Proton-coupled electron transfer in cytochrome oxidase

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase

This review focuses on the type A cytochrome c oxidases (CcO), which are found in all mitochondria and also in several aerobic bacteria. CcO catalyzes the respiratory reduction of dioxygen (O₂) to water by an intriguing mechanism, the details of which are fairly well understood today as a result of research for over four decades. Perhaps even more intriguingly, the membrane-bound CcO couples the O₂ reduction chemistry to translocation of protons across the membrane, thus contributing to generation of the electrochemical proton gradient that is used to drive the synthesis of ATP as catalyzed by the rotary ATP synthase in the same membrane. After reviewing the structure of the core subunits of CcO, the active site, and the transfer paths of electrons, protons, oxygen, and water, we describe the states of the catalytic cycle and point out the few remaining uncertainties. Finally, we discuss the mechanism of proton translocation and the controversies in that area that still prevail.

A Water Dimer Shift Activates a Proton Pumping Pathway in the PR → F Transition of ba3 Cytochrome c Oxidase

Broken-symmetry density functional calculations have been performed on the [Fe_a3⁴⁺,Cu_B²⁺] state of the dinuclear center (DNC) for the P_R → F part of the catalytic cycle of ba₃ cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H₂O molecules in the DNC affects the pK_a values of the residue side chains of Tyr237 and His376⁺, which are crucial for proton transfer/pumping in ba₃ CcO from Tt. The calculated lowest energy structure of the DNC in the [Fe_a3⁴⁺,Cu_B²⁺] state (state F) is of the form Fe_a3⁴⁺═O^2-···Cu_B²⁺, in which the H₂O ligand that resulted from protonation of the OH^- ligand in the P_R state is dissociated from the Cu_B²⁺ site. The calculated Fe_a3⁴⁺═O^2- distance in F (1.68 Å) is 0.03 Å longer than that in P_R (1.65 Å), which can explain the different Fe_a3⁴⁺═O^2- stretching modes in P (804 cm^-1) and F (785 cm^-1) identified by resonance Raman experiments. In this F state, the Cu_B²⁺···O^2- (ferryl-oxygen) distance is only around 2.4 Å. Hence, the subsequent O_H state [Fe_a3³⁺-OH^--Cu_B²⁺] with a μ-hydroxo bridge can be easily formed, as shown by our calculations.

Preparation and reactivity of half-sandwich dioxygen complexes of ruthenium

The preparation of dioxygen complexes [Ru(η⁵-C₅Me₅)(η²-O₂){P(OR)₃}L]BPh₄ and their intramolecular oxygen transfer reaction in the presence of acid affording bis(phosphate) derivatives are described.

The reductive phase of Rhodobacter sphaeroides cytochrome c oxidase disentangled by CO ligation

Cytochrome c oxidase (CcO) is a membrane protein of the respiratory chain that catalytically reduces molecular oxygen (O2) to water while translocating protons across the membrane. The enzyme hosts two copper and two heme iron moieties (heme a/heme a3). The atomic details of the sequential steps that go along with this redox-driven proton translocation are a matter of debate. Particularly for the reductive phase of CcO that precedes oxygen binding experimental data are scarce. Here, we use CcO under anaerobic conditions where carbon monoxide (CO) is bound to heme a3 which in tandem with CuB forms the binuclear center (BNC). Fourier-transform infrared (FTIR) absorption spectroscopy is combined with electro-chemistry to probe different redox and protonation states populated by variation of the external electrostatic potential. With this approach, the redox behavior of heme a and the BNC could be separated and the corresponding redox potentials were determined. We also infer the protonation of one of the propionate side chains of heme a3 to correlate with the oxidation of heme a. Experimental changes in the local electric field surrounding CO bound to heme a3 are determined by their vibrational Stark effect and agree well with electrostatic computations. The comparison of experimental and computational results indicates that changes of the heme a3/CuB redox state are coupled to proton transfer towards heme a3. The latter supports the role of the heme a3 propionate D as proton loading site.

Cavity hydration dynamics in cytochrome c oxidase and functional implications

Cytochrome c oxidase (CcO) is a transmembrane protein that uses the free energy of O₂ reduction to generate the proton concentration gradient across the membrane. The regulation of competitive proton transfer pathways has been established to be essential to the vectorial transport efficiency of CcO, yet the underlying mechanism at the molecular level remains lacking. Recent studies have highlighted the potential importance of hydration-level change in an internal cavity that connects the proton entrance channel, the site of O₂ reduction, and the putative proton exit route. In this work, we use atomistic molecular dynamics simulations to investigate the energetics and timescales associated with the volume fluctuation and hydration-level change in this central cavity. Extensive unrestrained molecular dynamics simulations (accumulatively [Formula: see text]4 [Formula: see text]s) and free energy computations for different chemical states of CcO support a model in which the volume and hydration level of the cavity are regulated by the protonation state of a propionate group of heme a₃ and, to a lesser degree, the redox state of heme a and protonation state of Glu286. Markov-state model analysis of [Formula: see text]2-[Formula: see text]s trajectories suggests that hydration-level change occurs on the timescale of 100-200 ns before the proton-loading site is protonated. The computed energetic and kinetic features for the cavity wetting transition suggest that reversible hydration-level change of the cavity can indeed be a key factor that regulates the branching of proton transfer events and therefore contributes to the vectorial efficiency of proton transport.

