Coordination of CuB in reduced and CO-liganded states of cytochrome bo3 from Escherichia coli. Is chloride ion a cofactor?

Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function

Heme-copper oxidases (HCOs) are terminal enzymes on the mitochondrial or bacterial respiratory electron transport chain, which utilize a unique heterobinuclear active site to catalyze the 4H+/4e- reduction of dioxygen to water. This process involves a proton-coupled electron transfer (PCET) from a tyrosine (phenolic) residue and additional redox events coupled to transmembrane proton pumping and ATP synthesis. Given that HCOs are large, complex, membrane-bound enzymes, bioinspired synthetic model chemistry is a promising approach to better understand heme-Cu-mediated dioxygen reduction, including the details of proton and electron movements. This review encompasses important aspects of heme-O2 and copper-O2 (bio)chemistries as they relate to the design and interpretation of small molecule model systems and provides perspectives from fundamental coordination chemistry, which can be applied to the understanding of HCO activity. We focus on recent advancements from studies of heme-Cu models, evaluating experimental and computational results, which highlight important fundamental structure-function relationships. Finally, we provide an outlook for future potential contributions from synthetic inorganic chemistry and discuss their implications with relevance to biological O2-reduction.

A water-soluble supramolecular complex that mimics the heme/copper hetero-binuclear site of cytochrome c oxidase

The O₂ adduct of an aqueous synthetic heme/copper model system built on a porphyrin/cyclodextrin supramolecular complex has been characterized.

In mitochondria, cytochrome c oxidase (CcO) catalyses the reduction of oxygen (O₂) to water by using a heme/copper hetero-binuclear active site. Here we report a highly efficient supramolecular approach for the construction of a water-soluble biomimetic model for the active site of CcO. A tridentate copper(ii) complex was fixed onto 5,10,15,20-tetrakis(4-sulfonatophenyl)porphinatoiron(iii) (Fe^IIITPPS) through supramolecular complexation between Fe^IIITPPS and a per-O-methylated β-cyclodextrin dimer linked by a (2,2′:6′,2′′-terpyridyl)copper(ii) complex (Cu^IITerpyCD₂). The reduced Fe^IITPPS/Cu^ITerpyCD₂ complex reacted with O₂ in an aqueous solution at pH 7 and 25 °C to form a superoxo-type Fe^III–O₂^–/Cu^I complex in a manner similar to CcO. The pH-dependent autoxidation of the O₂ complex suggests that water molecules gathered at the distal Cu site are possibly involved in the Fe^III–O₂^–/Cu^I superoxo complex in an aqueous solution. Electrochemical analysis using a rotating disk electrode demonstrated the role of the FeTPPS/CuTerpyCD₂ hetero-binuclear structure in the catalytic O₂ reduction reaction.

Oxygen as Acceptor

Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate-specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophosphate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and dimethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O₂ is served by two major oxidoreductases (oxidases), cytochrome bo₃ encoded by cyoABCDE and cytochrome bd encoded by cydABX. Terminal oxidases of aerobic respiratory chains of bacteria, which use O₂ as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo₃ and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo₃ and cytochrome bd. The E. coli membrane contains three types of quinones that all have an octaprenyl side chain (C₄₀). It has been proposed that the bo₃ oxidase can have two ubiquinone-binding sites with different affinities. "WHAT'S NEW" IN THE REVISED ARTICLE: The revised article comprises additional information about subunit composition of cytochrome bd and its role in bacterial resistance to nitrosative and oxidative stresses. Also, we present the novel data on the electrogenic function of appBCX-encoded cytochrome bd-II, a second bd-type oxidase that had been thought not to contribute to generation of a proton motive force in E. coli, although its spectral properties closely resemble those of cydABX-encoded cytochrome bd.

