermogram, with a maximum at 94 °C, while the CD spectra in the visible region indicate the presence of the type 1 copper center up to 80 °C. The reoxidation of the N. gonorrhoeae copper-containing nitrite reductase in the presence of nitrite were analyzed by visible spectroscopy and showed a pH dependence, being higher at pH 5.5-6.0. The high thermostability of this enzyme may be important to maintaining a high activity in the extracellular space and to making it less susceptible to denaturation and proteolysis, contributing to the proliferation of N. gonorrhoeae.

Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin

The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.

Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands

In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O₂ is reduced to H₂O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.

Cu+/Ag+ Competition in Type I Copper Proteins (T1Cu)

Due to the similarity in the basic coordination behavior of their mono-charged cations, silver biochemistry is known to be linked to that of copper in biological systems. Still, Cu⁺/²⁺ is an essential micronutrient in many organisms, while no known biological process requires silver. In human cells, copper regulation and trafficking is strictly controlled by complex systems including many cytosolic copper chaperones, whereas some bacteria exploit the so-called "blue copper" proteins. Therefore, evaluating the controlling factors of the competition between these two metal cations is of enormous interest. By employing the tools of computational chemistry, we aim to delineate the extent to which Ag⁺ might be able to compete with the endogenous copper in its Type I (T1Cu) proteins, and where and if, alternatively, it is handled uniquely. The effect of the surrounding media (dielectric constant) and the type, number, and composition of amino acid residues are taken into account when modelling the reactions in the present study. The obtained results clearly indicate the susceptibility of the T1Cu proteins to a silver attack due to the favorable composition and geometry of the metal-binding centers, along with the similarity between the Ag⁺/Cu⁺-containing structures. Furthermore, by exploring intriguing questions of both metals' coordination chemistry, an important background for understanding the metabolism and biotransformation of silver in organisms is provided.

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene ("BMIE"), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu⁺⁺ and Zn⁺⁺ in bidentate (N₂) and tridentate (N₂S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn⁺⁺, Cu⁺⁺, and Co⁺⁺. EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu⁺⁺ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H₂O/HO^-, tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn⁺⁺ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. These features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

Profiling charge transport: A new computational approach

To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.

Structural Analyses of the Multicopper Site of CopG Support a Role as a Redox Enzyme

Metal ions can be both essential components of cells as well as potential toxins if present in excess. Organisms utilize a variety of protein systems to maintain the concentration of metal ions within the appropriate range for cellular function, and to avoid concentrations where cellular damage can occur. In bacteria, numerous proteins contribute to copper homeostasis, including copper transporters, chelators, and redox enzymes. The genes that encode these proteins are often found in clusters, thus providing modular components that work together to achieve homeostasis. A better understanding of how these components function and cooperate to achieve metal ion resistance is needed, given the extensive use of metal ions, including copper, as broad-spectrum biocides in a variety of clinical and environmental settings. The copG gene is a common component of such copper resistance clusters, but its contribution to copper resistance is not well understood. In this review the available information about the CopG protein encoded by this gene is summarized. Comparison of the recent structure to diverse copper-containing metallochaperones, metalloenzymes, and electron transfer proteins suggests that CopG is a redox enzyme that uses multiple copper ions as active site redox cofactors to act on additional copper ion substrates. Mechanisms for both oxidase and reductase activity are proposed, and the biological advantages that these activities can contribute in conjunction with existing systems are described.

Prediction of Protein Function from Tertiary Structure of the Active Site in Heme Proteins by Convolutional Neural Network

Structure-function relationships in proteins have been one of the crucial scientific topics in recent research. Heme proteins have diverse and pivotal biological functions. Therefore, clarifying their structure-function correlation is significant to understand their functional mechanism and is informative for various fields of science. In this study, we constructed convolutional neural network models for predicting protein functions from the tertiary structures of heme-binding sites (active sites) of heme proteins to examine the structure-function correlation. As a result, we succeeded in the classification of oxygen-binding protein (OB), oxidoreductase (OR), proteins with both functions (OB-OR), and electron transport protein (ET) with high accuracy. Although the misclassification rate for OR and ET was high, the rates between OB and ET and between OB and OR were almost zero, indicating that the prediction model works well between protein groups with quite different functions. However, predicting the function of proteins modified with amino acid mutation(s) remains a challenge. Our findings indicate a structure-function correlation in the active site of heme proteins. This study is expected to be applied to the prediction of more detailed protein functions such as catalytic reactions.