The mechanism for oxygen reduction in cytochrome c dependent nitric oxide reductase (cNOR) as obtained from a combination of theoretical and experimental results

Bacterial NO-reductases (NOR) belong to the heme-copper oxidase (HCuO) superfamily, in which most members are O₂-reducing, proton-pumping enzymes. This study is one in a series aiming to elucidate the reaction mechanisms of the HCuOs, including the mechanisms for cellular energy conservation. One approach towards this goal is to compare the mechanisms for the different types of HCuOs, cytochrome c oxidase (CcO) and NOR, reducing the two substrates O₂ and NO. Specifically in this study, we describe the mechanism for oxygen reduction in cytochrome c dependent NOR (cNOR). Hybrid density functional calculations were performed on large cluster models of the cNOR binuclear active site. Our results are used, together with published experimental information, to construct a free energy profile for the entire catalytic cycle. Although the overall reaction is quite exergonic, we show that during the reduction of molecular oxygen in cNOR, two of the reduction steps are endergonic with high barriers for proton uptake, which is in contrast to oxygen reduction in CcO, where all reduction steps are exergonic. This difference between the two enzymes is suggested to be important for their differing capabilities for energy conservation. An additional result from this study is that at least three of the four reduction steps are initiated by proton transfer to the active site, which is in contrast to CcO, where electrons always arrive before the protons to the active site. The roles of the non-heme metal ion and the redox-active tyrosine in the active site are also discussed.

Mitochondrial cytochrome c oxidase: catalysis, coupling and controversies

Mitochondrial cytochrome c oxidase is a member of a diverse superfamily of haem-copper oxidases. Its mechanism of oxygen reduction is reviewed in terms of the cycle of catalytic intermediates and their likely chemical structures. This reaction cycle is coupled to the translocation of protons across the inner mitochondrial membrane in which it is located. The likely mechanism by which this occurs, derived in significant part from studies of bacterial homologues, is presented. These mechanisms of catalysis and coupling, together with current alternative proposals of underlying mechanisms, are critically reviewed.

Factors Determining the Rate and Selectivity of 4e-/4H+ Electrocatalytic Reduction of Dioxygen by Iron Porphyrin Complexes

Reactivity as well as selectivity are crucial in the activation and electrocatalytic reduction of molecular oxygen. Recent developments in the understanding of the mechanism of electrocatalytic O₂ reduction by iron porphyrin complexes in situ using surface enhanced resonance Raman spectroscopy coupled to rotating disc electrochemistry (SERRS-RDE) in conjunction with H/D isotope effects on electrocatalytic current reveals that the rate of O₂ reduction, ∼10⁴ to 10⁵ M^-1 s^-1 for simple iron porphyrins, is limited by the rate of O-O bond cleavage of an intermediate ferric peroxide species (Fe^III-OOH). SERRS-RDE probes the system in operando when it is under steady state such that any intermediate species that has a greater rate of formation relative to its rate of decay, including the rate determining species, would accumulate and can be identified. This technique is particularly well suited to investigate iron porphyrin electrocatalysts as the intense symmetric ligand vibrations allow determination of the oxidation and spin states of the bound iron with high fidelity. The rate of O₂ reduction could be tuned up by 3 orders of magnitude by incorporating residues in the catalyst design that can exert "push" or "pull" effects, that is, axial phenolate and thiolate ligands and distal arginine residues. Similarly the rate of O-O bond cleavage can be enhanced by several orders of magnitude upon incorporating a distal Cu site and installing the active site in a hydrophobic protein environment in synthetic models and biosynthetic protein scaffolds. The selectivity, however, is solely determined by the site of protonation of a ferric peroxide (Fe^III-OOH) intermediate and can be governed by installing preorganized second sphere residues in the distal pocket. The 4e^-/4H⁺ reduction of O₂ entails protonation of the distal oxygen of the Fe^III-OOH species, while 2e^-/2H⁺ reduction requires the proximal oxygen to be protonated. Mechanistic investigations of CO₂ reduction by iron porphyrins reveal that the rate-determining step is the C-O bond cleavage of a Fe^II-COOH species analogous to the O-O bond cleavage step of a Fe^III-OOH species in O₂ reduction. The selectivity, resulting in either CO or HCOOH, is determined by the site of protonation of this species. These similarities suggests that the chemical principles governing the rate and selectivity of reduction of small molecules like O₂, CO₂, NO_x, and SO_x may be quite similar in nature.