A combined quantum chemical and crystallographic study on the oxidized binuclear center of cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain. By reducing oxygen to water, it generates a proton gradient across the mitochondrial or bacterial membrane. Recently, two independent X-ray crystallographic studies ((Aoyama et al. Proc. Natl. Acad. Sci. USA 106 (2009) 2165-2169) and (Koepke et al. Biochim. Biophys. Acta 1787 (2009) 635-645)), suggested that a peroxide dianion might be bound to the active site of oxidized CcO. We have investigated this hypothesis by combining quantum chemical calculations with a re-refinement of the X-ray crystallographic data and optical spectroscopic measurements. Our data suggest that dianionic peroxide, superoxide, and dioxygen all form a similar superoxide species when inserted into a fully oxidized ferric/cupric binuclear site (BNC). We argue that stable peroxides are unlikely to be confined within the oxidized BNC since that would be expected to lead to bond splitting and formation of the catalytic P intermediate. Somewhat surprisingly, we find that binding of dioxygen to the oxidized binuclear site is weakly exergonic, and hence, the observed structure might have resulted from dioxygen itself or from superoxide generated from O(2) by the X-ray beam. We show that the presence of O(2) is consistent with the X-ray data. We also discuss how other structures, such as a mixture of the aqueous species (H(2)O+OH(-) and H(2)O) and chloride fit the experimental data.

Oxygen as Acceptor

Like most bacteria, Escherichia coli has a flexible and branched respiratory chain that enables the prokaryote to live under a variety of environmental conditions, from highly aerobic to completely anaerobic. In general, the bacterial respiratory chain is composed of dehydrogenases, a quinone pool, and reductases. Substrate specific dehydrogenases transfer reducing equivalents from various donor substrates (NADH, succinate, glycerophoshate, formate, hydrogen, pyruvate, and lactate) to a quinone pool (menaquinone, ubiquinone, and demethylmenoquinone). Then electrons from reduced quinones (quinols) are transferred by terminal reductases to different electron acceptors. Under aerobic growth conditions, the terminal electron acceptor is molecular oxygen. A transfer of electrons from quinol to O2 is served by two major oxidoreductases (oxidases), cytochrome bo3 and cytochrome bd. Terminal oxidases of aerobic respiratory chains of bacteria, which use O2 as the final electron acceptor, can oxidize one of two alternative electron donors, either cytochrome c or quinol. This review compares the effects of different inhibitors on the respiratory activities of cytochrome bo3 and cytochrome bd in E. coli. It also presents a discussion on the genetics and the prosthetic groups of cytochrome bo3 and cytochrome bd. The E. coli membrane contains three types of quinones which all have an octaprenyl side chain (C40). It has been proposed that the bo3 oxidase can have two ubiquinone-binding sites with different affinities. The spectral properties of cytochrome bd-II closely resemble those of cydAB-encoded cytochrome bd.

The chemistry of the CuB site in cytochrome c oxidase and the importance of its unique His-Tyr bond

The CuB metal center is at the core of the active site of the heme-copper oxidases, comprising a copper atom ligating three histidine residues one of which is covalently bonded to a tyrosine residue. Using quantum chemical methodology, we have studied the CuB site in several redox and ligand states proposed to be intermediates of the catalytic cycle. The importance of the His-Tyr crosslink was investigated by comparing energetics, charge, and spin distributions between systems with and without the crosslink. The His-Tyr bond was shown to decrease the proton affinity and increase the electron affinity of both Tyr-244 and the copper. A previously unnoticed internal electronic equilibrium between the copper atom and the tyrosine was observed, which seems to be coupled to the unique structure of the system. In certain states the copper and Tyr-244 compete for the unpaired electron, the localization of which is determined by the oxygenous ligand of the copper. This electronic equilibrium was found to be sensitive to the presence of a positive charge 10 A away from the center, simulating the effect of Lys-319 in the K-pathway of proton transfer. The combined results provide an explanation for why the heme-copper oxidases need two pathways of proton uptake, and why the K-pathway is active only in the second half of the reaction cycle.