Oxygen versus Sulfur Coordination in Cobalt Superoxo Complexes: Spectroscopic Properties, O2 Binding, and H-Atom Abstraction Reactivity

A five-coordinate, disiloxide-ligated cobalt(II) (S = 3/2) complex (1) was prepared as an oxygen-ligated analogue to the previously reported silanedithiolate-ligated CoII(Me3TACN)(S2SiMe2) (J. Am. Chem. Soc., 2019, 141, 3641-3653). The structural and spectroscopic properties of 1 were analyzed by single-crystal X-ray diffraction, electron paramagnetic resonance (EPR), and NMR spectroscopies. The reactivity of 1 with dioxygen was examined, and it was shown to bind O2 reversibly in a range of solvents at low temperatures. A cobalt(III)-superoxo complex, CoIII(O2·-)(Me3TACN)((OSi2Ph)2O) (2), was generated, and was analyzed by UV-vis, EPR, and resonance Raman spectroscopies. Unlike its sulfur-ligated analogue, complex 2 can thermally release O2 to regenerate 1. Vibrational assignments for selective 18O isotopic labeling of both O2 and disiloxide ligands in 2 are consistent with a 6-coordinate, Co(η1-O2·-)("end-on") complex. Complex 2 reacts with the O-H bond of 4-methoxy-2,2,6,6-tetramethylpiperidin-1-ol (4-MeO-TEMPOH) via H-atom abstraction with a rate of 0.58(2) M-1 s-1 at -105 °C, but it is unable to oxidize phenol substrates. This bracketed reactivity suggests that the O-H bond being formed in the putative CoIII(OOH) product has a relatively weak O-H bond strength (BDFE ∼66-74 kcal mol-1). These thermodynamic and kinetic parameters are similar to those seen for the sulfur-ligated Co(O2)(Me3TACN)(S2SiMe2), indicating that the differences in the electronic structure for O versus S ligation do not have a large impact on H-atom abstraction reactivity.

A Novel Strategy for Selective Thyroid Hormone Determination Based on an Electrochemical Biosensor with Graphene Nanocomposite

This article presents a novel and selective electrochemical bioassay with antibody and laccase for the determination of free thyroid hormone (free triiodothyronine, fT3). The biosensor was based on a glassy carbon electrode modified with a Fe₃O₄@graphene nanocomposite with semiconducting properties, an antibody (anti-PDIA3) with high affinity for fT3, and laccase, which was responsible for catalyzing the redox reaction of fT3. The electrode modification procedure was investigated using a cyclic voltammetry technique, based on the response of the peak current after modifications. All characteristic working parameters of the developed biosensor were analyzed using differential pulse voltammetry. Obtained experimental results showed that the biosensor revealed a sensitive response to fT3 in a concentration range of 10-200 µM, a detection limit equal to 27 nM, and a limit of quantification equal to 45.9 nM. Additionally, the constructed biosensor was selective towards fT3, even in the presence of interference substances: ascorbic acid, tyrosine, and levothyroxine, and was applied for the analysis of fT3 in synthetic serum samples with excellent recovery results. The designed biosensor also exhibited good stability and can find application in future medical diagnostics.

Switchable catalysis and CO2 sensing by reduction resistant, luminescent copper-thiolate complexes

Metal-thiolate complexes have been the focus of research for several years because of their unique photophysical properties and their use as a precursor for synthesizing various well-defined metal nanoclusters. A rational understanding of their structure-property relationship is necessary to realize their full potential in practical applications. Herein, we demonstrate the synthesis of a unique copper-thiolate complex with reversibly switchable catalytic and photoluminescence (PL) properties. The as-synthesized complex at basic pH (Complex B) showed cyan PL with a strong peak at ∼488 nm (cyan) and a small shoulder peak at ∼528 nm (green). When the pH of the complex was changed to acidic (Complex A), the PL was switched to light green. Such pH-responsive PL properties were demonstrated to be useful for pH and CO₂ sensing. The switchable properties originate from their two distinct structural states at two different pHs. We found that Complex A was resistant to high concentrations of a strong reducing agent, and had an intermediate oxidation state of copper (Cu⁺) with good thermodynamic stability. Furthermore, the switchable catalytic property was investigated with a 4-nitrophenol reduction and 3,3',5,5'-tetramethylbenzidine (TMB) oxidation reaction. The reduction kinetics followed pseudo-first-order, where the catalytic activity was enhanced by more than 10³ times when Complex B was switched to Complex A. A similar trend was also observed for TMB oxidation. Our design strategy demonstrates that redox switchable metal-thiolate complexes could be a powerful candidate for a plethora of applications.