Synchronized Collective Proton-Assisted Electron Transfer in Solid State by Hydrogen-Bonding Ru(II)/Ru(III) Mixed-Valence Molecular Crystals

A proton-coupled electron transfer (PCET) reaction was widely studied with isolated organic molecules and metal complexes in solution in view of the biological catalytic reaction, while studying this reaction in the crystalline or solid-state phase, which has a novel example, would give insight into the rather internal environment of proteins without solvation and a creation of new molecular materials. We tried to crystallize a hydrogen-bonded (H-bonded) coordination polymer with one-dimensional nanoporous channels, formed from redox-active Ru^III complexes, [Ru^III(Hbim)₃] (Hbim^- = 2,2'-biimidazolate monoanion). As a result, a synchronized collective PCET phenomenon was observed for the molecular nanoporous crystal by novel solid-state cyclic voltammetry (CV), which could be measured by only setting some crystals on the electrode surface. The nanoporous crystals, {[Ru^III(Hbim)₃]}_n (1), are simultaneously induced to a synchronized collective Ru^IIRu^III mixed-valence state, {Ru^IIRu^III}_n, with alternating arrays of Ru^II and Ru^III complexes by PCET in a way of the reductive state of {Ru^IIRu^II}_n. Further, a new crystal with {Ru^IIRu^III}_n, {[Ru^II(H₂bim)(Hbim)₂][Ru^III(bim) (Hbim)₂][K(MeOBz)₆]}_n (2), was also prepared, and the solid-state CV revealed the same electrochemical behavior of {Ru^IIRu^III}_n with 1. The single crystal with {Ru^IIRu^III}_n of 2 was unusually a semiconductor with 5.12 × 10^-6 S/cm conductivity at 298 K by an impedance method (8.01 × 10^-6 S/cm by a direct-current method at 277 K). Thus, an unprecedented electron-hopping conductor driven by a low-barrier proton transfer through a PCET mechanism (E_a = 0.30 eV) was realized in the H-bonding molecular crystal with {Ru^IIRu^III}_n. Such studies on a PCET reaction in the crystalline state is not only worthwhile as a model of essential biological reactions without solvation, but also proposed to a new design of molecular materials to occur an electron transfer by using an intermolecular H-bond.

Symmetry-related proton transfer pathways in respiratory complex I

Complex I functions as the initial electron acceptor in aerobic respiratory chains of most organisms. This gigantic redox-driven enzyme employs the energy from quinone reduction to pump protons across its complete approximately 200-Å membrane domain, thermodynamically driving synthesis of ATP. Despite recently resolved structures from several species, the molecular mechanism by which complex I catalyzes this long-range proton-coupled electron transfer process, however, still remains unclear. We perform here large-scale classical and quantum molecular simulations to study the function of the proton pump in complex I from Thermus thermophilus The simulations suggest that proton channels are established at symmetry-related locations in four subunits of the membrane domain. The channels open up by formation of quasi one-dimensional water chains that are sensitive to the protonation states of buried residues at structurally conserved broken helix elements. Our combined data provide mechanistic insight into long-range coupling effects and predictions for site-directed mutagenesis experiments.

Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

Cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) with an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a₃ iron atom, with a bent Fe-C-O angle of ∼142°. In contrast, in the synchrotron structure, the Fe-CO bond is cleaved; CO relocates to a new site near Cu_B, which, in turn, moves closer to the heme a₃ iron by ∼0.38 Å. Structural comparison reveals that ligand binding to the heme a₃ iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a₃, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.

Serial femtosecond crystallography structure of cytochrome c oxidase at room temperature

Cytochrome c oxidase catalyses the reduction of molecular oxygen to water while the energy released in this process is used to pump protons across a biological membrane. Although an extremely well-studied biological system, the molecular mechanism of proton pumping by cytochrome c oxidase is still not understood. Here we report a method to produce large quantities of highly diffracting microcrystals of ba₃-type cytochrome c oxidase from Thermus thermophilus suitable for serial femtosecond crystallography. The room-temperature structure of cytochrome c oxidase is solved to 2.3 Å resolution from data collected at an X-ray Free Electron Laser. We find overall agreement with earlier X-ray structures solved from diffraction data collected at cryogenic temperature. Previous structures solved from synchrotron radiation data, however, have shown conflicting results regarding the identity of the active-site ligand. Our room-temperature structure, which is free from the effects of radiation damage, reveals that a single-oxygen species in the form of a water molecule or hydroxide ion is bound in the active site. Structural differences between the ba₃-type and aa₃-type cytochrome c oxidases around the proton-loading site are also described.

A High-Valent Non-Heme μ-Oxo Manganese(IV) Dimer Generated from a Thiolate-Bound Manganese(II) Complex and Dioxygen

This study deals with the unprecedented reactivity of dinuclear non-heme MnII -thiolate complexes with O2 , which dependent on the protonation state of the initial MnII dimer selectively generates either a di-μ-oxo or μ-oxo-μ-hydroxo MnIV complex. Both dimers have been characterized by different techniques including single-crystal X-ray diffraction and mass spectrometry. Oxygenation reactions carried out with labeled 18 O2 unambiguously show that the oxygen atoms present in the MnIV dimers originate from O2 . Based on experimental observations and DFT calculations, evidence is provided that these MnIV species comproportionate with a MnII precursor to yield μ-oxo and/or μ-hydroxo MnIII dimers. Our work highlights the delicate balance of reaction conditions to control the synthesis of non-heme high-valent μ-oxo and μ-hydroxo Mn species from MnII precursors and O2 .