Accommodation of two diatomic molecules in cytochrome bo: insights into NO reductase activity in terminal oxidases

Bacterial heme-copper terminal oxidases react quickly with NO to form a heme-nitrosyl complex, which, in some of these enzymes, can further react with a second NO molecule to produce N(2)O. Previously, we characterized the heme a(3)-NO complex formed in cytochrome ba(3) from Thermus thermophilus and the product of its low-temperature illumination. We showed that the photolyzed NO group binds to Cu(B)(I) to form an end-on NO-Cu(B) or a side-on copper-nitrosyl complex, which is likely to represent the binding characteristics of the second NO molecule at the heme-copper active site. Here we present a comparative study with cytochrome bo(3) from Escherichia coli. Both terminal oxidases are shown to catalyze the same two-electron reduction of NO to N(2)O. The EPR and resonance Raman signatures of the heme o(3)-NO complex are comparable to those of the a(3)-NO complex. However, low-temperature FTIR experiments reveal that photolysis of the heme o(3)-NO complex does not produce a Cu(B)-nitrosyl complex, but that instead, the NO remains unbound in the active-site cavity. Additional FTIR photolysis experiments on the heme-nitrosyl complexes of these terminal oxidases, in the presence of CO, demonstrate that an [o(3)-NO.OC-Cu(B)] tertiary complex can form in bo(3) but not in ba(3). We assign these differences to a greater iron-copper distance in the reduced form of bo(3) compared to that of ba(3). Because this difference in metal-metal distance does not appear to affect the NO reductase activity, our results suggest that the coordination of the second NO to Cu(B) is not an essential step of the reaction mechanism.

Copper-Carbon Bonds in Mechanistic and Structural Probing of Proteins as well as in Situations where Copper is a Catalytic or Receptor Site

While copper-carbon bonds are well appreciated in organometallic synthetic chemistry, such occurrences are less known in biological settings. By far, the greatest incidence of copper-carbon moieties is in bioinorganic research aimed at probing copper protein active site structure and mechanism; for example, carbon monoxide (CO) binding as a surrogate for O2. Using infrared (IR) spectroscopy, CO coordination to cuprous sites has proven to be an extremely useful tool for determining active site copper ligation (e.g., donor atom number and type). The coupled (hemocyanin, tyrosinase, catechol oxidase) and non-coupled (peptidylglycine α-hydroxylating monooxygenase, dopamine β-monooxygenase) binuclear copper proteins as well as the heme-copper oxidases (HCOs) have been studied extensively via this method. In addition, environmental changes within the vicinity of the active site have been determined based on shifts in the CO stretching frequencies, such as for copper amine oxidases, nitrite reductases and again in the binuclear proteins and HCOs. In many situations, spectroscopic monitoring has provided kinetic and thermodynamic data on CuI-CO formation and CO dissociation from copper(I); recently, processes occurring on a femtosecond timescale have been reported. Copper-cyano moieties have also been useful for obtaining insights into the active site structure and mechanisms of copper-zinc superoxide dismutase, azurin, nitrous oxide reductase, and multi-copper oxidases. Cyanide is a good ligand for both copper(I) and copper(II), therefore multiple physical-spectroscopic techniques can be applied. A more obvious occurrence of a “Cu-C” moiety was recently described for a CO dehydrogenase which contains a novel molybdenum-copper catalytic site. A bacterial copper chaperone (CusF) was recently established to have a novel d-π interaction comprised of copper(I) with the arene containing side-chain of a tryptophan amino acid residue. Meanwhile, good evidence exists that a plant receptor site (ETR1) utilizes copper(I) to sense ethylene, a growth hormone. A copper olfactory receptor has also been suggested. All of the above mentioned occurrences or uses of carbon-containing substrates and/or probes are reviewed and discussed within the framework of copper proteins and other relevant systems.

Charge parameterization of the metal centers in cytochrome c oxidase

Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near-neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between C--H bonds and C--C bonds at the border vanishes. We apply the procedure to the four redox-active metal centers of cytochrome c oxidase: Cu(A), haem a, haem a(3), and Cu(B). Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented.

Calculated reaction cycle of cytochrome c oxidase

The catalytic cycle of cytochrome c oxidase has been simulated by means of quantum mechanical calculations. The experimental energetics of the catalytic cycle is nearly reproduced. The atomic structures of the intermediates are suggested. In particular, the structures of nonactive "resting" intermediates are proposed.