The redox-active Cu-FomA complex: the mode that provides coordination of CuII/CuI ions during the reduction/oxidation cycle

Colorectal cancer (CRC) is the third most commonly diagnosed form of cancer worldwide. Recent studies have indicated a strong correlation between microbial imbalance and the development of CRC. An abundance of Fusobacterium nucleatum, an anaerobic Gram-negative bacterium, has been considered a biomarker of CRC progression. Several investigations have also proposed that binding copper ions to various bacterial proteins enhances the Cu^II + e^- ⇄ Cu^I redox cycle, which consequently promotes uncontrolled production of reactive oxygen species (ROS) and propels colorectal carcinogenesis. In this work, a multidisciplinary approach was applied to study the molecular relation of copper with the peptide models of FomA, a protein expressed by Fusobacterium nucleatum. The main goal was to investigate all the factors that tune the Cu^II + e^- ⇄ Cu^I equilibrium. A linear peptide Fom1 (Ac-KGHGNGEEGTPTVHNE-NH₂) and cyclic peptide Fom2 (cyclo-(KGHGNGEEGTPTVHNE)) were used as ligands. The coordination of Cu^I was deduced from the NMR data. The conditional dissociation constants KcondD defined the stability of Cu^I complexes. The electrochemical activity of Cu^II and Cu^I compounds was analysed using cyclic voltammetry. A quasi-reversible redox conversion Cu^II-peptide + e^- ⇄ Cu^I-peptide was revealed for all studied systems. In the presence of ascorbic acid (HAsc), Cu^II complexes were immediately reduced to Cu^I species; however, their re-oxidation was kinetically sluggish. The HAsc-induced redox cycle provoked the metal-catalyzed oxidation (MCO) effect. That in the end prevented coordination of the re-appearing Cu^II ion to its initial binding site. The toxicity of the FomA-Cu^II/Cu^I complexes and their role in CRC progression were briefly discussed.

Cu(Proline)2 Complex: A Model of Bio-Copper Structural Ambivalence

Complexes of Cu²⁺(d⁹) with proline may be considered a simple model to address the structural flexibility and electronic properties of copper metalloproteins. To discuss optical electronic spectra and infrared spectral responses, we use quantum chemistry applied to model systems prepared under different geometries and degree of hydration. A comparison of experimental data with calculations indicates that first explicit neighbor water clustering next to the Cu²⁺(d⁹) complex is critical for a correct description of the electronic properties of this system. We deduce that the moderately hydrated trans conformer is the main structural form of the complex in water. Further, we suggest that the antisymmetric stretching mode of the carbonyl moieties of the conformer is dominant in the spectrally broadened infrared resonance at 1605 cm⁻¹, where inhomogeneity of the transition at the blue side can be ascribed to a continuum of less optimal interactions with the solvent. Extracted structural properties and hydration features provide information on the structural flexibility/plasticity specific to Cu²⁺(d⁹) systems in correlation with the electronic behavior upon photoexcitation. We discuss the role and the nature of the axial ligand in bio-copper structural ambivalence and reactivity.

Hollow Bioelectrodes Based on Buckypaper Assembly. Application to the Electroenzymatic Reduction of O2

A new concept of hollow electrode based on the assembly of two buckypapers creating a microcavity which contains a biocatalyst is described. To illustrate this innovative concept, hollow bioelectrodes containing 0.16–4 mg bilirubin oxidase in a microcavity were fabricated and applied to electroenzymatic reduction of O2 in aqueous solution. For hemin-modified buckypaper, the bioelectrode shows a direct electron transfer between multi-walled carbon nanotubes and bilirubin oxidase with an onset potential of 0.77 V vs. RHE. The hollow bioelectrodes showed good storage stability in solution with an electroenzymatic activity of 30 and 11% of its initial activity after 3 and 6 months, respectively. The co-entrapment of bilirubin oxidase and 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) in the microcavity leads to a bioelectrode exhibiting mediated electron transfer. After 23 h of intermittent operation, 5.66 × 10−4 mol of O2 were electroreduced (turnover number of 19,245), the loss of catalytic current being only 54% after 7 days.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Artificial Metalloproteins: At the Interface between Biology and Chemistry