Effects of membrane curvature and pH on proton pumping activity of single cytochrome bo3 enzymes

The molecular mechanism of proton pumping by heme-copper oxidases (HCO) has intrigued the scientific community since it was first proposed. We have recently reported a novel technology that enables the continuous characterisation of proton transport activity of a HCO and ubiquinol oxidase from Escherichia coli, cytochrome bo₃, for hundreds of seconds on the single enzyme level (Li et al. J Am Chem Soc 137 (2015) 16055-16063). Here, we have extended these studies by additional experiments and analyses of the proton transfer rate as a function of proteoliposome size and pH at the N- and P-side of single HCOs. Proton transport activity of cytochrome bo₃ was found to decrease with increased curvature of the membrane. Furthermore, proton uptake at the N-side (proton entrance) was insensitive to pH between pH6.4-8.4, while proton release at the P-side had an optimum pH of ~7.4, suggesting that the pH optimum is related to proton release from the proton exit site. Our previous single-enzyme experiments identified rare, long-lived conformation states of cytochrome bo₃ where protons leak back under turn-over conditions. Here, we analyzed and found that ~23% of cytochrome bo₃ proteoliposomes show ΔpH half-lives below 50s after stopping turnover, while only ~5% of the proteoliposomes containing a non-pumping mutant, E286C cytochrome bo₃ exhibit such fast decays. These single-enzyme results confirm our model in which HCO exhibit heterogeneous pumping rates and can adopt rare leak states in which protons are able to rapidly flow back.

Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O2 Reduction in Heme-Copper Oxidases

This study evaluates the reaction of a biomimetic heme-peroxo-copper complex, {[(DCHIm)(F8)FeIII]-(O22-)-[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O-O bond that produces FeIV═O, CuII-OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme-copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O-O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O-O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O-O homolysis mechanism. The consequences of these findings are discussed in relation to O-O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e- required for O-O cleavage derive from the cross-linked Tyr residue present at the active site.

Reversible Bond/Cation-Coupled Electron Transfer on Phenylenediamine-Based Rhodamine B and Its Application on Electrochromism

A biomimetic system on reversible bond-coupled electron transfer (BCET) has been proposed and investigated in a switchable Rh-N molecule with redox active subunits. We discover that energy barrier of C-N bond breaking is reduced dramatically to less than 1/7 (from 40.4 to 5.5 kcal/mol), and 1/3 of the oxidation potential is simultaneously lowered (from 0.67 to 0.43 V) with the oxidation of Rh-N. The concept, cation-coupled electron transfer (CCET), is highly recommended by analyzing existing proton coupled electron transfer (PCET) and metal coupled electron transfer (MCET) along with aforementioned BCET, which have same characteristic of transferring positive charges, such as proton, metal ion, and organic cation. Molecular switch can be controlled directly by electricity through BCET process. Solid electrochromic device was fabricated with extremely high coloration efficiency (720 cm²/C), great reversibility (no degradation for 600 cycles), and quick respond time (30 ms).

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na⁺ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521:48-53]. To elucidate its molecular mechanism for Na⁺ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na⁺ binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase

Cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water and uses the released free energy to pump protons against the transmembrane proton gradient. To better understand the proton-pumping mechanism of the wild-type (WT) CcO, much attention has been given to the mutation of amino acid residues along the proton translocating D-channel that impair, and sometimes decouple, proton pumping from the chemical catalysis. Although their influence has been clearly demonstrated experimentally, the underlying molecular mechanisms of these mutants remain unknown. In this work, we report multiscale reactive molecular dynamics simulations that characterize the free-energy profiles of explicit proton transport through several important D-channel mutants. Our results elucidate the mechanisms by which proton pumping is impaired, thus revealing key kinetic gating features in CcO. In the N139T and N139C mutants, proton back leakage through the D-channel is kinetically favored over proton pumping due to the loss of a kinetic gate in the N139 region. In the N139L mutant, the bulky L139 side chain inhibits timely reprotonation of E286 through the D-channel, which impairs both proton pumping and the chemical reaction. In the S200V/S201V double mutant, the proton affinity of E286 is increased, which slows down both proton pumping and the chemical catalysis. This work thus not only provides insight into the decoupling mechanisms of CcO mutants, but also explains how kinetic gating in the D-channel is imperative to achieving high proton-pumping efficiency in the WT CcO.

Splitting of the O-O bond at the heme-copper catalytic site of respiratory oxidases

Heme-copper oxidases catalyze the four-electron reduction of O₂ to H₂O at a catalytic site that is composed of a heme group, a copper ion (Cu_B), and a tyrosine residue. Results from earlier experimental studies have shown that the O-O bond is cleaved simultaneously with electron transfer from a low-spin heme (heme a/b), forming a ferryl state (P_R ; Fe⁴⁺=O^2-, Cu_B²⁺-OH^-). We show that with the Thermus thermophilus ba₃ oxidase, at low temperature (10°C, pH 7), electron transfer from the low-spin heme b to the catalytic site is faster by a factor of ~10 (τ ≅ 11 μs) than the formation of the P_R ferryl (τ ≅110 μs), which indicates that O₂ is reduced before the splitting of the O-O bond. Application of density functional theory indicates that the electron acceptor at the catalytic site is a high-energy peroxy state [Fe³⁺-O^--O^-(H⁺)], which is formed before the P_R ferryl. The rates of heme b oxidation and P_R ferryl formation were more similar at pH 10, indicating that the formation of the high-energy peroxy state involves proton transfer within the catalytic site, consistent with theory. The combined experimental and theoretical data suggest a general mechanism for O₂ reduction by heme-copper oxidases.