Spectroscopic characterization of heme iron-nitrosyl species and their role in NO reductase mechanisms in diiron proteins

Nitric oxide (NO) plays an important role in cell signalling and in the mammalian immune response to infection. On its own, NO is a relatively inert radical, and when it is used as a signalling molecule, its concentration remains within the picomolar range. However, at infection sites, the NO concentration can reach the micromolar range, and reactions with other radical species and transition metals lead to a broad toxicity. Under aerobic conditions, microorganisms cope with this nitrosative stress by oxidizing NO to nitrate (NO3−). Microbial hemoglobins play an essential role in this NO-detoxifying process. Under anaerobic conditions, detoxification occurs via a 2-electron reduction of two NO molecules to N2O. In many bacteria and archaea, this NO-reductase reaction is catalyzed by diiron proteins. Despite the importance of this reaction in providing microorganisms with a resistance to the mammalian immune response, its mechanism remains ill-defined. Because NO is an obligatory intermediate of the denitrification pathway, respiratory NO reductases also provide resistance to toxic concentrations of NO. This family of enzymes is the focus of this review. Respiratory NO reductases are integral membrane protein complexes that contain a norB subunit evolutionarily related to subunit I of cytochrome c oxidase (Cc O). NorB anchors one high-spin heme b3 and one non-heme iron known as FeB, i.e ., analogous to CuB in Cc O. A second group of diiron proteins with NO-reductase activity is comprised of the large family of soluble flavoprotein A found in strict and facultative anaerobic bacteria and archaea. These soluble detoxifying NO reductases contain a non-heme diiron cluster with a Fe–Fe distance of 3.4 Å and are only briefly mentioned here as a promising field of research. This article describes possible mechanisms of NO reduction to N2O in denitrifying NO-reductase (NOR) proteins and critically reviews recent experimental results. Relevant theoretical model calculations and spectroscopic studies of the NO-reductase reaction in heme/copper terminal oxidases are also overviewed.

Thermodynamics of carbon monoxide photodissociation from the fully reduced cytochrome aa3 oxidase from Rb. sphaeroides

Photodissociation of the fully reduced carbonmonoxy bound cytochrome aa3 from Rb. sphaeroides results in ultrafast ligand transfer between heme a3 and CuB, which is followed by thermal dissociation from CuB on longer time scales. We have utilized photoacoustic calorimetry to obtain a detailed thermodynamic description of the mechanism of ligand photodissociation and transfer between heme a3 and CuB. Subsequent to ligand photodissociation an additional process, which has not been characterized previously, was observed with the lifetime of 485 ns at 18 degrees C and is coupled to a volume expansion of 3.3 ml mol(-1). From the temperature dependence, an activation barrier of 4 kcal mol(-1) was determined. We attribute the observed 500 ns process to changes in CuB ligation subsequent to ligand translocation. In a photoacoustic study on CO photodissociation from bovine heart aa3 oxidase, no volume changes were observed on the ns timescale, indicating that a different mechanism may control ligand dissociation and binding within the binuclear center of the bacterial and bovine enzymes.

Time-resolved thermodynamic profiles for CO photolsysis from the mixed valence form of bovine heart cytochrome c oxidase

Photoacoustic calorimetry has been utilized to probe the thermodynamics accompanying photodissociation of the CO mixed valence form of bovine heart cytochrome c oxidase (COMV CcO). At pH's below 9 photolysis of the COMV CcO results in three kinetic phases with the first phase occurring faster than the time resolution of the instrument (i.e., < approximately 50 ns), a second phase occurring with a lifetime of approximately 100 ns and a third phase occurring with a lifetime of approximately 2 micros. The corresponding volume and enthalpy changes for these processes are: DeltaH1, DeltaV1 = +79 +/- 10 kcal mol(-1), +9 +/- 1 mL mol(-1); DeltaH2, DeltaV2 = -79 +/- 5 kcal mol(-1), -9 +/- 2 mL mol(-1); DeltaH3, DeltaV3 = +54 +/- 7 kcal mol(-1), +8 +/- 1 mL mol(-1). At pH's above 9 only one phase is observed, a prompt phase occurring in < 50 ns. The overall volume change is negligible above pH 9 and the enthalpy change is +29 +/- 5 kcal mol(-1). The data are consistent with the prompt phase being associated with CO-Fe(a3) bond cleavage, CO-CuB+ bond formation, Fe(a3) low-spin to high-spin transition and fast electron transfer (ET) from heme a3 to heme a followed by proton transfer from Glu242 to Arg38 on an approximately 100 ns timescale. The slow phase is likely a combination of CO thermal dissociation from CuB and additional ET between heme a3 to heme a. Interestingly, this phase is not evident above pH 9 suggesting linkage between CO dissociation/ET and the protonation state of a group or groups near the binuclear center.