Artificial metalloproteins (ArMs) have recently gained significant interest due to their potential to address issues in a broad scope of applications, including biocatalysis, biotechnology, protein assembly, and model chemistry. ArMs are assembled by the incorporation of a non-native metallocofactor into a protein scaffold. This can be achieved by a number of methods that apply tools of chemical biology, computational de novo design, and synthetic chemistry. In this Perspective, we highlight select systems in the hope of demonstrating the breadth of ArM design strategies and applications and emphasize how these systems address problems that are otherwise difficult to do so with strictly biochemical or synthetic approaches.

Metal Centers and Organic Ligands Determine Electrochemistry of Metal-Organic Frameworks

The properties and applications of metal-organic frameworks (MOFs) can be tuned by their metal centers and organic ligands. To reveal experimentally and theoretically the influence of metal centers and ligands on electrochemical performance of MOFs, three MOFs with copper or zinc centers and organic ligands of 2-methylimidazole (2MI) or 1,3,5-benzenetricarboxylic acid (H₃ BTC) are synthesized and characterized in this study. 2D and porous Cu-2MI exhibits a larger active area, faster electron transfer capability, and stronger adsorption capacity than bulk Cu-BTC and dodecahedron Zn-2MI. Density functional theory calculations of adsorption ability of three MOFs toward xanthine (XA), hypoxanthine (HXA), and malachite green (MG) prove that 2D Cu-2MI has the strongest adsorption energies to three targets. Rotating disk electrode measurements reveal that 2D Cu-2MI features the biggest intrinsic heterogeneous rate constant toward three analytes. On 2D Cu-2MI sensitive and selective monitoring of XA, HXA, and MG is then achieved using differential pulse voltammetry. Their monitoring in real samples on 2D Cu-2MI is accurate and comparable with that using high-performance liquid chromatography. In summary, regulation of electrochemical sensing features of MOFs is realized through defining selected metal centers and organic ligands.

Frustration Dynamics and Electron-Transfer Reorganization Energies in Wild-Type and Mutant Azurins

Long-range electron tunneling through metalloproteins is facilitated by evolutionary tuning of donor–acceptor electronic couplings, formal electrochemical potentials, and active-site reorganization energies. Although the minimal frustration of the folding landscape enables this tuning, residual frustration in the vicinity of the metallocofactor can allow conformational fluctuations required for protein function. We show here that the constrained copper site in wild-type azurin is governed by an intricate pattern of minimally frustrated local and distant interactions that together enable rapid electron flow to and from the protein. In contrast, sluggish electron transfer reactions (unfavorable reorganization energies) of active-site azurin variants are attributable to increased frustration near to as well as distant from the copper site, along with an exaggerated oxidation-state dependence of both minimally and highly frustrated interaction patterns.

Acceleration of oxidation promoted by laccase irradiation with red light

Irradiation with red light is able to improve yields and shorten the reaction time in enzymatic reactions.

Spiers Memorial Lecture: Activating Metal Sites for Biological Electron Transfer

Metal sites in biology often exhibit unique spectroscopic features that reflect novel geometric and electronic structures imposed by the protein that are key to reactivity. The Blue copper active site...

Mononuclear copper(ii) Schiff base complexes as effective models for phenoxazinone synthase

Copper(ii) complexes of tridentate (N2O) Schiff base ligands as efficient catalysts for 2-aminophenol oxidation to 2-aminophenoxazin-3-one with excellent reaction rates.

Altered coordination in a blue copper protein upon association with redox partner revealed by carbon-deuterium vibrational probes

Proteins tune the reactivity of metal sites; less understood is the impact of association with a redox partner. We demonstrate the utility of carbon-deuterium labels for selective analysis of delicate...