Why copper is preferred over iron for oxygen activation and reduction in haem-copper oxidases

Haem-copper oxidase (HCO) catalyses the natural reduction of oxygen to water using a haem-copper centre. Despite decades of research on HCOs, the role of non-haem metal and the reason for nature's choice of copper over other metals such as iron remains unclear. Here, we use a biosynthetic model of HCO in myoglobin that selectively binds different non-haem metals to demonstrate 30-fold and 11-fold enhancements in the oxidase activity of Cu- and Fe-bound HCO mimics, respectively, as compared with Zn-bound mimics. Detailed electrochemical, kinetic and vibrational spectroscopic studies, in tandem with theoretical density functional theory calculations, demonstrate that the non-haem metal not only donates electrons to oxygen but also activates it for efficient O-O bond cleavage. Furthermore, the higher redox potential of copper and the enhanced weakening of the O-O bond from the higher electron density in the d orbital of copper are central to its higher oxidase activity over iron. This work resolves a long-standing question in bioenergetics, and renders a chemical-biological basis for the design of future oxygen-reduction catalysts.

Formal Reduction Potentials of Difluorotyrosine and Trifluorotyrosine Protein Residues: Defining the Thermodynamics of Multistep Radical Transfer

Redox-active tyrosines (Ys) play essential roles in enzymes involved in primary metabolism including energy transduction and deoxynucleotide production catalyzed by ribonucleotide reductases (RNRs). Thermodynamic characterization of Ys in solution and in proteins remains a challenge due to the high reduction potentials involved and the reactive nature of the radical state. The structurally characterized α₃Y model protein has allowed the first determination of formal reduction potentials (E°') for a Y residing within a protein (Berry, B. W.; Martı́nez-Rivera, M. C.; Tommos, C. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 9739-9743). Using Schultz's technology, a series of fluorotyrosines (F_nY, n = 2 or 3) was site-specifically incorporated into α₃Y. The global protein properties of the resulting α₃(3,5)F₂Y, α₃(2,3,5)F₃Y, α₃(2,3)F₂Y and α₃(2,3,6)F₃Y variants are essentially identical to those of α₃Y. A protein film square-wave voltammetry approach was developed to successfully obtain reversible voltammograms and E°'s of the very high-potential α₃F_nY proteins. E°'(pH 5.5; α₃F_nY(O•/OH)) spans a range of 1040 ± 3 mV to 1200 ± 3 mV versus the normal hydrogen electrode. This is comparable to the potentials of the most oxidizing redox cofactors in nature. The F_nY analogues, and the ability to site-specifically incorporate them into any protein of interest, provide new tools for mechanistic studies on redox-active Ys in proteins and on functional and aberrant hole-transfer reactions in metallo-enzymes. The former application is illustrated here by using the determined α₃F_nY ΔE°'s to model the thermodynamics of radical-transfer reactions in F_nY-RNRs and to experimentally test and support the key prediction made.

Copper-Oxygen Complexes Revisited: Structures, Spectroscopy, and Reactivity

A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E. A.; Tolman, W. B. Chem. Rev. 2004, 104, 1047-1076), the field has seen significant expansion in the (1) range of cores synthesized and characterized, (2) amount of mechanistic work performed, particularly in the area of organic substrate oxidation, and (3) use of computational methods for both the corroboration and prediction of proposed intermediates. The scope of this review has been limited to well-characterized examples of copper-oxygen species but seeks to provide a thorough picture of the spectroscopic characteristics and reactivity trends of the copper-oxygen cores discussed.

Reactivity of the copper(iii)-hydroxide unit with phenols

Kinetic studies of the reactions of two previously characterized copper(iii)-hydroxide complexes (LCuOH and NO2 LCuOH, where L = N,N'-bis(2,6-diisopropylphenyl)-2,6-pyridine-dicarboxamide and NO2 L = N,N'-bis(2,6-diisopropyl-4-nitrophenyl)pyridine-2,6-dicarboxamide) with a series of para substituted phenols (XArOH where X = NMe2, OMe, Me, H, Cl, NO2, or CF3) were performed using low temperature stopped-flow UV-vis spectroscopy. Second-order rate constants (k) were determined from pseudo first-order and stoichiometric experiments, and follow the trends CF3 < NO2 < Cl < H < Me < OMe < NMe2 and LCuOH < NO2 LCuOH. The data support a concerted proton-electron transfer (CPET) mechanism for all but the most acidic phenols (X = NO2 and CF3), for which a more complicated mechanism is proposed. For the case of the reactions between NO2 ArOH and LCuOH in particular, competition between a CPET pathway and one involving initial proton transfer followed by electron transfer (PT/ET) is supported by multiwavelength global analysis of the kinetic data, formation of the phenoxide NO2 ArO- as a reaction product, observation of an intermediate [LCu(OH2)]+ species derived from proton transfer from NO2 ArOH to LCuOH, and thermodynamic arguments indicating that initial PT should be competitive with CPET.