Structure and coordination of CuB in the Acidianus ambivalens aa3 quinol oxidase heme-copper center

The coordination environment of the Cu(B) center of the quinol oxidase from Acidianus ambivalens, a type B heme-copper oxygen reductase, was investigated by Fourier transform (FT) IR and extended X-ray absorption fine structure (EXAFS) spectroscopy. The comparative structural chemistry of dinuclear Fe-Cu sites of the different types of oxygen reductases is of great interest. Fully reduced A. ambivalens quinol oxidase binds CO at the heme a (3) center, with nu(CO)=1,973 cm(-1). On photolysis, the CO migrated to the Cu(B) center, forming a Cu (B) (I) -CO complex with nu(CO)=2,047 cm(-1). Raising the temperature of the samples to 25 degrees C did not result in a total loss of signal in the FTIR difference spectrum although the intensity of these signals was reduced sevenfold. This observation is consistent with a large energy barrier against the geminate rebinding of CO to the heme iron from Cu(B), a restricted limited access at the active-site pocket for a second binding, and a kinetically stable Cu(B)-CO complex in A. ambivalens aa (3). The Cu(B) center was probed in a number of different states using EXAFS spectroscopy. The oxidized state was best simulated by three histidines and a solvent O scatterer. On reduction, the site became three-coordinate, but in contrast to the bo (3) enzyme, there was no evidence for heterogeneity of binding of the coordinated histidines. The Cu(B) centers in both the oxidized and the reduced enzymes also appeared to contain substoichiometric amounts (0.2 mol equiv) of nonlabile chloride ion. EXAFS data of the reduced carbonylated enzyme showed no difference between dark and photolyzed forms. The spectra could be well fit by 2.5 imidazoles, 0.5 Cl(-) and 0.5 CO ligands. This arrangement of scatterers would be consistent with about half the sites remaining as unligated Cu(his)(3) and half being converted to Cu(his)(2)Cl(-)CO, a 50/50 ratio of Cu(his)(2)Cl(-) and Cu(his)(3)CO, or some combination of these formulations.

Photothermal studies of CO photodissociation from mixed valence Escherichia coli cytochrome bo3

Here, we report the volume and enthalpy changes accompanying CO photodissociation from the mixed valence form of cytochrome bo3 oxidase from Escherichia coli. The results of photoacoustic calorimetry indicate two kinetic phases with distinct volume and enthalpy changes accompanying CO photodissociation from heme o3 and its transfer to CuB. The first phase occurring on a timescale of <50 ns is characterized by a volume decrease of -1.3+/-0.3 mL mol-1 and enthalpy change of 32+/-1.6 kcal mol-1. Subsequently, a volume increase of 2.9 mL mol-1 with an enthalpy change of -5.3+/-2.5 kcal mol-1 is observed with the lifetime of approximately 250 ns (this phase has not been detected in previous optical studies). These volume and enthalpy changes differ from the volume and enthalpy changes observed for CO dissociation from fully reduced cytochrome bo3 oxidase indicating that the heme o3/CuB active site dynamics are affected by the redox state of heme b.