Recent advances in tuning redox properties of electron transfer centers in metalloenzymes catalyzing oxygen reduction reaction and H2 oxidation important for fuel cells design

Current fuel-cell catalysts for oxygen reduction reaction (ORR) and H₂ oxidation use precious metals and, for ORR, require high overpotentials. In contrast, metalloenzymes perform their respective reaction at low overpotentials using earth-abundant metals, making metalloenzymes ideal candidates for inspiring electrocatalytic design. Critical to the success of these enzymes are redox-active metal centers surrounding the enzyme active sites that ensure fast electron transfer (ET) to or away from the active site, by tuning the catalytic potential of the reaction as observed in multicopper oxidases but also in dictating the catalytic bias of the reaction as realized in hydrogenases. This review summarizes recent advances in studying these ET centers in multicopper oxidases and heme-copper oxidases that perform ORR and hydrogenases in carrying out H₂ oxidation. Insights gained from understanding how the reduction potential of the ET centers effects reactivity at the active site in both the enzymes and their models are provided.

1.3 V Inorganic Sequential Redox Chain with an All-Anionic Couple 1-/2- in a Single Framework

The relatively low symmetry of [3,3′-Co(1,2-C₂B₉H₁₁)₂]⁻ ([1]⁻), along with the high number of available substitution sites, 18 on the boron atoms and 4 on the carbon atoms, allows a fairly regioselective and stepwise chlorination of the platform and therefore a very controlled tuning of the electrochemical potential tuning. This is not so easily found in other systems, e.g., ferrocene. In this work, we show how a single platform with boron and carbon in the ligand, and only cobalt can produce a tuning of potentials in a stepwise manner in the 1.3 V range. The platform used is made of two icosahedra sharing one vertex. The E_1/2 tuning has been achieved from [1]⁻ by sequential chlorination, which has given potentials whose values increase sequentially and linearly with the number of chloro groups in the platform. [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ have been obtained, which are added to the existing [Cl-1]⁻, [Cl₂-1]⁻, [Cl₄-1]⁻, and [Cl₆-1]⁻ described earlier to give the 1.3 V range. It is envisaged to extend this range also sequentially by changing the metal from cobalt to iron. The last successful synthesis of the highest chlorinated derivatives of cobaltabis(dicarbollide) dates back to 1982, and since then, no more advances have occurred toward more substituted metallacarborane chlorinated compounds. [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ are made with an easy and fast method. The key point of the reaction is the use of the protonated form of [Co(C₂B₉H₁₁)₂]⁻, as a starting material, and the use of sulfuryl chloride, a less hazardous and easier to use chlorinating agent. In addition, we present a complete, spectroscopic, crystallographic, and electrochemical characterization, together with a study of the influence of the chlorination position in the electrochemical properties.

By sequential halogenation of [Co(C₂B₉H₁₁)₂]⁻ ([1]⁻) with chlorine, the [Cl₈-1]⁻, [Cl₁₀-1]⁻, and [Cl₁₂-1]⁻ derivatives of [1]⁻ have been prepared and isolated. The E_1/2 values increase sequentially and linearly with the number of chloro groups in the platform. If these potentials are added to the existing E_1/2 values due to [Cl-1]⁻, [Cl₂-1]⁻, [Cl₄-1]⁻, and [Cl₆-1]⁻ described earlier, a 1.3 V range is obtained. This allows tuning of the desired potentials for the purposes of nature.

Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator

We report the crystal structure of the copper-containing nitrite reductase (NirK) from the Gram-negative bacterium Sinorhizobium meliloti 2011 (Sm), together with complex structural alignment and docking studies with both non-cognate and the physiologically related pseudoazurins, SmPaz1 and SmPaz2, respectively. S. meliloti is a rhizobacterium used for the formulation of Medicago sativa bionoculants, and SmNirK plays a key role in this symbiosis through the denitrification pathway. The structure of SmNirK, solved at a resolution of 2.5 Å, showed a striking resemblance with the overall structure of the well-known Class I NirKs composed of two Greek key β-barrel domains. The activity of SmNirK is ~12% of the activity reported for classical NirKs, which could be attributed to several factors such as subtle structural differences in the secondary proton channel, solvent accessibility of the substrate channel, and that the denitrifying activity has to be finely regulated within the endosymbiont. In vitro kinetics performed in homogenous and heterogeneous media showed that both SmPaz1 and SmPaz2, which are coded in different regions of the genome, donate electrons to SmNirK with similar performance. Even though the energetics of the interprotein electron transfer (ET) process is not favorable with either electron donors, adduct formation mediated by conserved residues allows minimizing the distance between the copper centers involved in the interprotein ET process.