Cytochrome c Oxidase Biogenesis and Metallochaperone Interactions: Steps in the Assembly Pathway of a Bacterial Complex

Biogenesis of mitochondrial cytochrome c oxidase (COX) is a complex process involving the coordinate expression and assembly of numerous subunits (SU) of dual genetic origin. Moreover, several auxiliary factors are required to recruit and insert the redox-active metal compounds, which in most cases are buried in their protein scaffold deep inside the membrane. Here we used a combination of gel electrophoresis and pull-down assay techniques in conjunction with immunostaining as well as complexome profiling to identify and analyze the composition of assembly intermediates in solubilized membranes of the bacterium Paracoccus denitrificans. Our results show that the central SUI passes through at least three intermediate complexes with distinct subunit and cofactor composition before formation of the holoenzyme and its subsequent integration into supercomplexes. We propose a model for COX biogenesis in which maturation of newly translated COX SUI is initially assisted by CtaG, a chaperone implicated in CuB site metallation, followed by the interaction with the heme chaperone Surf1c to populate the redox-active metal-heme centers in SUI. Only then the remaining smaller subunits are recruited to form the mature enzyme which ultimately associates with respiratory complexes I and III into supercomplexes.

Critical Aspects of Heme-Peroxo-Cu Complex Structure and Nature of Proton Source Dictate Metal-O(peroxo) Breakage versus Reductive O-O Cleavage Chemistry

The 4H+/4e- reduction of O2 to water, a key fuel-cell reaction also carried out in biology by oxidase enzymes, includes the critical O-O bond reductive cleavage step. Mechanistic investigations on active-site model compounds, which are synthesized by rational design to incorporate systematic variations, can focus on and resolve answers to fundamental questions, including protonation and/or H-bonding aspects, which accompany electron transfer. Here, we describe the nature and comparative reactivity of two low-spin heme-peroxo-Cu complexes, LS-4DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)4]+, and LS-3DCHIm, [(DCHIm)F8FeIII-(O22-)-CuII(DCHIm)3]+ (F8 = tetrakis(2,6-difluorophenyl)-porphyrinate; DCHIm = 1,5-dicyclohexylimidazole), toward different proton (4-nitrophenol and [DMF·H+](CF3SO3-)) (DMF = dimethyl-formamide) or electron (decamethylferrocene (Fc*)) sources. Spectroscopic reactivity studies show that differences in structure and electronic properties of LS-3DCHIm and LS-4DCHIm lead to significant differences in behavior. LS-3DCHIm is resistant to reduction, is unreactive toward weakly acidic 4-NO2-phenol, and stronger acids cleave the metal-O bonds, releasing H2O2. By contrast, LS-4DCHIm forms an adduct with 4-NO2-phenol, which includes an H-bond to the peroxo O-atom distal to Fe (resonance Raman (rR) spectroscopy and DFT). With addition of Fc* (2 equiv overall required), O-O reductive cleavage occurs, giving water, Fe(III), and Cu(II) products; however, a kinetic study reveals a one-electron rate-determining process, ket = 1.6 M-1 s-1 (-90 °C). The intermediacy of a high-valent [(DCHIm)F8FeIV═O] species is thus implied, and separate experiments show that one-electron reduction-protonation of [(DCHIm)F8FeIV═O] occurs faster (ket2 = 5.0 M-1 s-1), consistent with the overall postulated mechanism. The importance of the H-bonding interaction as a prerequisite for reductive cleavage is highlighted.

Decoding Proton-Coupled Electron Transfer with Potential-pKa Diagrams

Aqueous potential-pH diagrams, commonly called Pourbaix diagrams, were originally developed to study metal corrosion in the 1930s and 1940s. Pourbaix diagrams have since been widely adopted for use across chemistry disciplines, particularly for the study of aqueous proton-coupled electron transfer reactions. Despite this enormous versatility, a clear extension of analogous diagrams to nonaqueous solvents is lacking. The problem hinges on the difficulty of defining the nonaqueous solution pH. Here, we address this issue by reporting the development of diagrams based on nonaqueous pK_a scales. We experimentally construct diagrams for two transition-metal complexes that undergo proton-coupled electron transfer reactivity by recording their reduction potentials in the presence of acids with varying pK_a values. These experimental diagrams validate the potential-pK_a theory and provide valuable thermochemical information for proton-coupled electron transfer reactions, including for fleetingly stable species.

A New Domain of Reactivity for High-Valent Dinuclear [M(μ-O)2 M'] Complexes in Oxidation Reactions

The strikingly different reactivity of a series of homo- and heterodinuclear [(MIII )(μ-O)2 (MIII )']2+ (M=Ni; M'=Fe, Co, Ni and M=M'=Co) complexes with β-diketiminate ligands in electrophilic and nucleophilic oxidation reactions is reported, and can be correlated to the spectroscopic features of the [(MIII )(μ-O)2 (MIII )']2+ core. In particular, the unprecedented nucleophilic reactivity of the symmetric [NiIII (μ-O)2 NiIII ]2+ complex and the decay of the asymmetric [NiIII (μ-O)2 CoIII ]2+ core through aromatic hydroxylation reactions represent a new domain for high-valent bis(μ-oxido)dimetal reactivity.