A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

The formation of water chains in cytochrome c oxidase (CcO) is studied by molecular dynamics (MD). Focus is on water chains in the K channel that can supply a proton to the binuclear center (the heme a3 Fe/CuB region), the site of O2 reduction. By assessing the presence of chains of any length on a short time scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. Chains from the entry of the channel on the inner membrane to Thr359 (Rhodobacter sphaeroides numbering) are often present but are blocked at that point until a rotation of the Thr359 side chain occurs, permitting formation of chains from Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains are found connecting Thr359 and the binuclear center. Instead, waters hydrogen bond from Thr359 to the hydroxyl of the heme a3 farnesyl and then continue to the binuclear center via Tyr288, which has been identified as a source of a proton for O2 reduction. Three hydrogen-bonded waters are found to be present in the binuclear center after a sufficiently long simulation time. One is ligated to the CuB and could be associated with a water (or hydroxyl) identified in the crystal structure as the fourth ligand of CuB. The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O2 reduction. The third water is located where O2 is often suggested to reside in mechanistic studies of O2 reduction.

Implications of ligand binding studies for the catalytic mechanism of cytochrome c oxidase

The reaction of oxidized bovine heart cytochrome c oxidase (CcO) with one equivalent of hydrogen peroxide results in the formation of two spectrally distinct species. The yield of these two forms is controlled by the ionization of a group with a pK(a) of 6.6. At basic pH, where this group is deprotonated, an intermediate called P dominates (P, because it was initially believed to be a peroxy compound). At acidic pH where the group is protonated, a different species, called F (ferryl intermediate) is obtained. We previously proposed that the only difference between these two species is the presence of one proton in the catalytic center of F that is absent in P. It is now suggested that the catalytic center of this F form has the same redox and protonation state as a second ferryl intermediate produced at basic pH by two equivalents of hydrogen peroxide; the role of the second equivalent of H(2)O(2) is that of a proton donor in the conversion of P to F. Two chloride-binding sites have been detected in oxidized CcO. One site is located at the binuclear center; the second site was identified from the sensitivity of g=3 signal of cytochrome a to chloride in the EPR spectra of oxidized CcO. Turnover of CcO releases chloride from the catalytic center into the medium probably by one of the hydrophobic channels, proposed for oxygen access, with an orientation parallel to the membrane plane. Chloride in the binuclear center is most likely not involved in CcO catalysis. The influence of the second chloride site upon several reactions of CcO has been assessed. No correlation was found between chloride binding to the second site and the reactions that were examined.

Two Sites of Interaction of Anions with Cytochrome a in Oxidized Bovine Cytochrome c Oxidase

An interaction between cytochrome a in oxidized cytochrome c oxidase (CcO) and anions has been characterized by EPR spectroscopy. Those anions that affect the EPR g = 3 signal of cytochrome a can be divided into two groups. One group consists of halides (Cl-, Br-, and I-) and induces an upfield shift of the g = 3 signal. Nitrogen-containing anions (CN-, NO2-, N3-, NO3-) are in the second group and shift the g = 3 signal downfield. The shifts in the EPR spectrum of CcO are unrelated to ligand binding to the binuclear center. The binding properties of one representative from each group, azide and chloride, were characterized in detail. The dependence of the shift on chloride concentration is consistent with a single binding site in the isolated oxidized enzyme with a Kd of approximately 3 mm. In mitochondria, the apparent Kd was found to be about four times larger than that of the isolated enzyme. The data indicate it is the chloride anion that is bound to CcO, and there is a hydrophilic size-selective access channel to this site from the cytosolic side of the mitochondrial membrane. An observed competition between azide and chloride is interpreted by azide binding to three sites: two that are apparent in the x-ray structure plus the chloride-binding site. It is suggested that either Mg2+ or Arg-438/Arg-439 is the chloride-binding site, and a mechanism for the ligand-induced shift of the g = 3 signal is proposed.