OH cleavage from tyrosine: debunking a myth

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.

Energy-Related Small Molecule Activation Reactions: Oxygen Reduction and Hydrogen and Oxygen Evolution Reactions Catalyzed by Porphyrin- and Corrole-Based Systems

Globally increasing energy demands and environmental concerns related to the use of fossil fuels have stimulated extensive research to identify new energy systems and economies that are sustainable, clean, low cost, and environmentally benign. Hydrogen generation from solar-driven water splitting is a promising strategy to store solar energy in chemical bonds. The subsequent combustion of hydrogen in fuel cells produces electric energy, and the only exhaust is water. These two reactions compose an ideal process to provide clean and sustainable energy. In such a process, a hydrogen evolution reaction (HER), an oxygen evolution reaction (OER) during water splitting, and an oxygen reduction reaction (ORR) as a fuel cell cathodic reaction are key steps that affect the efficiency of the overall energy conversion. Catalysts play key roles in this process by improving the kinetics of these reactions. Porphyrin-based and corrole-based systems are versatile and can efficiently catalyze the ORR, OER, and HER. Because of the significance of energy-related small molecule activation, this review covers recent progress in hydrogen evolution, oxygen evolution, and oxygen reduction reactions catalyzed by porphyrins and corroles.

Using Biosynthetic Models of Heme-Copper Oxidase and Nitric Oxide Reductase in Myoglobin to Elucidate Structural Features Responsible for Enzymatic Activities

In biology, a heme-Cu center in heme-copper oxidases (HCOs) is used to catalyze the four-electron reduction of oxygen to water, while a heme-nonheme diiron center in nitric oxide reductases (NORs) is employed to catalyze the two-electron reduction of nitric oxide to nitrous oxide. Although much progress has been made in biochemical and biophysical studies of HCOs and NORs, structural features responsible for similarities and differences within the two enzymatic systems remain to be understood. Here, we discuss the progress made in the design and characterization of myoglobin-based enzyme models of HCOs and NORs. In particular, we focus on use of these models to understand the structure-function relations between HCOs and NORs, including the role of nonheme metals, conserved amino acids in the active site, heme types and hydrogen-bonding network in tuning enzymatic activities and total turnovers. Insights gained from these studies are summarized and future directions are proposed.

Rapid Electron Transfer within the III-IV Supercomplex in Corynebacterium glutamicum

Complex III in C. glutamicum has an unusual di-heme cyt. c₁ and it co-purifies with complex IV in a supercomplex. Here, we investigated the kinetics of electron transfer within this supercomplex and in the cyt. aa₃ alone (cyt. bc₁ was removed genetically). In the reaction of the reduced cyt. aa₃ with O₂, we identified the same sequence of events as with other A-type oxidases. However, even though this reaction is associated with proton uptake, no pH dependence was observed in the kinetics. For the cyt. bc₁-cyt. aa₃ supercomplex, we observed that electrons from the c-hemes were transferred to Cu_A with time constants 0.1–1 ms. The b-hemes were oxidized with a time constant of 6.5 ms, indicating that this electron transfer is rate-limiting for the overall quinol oxidation/O₂ reduction activity (~210 e⁻/s). Furthermore, electron transfer from externally added cyt. c to cyt. aa₃ was significantly faster upon removal of cyt. bc₁ from the supercomplex, suggesting that one of the c-hemes occupies a position near Cu_A. In conclusion, isolation of the III-IV-supercomplex allowed us to investigate the kinetics of electron transfer from the b-hemes, via the di-heme cyt. c₁ and heme a to the heme a₃-Cu_B catalytic site of cyt. aa₃.

Role of a Conserved Tyrosine Residue in the FMN-Heme Interdomain Electron Transfer in Inducible Nitric Oxide Synthase

The interdomain electron transfer (IET) between the flavin mononucleotide (FMN) and heme domains is essential in the biosynthesis of nitric oxide (NO) by the NO synthase (NOS) enzymes. A conserved tyrosine residue in the FMN domain (Y631 in human inducible NOS) was proposed to be a key part of the electron transfer pathway in the FMN/heme docked complex model. In the present study, the FMN-heme IET kinetics in the Y631F mutant and wild type of a bidomain oxygenase/FMN construct of human inducible NOS were determined by laser flash photolysis. The rate constant of the Y631F mutant is significantly decreased by ∼75% (compared to the wild type), showing that the tyrosine residue indeed facilitates the FMN-heme IET through the protein medium. The IET rate constant of the wild type protein decreases from 345 to 242 s^-1 on going from H₂O to 95% D₂O, giving a solvent kinetic isotope effect of 1.4. In contrast, no deuterium isotope effect was observed for the Tyr-to-Phe mutant. Moreover, an appreciable change in the wild type iNOS IET rate constant value was observed upon changing pH. These results indicate that the FMN-heme IET is proton coupled, in which the conserved tyrosine residue may play an important role.