Active site structure of the aa3 quinol oxidase of Acidianus ambivalens

The membrane bound aa(3)-type quinol:oxygen oxidoreductase from the hyperthermophilic archaeon, Acidianus ambivalens, which thrives at a pH of 2.5 and a temperature of 80 degrees C, has several unique structural and functional features as compared to the other members of the heme-copper oxygen reductase superfamily, but shares the common redox-coupled, proton-pumping function. To better understand the properties of the heme a(3)-Cu(B) catalytic site, a resonance Raman spectroscopic study of the enzyme under a variety of conditions and in the presence of various ligands was carried out. Assignments of several heme vibrational modes as well as iron-ligand stretching modes are made to serve as a basis for comparing the structure of the enzyme to that of other oxygen reductases. The CO-bound oxidase has conformations that are similar to those of other oxygen reductases. However, the addition of CO to the resting enzyme does not generate a mixed valence species as in the bovine aa(3) enzyme. The cyanide complex of the oxidized enzyme of A. ambivalens does not display the high stability of its bovine counterpart, and a redox titration demonstrates that there is an extensive heme-heme interaction reflected in the midpoint potentials of the cyanide adduct. The A. ambivalens oxygen reductase is very stable under acidic conditions, but it undergoes an earlier alkaline transition than the bovine enzyme. The A. ambivalens enzyme exhibits a redox-linked reversible conformational transition in the heme a(3)-Cu(B) center. The pH dependence and H/D exchange demonstrate that the conformational transition is associated with proton movements involving a group or groups with a pK(a) of approximately 3.8. The observed reversibility and involvement of protons in the redox-coupled conformational transition support the proton translocation model presented earlier. The implications of such conformational changes are discussed in relation to general redox-coupled proton pumping mechanisms in the heme-copper oxygen reductases.

Could the tyrosine-histidine ligand to CuB in cytochrome c oxidase be coordinatively labile? Implications from a quantum chemical model study of histidine substitutional lability and the effects of the covalent tyrosine-histidine cross-link

Density functional theory calculations have been used to evaluate the effects of inter-ring interactions within a covalently linked histidine-tyrosine cofactor such as that which is a ligand to the Cu(B) centre in cytochrome c oxidases and to investigate the energetics of histidine substitution at the Cu(B) centre. Small, but significant, perturbations of the redox potentials and/or p K(a) values of the histidine imidazole, the tyrosine phenol and the copper ion are found. The Cu(B)-N(cofactor) bond is estimated to be weaker than the Cu(B)-N(histidine coligand) bonds in the Cu(B)(I) state and in the Cu(B) (II) state when the cofactor is oxidized, by approximately 13 kJ/mol and approximately 23 kJ/mol, respectively. The calculations reveal that displacement of a histidine ligand from the Cu(B) centre, as is suggested in proposals of "histidine cycle" mechanisms for proton pumping in cytochrome c oxidases, is only energetically feasible if accompanied by protonation of the histidine imidazole and coupled to an endothermic process. It is proposed that the histidine-tyrosine cofactor ought to be considered as the substitutionally labile ligand to Cu(B) as the covalent crosslink would ensure displacement of the cofactor from Cu(B)-driven helix deformation. It is estimated that this process could store up to approximately 70 kJ/mol, which, based upon thermodynamic considerations, is sufficient for the pumping of two protons in the later steps (reductive phase) of the catalytic cycle. Ramifications of this proposition for the mechanism of proton pumping in cytochrome c oxidases are discussed.

Metal-bridging mechanism for O-O bond cleavage in cytochrome C oxidase

Density functional theory (B3LYP) has been applied to large models of the Fe(II)-Cu(I) binuclear center in cytochrome oxidase, investigating the mechanism of O-O bond cleavage in the mixed valence form of the enzyme. To comply with experimental information, the O(2) molecule is assumed to be bridging between iron and copper during the O-O bond cleavage, leading to the formation of a ferryl-oxo group and a cupric hydroxide. In accord with previous suggestions, the calculations show that it is energetically feasible to take the fourth electron needed in this reaction from the tyrosine residue that is cross-linked to one of the copper ligands, resulting in the formation of a neutral tyrosyl radical. However, the calculations indicate that simultaneous transfer of an electron and a proton from the tyrosine to dioxygen during bond cleavage leads to a barrier more than 10 kcal/mol higher than that experimentally determined. This may be overcome in two ways. If an extra proton in the binuclear center assists in the mechanism, the calculated reaction barrier agrees with experiment. Alternatively, the fourth electron might initially be supplied by a residue in the vicinity other than the tyrosine.