Design and engineering of artificial oxygen-activating metalloenzymes

Many efforts are being made in the design and engineering of metalloenzymes with catalytic properties fulfilling the needs of practical applications. Progress in this field has recently been accelerated by advances in computational, molecular and structural biology. This review article focuses on the recent examples of oxygen-activating metalloenzymes, developed through the strategies of de novo design, miniaturization processes and protein redesign. Considerable progress in these diverse design approaches has produced many metal-containing biocatalysts able to adopt the functions of native enzymes or even novel functions beyond those found in Nature.

Molecular cloning and expression analysis of cytochrome c oxidase subunit II from Sitophilus zeamais

Cytochrome c oxidase subunit II (COX II) containing a dual core CuA active site is one of the core subunits of mitochondrial Cytochrome c oxidase (Cco), which plays a significant role in the physiological process. In this report, the full-length cDNA of COXII gene was cloned from Sitophilus zeamais, which had an open reading frame (ORF) of 684 bp encoding 227 amino acids residues. The predicted COXII protein had a molecular mass of 26.2 kDa with pI value of 6.37. multiple sequence alignment and phylogenetic analysis indicated that Sitophilus zeamais COXII had high sequence identity with the COXII of other insect species. The gene was subcloned into the expression vector pET-32a, and induced by isopropyl β-d-thiogalactopyranoside (IPTG) in E. coli Transetta (DE3) expression system. Finally the recombinant COXII with 6-His tag was purified using affinity chromatography with Ni(2+)-NTA agarose. Western Blotting (WB) showed the recombinant protein was about 44 kD, and the concentration of fusion protein was 50 μg/mL. UV-spectrophotometer and infrared spectrometer analysis showed that recombinant COXII could catalyze the oxidation of substrate Cytochrome C (Cyt c), and influenced by allyl isothiocyanate (AITC). By using molecular docking method, It was found that a sulfur atom of AITC structure could form a length of 2.9 Å hydrogen bond with Leu-31. These results suggested that tag-free COXII was functional and one of the action sites of AITC, which will be helpful to carry out a point mutation in binding sites for the future research.

A Protonated Water Cluster as a Transient Proton-Loading Site in Cytochrome c Oxidase

Cytochrome c oxidase (CcO) is a redox-driven proton pump that powers aerobic respiratory chains. We show here by multi-scale molecular simulations that a protonated water cluster near the active site is likely to serve as the transient proton-loading site (PLS) that stores a proton during the pumping process. The pKa of this water cluster is sensitive to the redox states of the enzyme, showing distinct similarities to other energy converting proton pumps.

Copper(I)-Dioxygen Adducts and Copper Enzyme Mechanisms

Primary copper(I)-dioxygen (O₂) adducts, cupric-superoxide complexes, have been proposed intermediates in copper-containing dioxygen-activating monooxygenase and oxidase enzymes. Here, mechanisms of C-H activation by reactive copper-(di)oxygen intermediates are discussed, with an emphasis on cupric-superoxide species. Over the past 25 years, many synthetically derived cupric-superoxide model complexes have been reported. Due to the thermal instability of these intermediates, early studies focused on increasing their stability and obtaining physical characterization. More recently, in an effort to gain insight into the possible substrate oxidation step in some copper monooxygenases, several cupric-superoxide complexes have been used as surrogates to probe substrate scope and reaction mechanisms. These cupric superoxides are capable of oxidizing substrates containing weak O-H and C-H bonds. Mechanistic studies for some enzymes and model systems have supported an initial hydrogen-atom abstraction via the cupric-superoxide complex as the first step of substrate oxidation.

Regulatory role of the respiratory supercomplex factors in Saccharomyces cerevisiae

The respiratory supercomplex factors (Rcf) 1 and 2 mediate supramolecular interactions between mitochondrial complexes III (ubiquinol-cytochrome c reductase; cyt. bc1) and IV (cytochrome c oxidase; CytcO). In addition, removal of these polypeptides results in decreased activity of CytcO, but not of cyt. bc1 In the present study, we have investigated the kinetics of ligand binding, the single-turnover reaction of CytcO with O2, and the linked cyt. bc1-CytcO quinol oxidation-oxygen-reduction activities in mitochondria in which Rcf1 or Rcf2 were removed genetically (strains rcf1Δ and rcf2Δ, respectively). The data show that in the rcf1Δ and rcf2Δ strains, in a significant fraction of the population, ligand binding occurs over a time scale that is ∼100-fold faster (τ ≅ 100 μs) than observed with the wild-type mitochondria (τ ≅ 10 ms), indicating structural changes. This effect is specific to removal of Rcf and not dissociation of the cyt. bc1-CytcO supercomplex. Furthermore, in the rcf1Δ and rcf2Δ strains, the single-turnover reaction of CytcO with O2 was incomplete. This observation indicates that the lower activity of CytcO is caused by a fraction of inactive CytcO rather than decreased CytcO activity of the entire population. Furthermore, the data suggest that the Rcf1 polypeptide mediates formation of an electron-transfer bridge from cyt. bc1 to CytcO via a tightly bound cyt. c We discuss the significance of the proposed regulatory mechanism of Rcf1 and Rcf2 in the context of supramolecular interactions between cyt. bc1 and CytcO.