Kinetics of intramolecular electron transfer in cytochrome bo3 from Escherichia coli

We have examined the temperature dependence of the intramolecular electron transfer (ET) between heme b and heme o(3) in CO-mixed valence cytochrome bo(3) (Cbo) from Escherichia coli. Upon photolysis of CO-mixed valence Cbo rapid ET occurs between heme o(3) and heme b with a rate constant of 2.2 x 10(5) s(-1) at room temperature. The corresponding rate of CO recombination is found to be 86 s(-1). From Eyring plots the activation energies for these two processes are found to be 3.4 kcal/mol and 6.7 kcal/mol for the ligand binding and ET reactions, respectively. Using variants of the Marcus equation the reorganization energy (lambda), electronic coupling factor (H(AB)), and the ET distance were found to be 1.4 +/- 0.2 eV, (2 +/- 1) x 10(-3) eV, and 9 +/- 1 A, respectively. These values are quite distinct from the analogous values previously obtained for bovine heart cytochrome c oxidase (CcO) (0.76 eV, 9.9 x 10(-5) eV, 13.2 A). The differences in mechanisms/pathways for heme b/heme o(3) and heme a/heme a(3) ET suggested by the Marcus parameters can be attributed to structural changes at the Cu(B) site upon change in oxidation state as well as differences in electronic coupling pathways between Heme b and heme o(3).

Characterization of the zinc-binding site of the histidine-proline-rich glycoprotein associated with rabbit skeletal muscle AMP deaminase

The AMP deaminase-associated variant of histidine-proline-rich glycoprotein (HPRG) is isolated from rabbit skeletal muscle by a modification of the protocol previously used for the purification of AMP deaminase. This procedure yields highly pure HPRG suitable for investigation by x-ray absorption spectroscopy of the zinc-binding behavior of the protein. X-ray absorption spectroscopy analysis of a 2:1 zinc-HPRG complex shows that zinc is bound to the protein, most probably in a dinuclear cluster where each Zn(2+) ion is coordinated, on average, by three histidine ligands and one heavier ligand, likely a sulfur from a cysteine. 11 cysteines of HPRG from different species are totally conserved, suggesting that five disulfide bridges are essential for the proper folding of the protein. At least another cysteine is present at different positions in the histidine-proline-rich domain of HPRG in all species, suggesting that this cysteine is the candidate for zinc ligation in the muscle variant of HPRG. The same conclusion is likely to be true for the six histidines used by the protein as zinc ligands. The presence in muscle HPRG of a specific zinc-binding site permits us to envisage the addition of HPRG into the family of metallochaperones. In this view, HPRG may enhance the in vivo stability of metalloenzymes such as AMP deaminase.

Activation volumes for intramolecular electron transfer in Escherichia coli cytochrome bo(3)

In this report we describe the activation volumes associated with the heme-heme electron transfer (ET) and CO rebinding to the binuclear center subsequent to photolysis of the CO-mixed-valence derivative of Escherichia coli cytochrome bo(3) (Cbo). The activation volumes associated with the heme-heme ET (k=1.2 x 10(5) s(-1)), and CO rebinding (k=57 s(-1)) are found to be +27.4 ml/mol and -2.6 ml/mol, respectively. The activation volume associated with the rebinding of CO is consistent with previous Cu X-ray absorption studies of Cbo where a structural change was observed at the Cu(B) site (loss of a histidine ligand) due to a change in the redox state of the binuclear center. In addition, the volume of activation for the heme-heme ET was found to be quite distinct from the activation volumes obtained for heme-heme ET in bovine heart Cytochrome c oxidase. Differences in mechanisms/pathways for heme b/heme o(3) and heme a/heme a(3) ET are suggested based on the associated activation volumes and previously obtained Marcus parameters.

Cytochrome bo(3) from Escherichia coli: the binding and turnover of nitric oxide

The reaction of nitric oxide (NO) with fast and reduced cytochrome bo(3)(cyt bo(3)) from Escherichia coli has been investigated. The stoichiometry of NO binding to cyt bo(3) was determined using an NO electrode in the [NO] range 1-14 microM. Under reducing conditions, the initial decrease in [NO] following the addition of cyt bo(3) corresponded to binding of 1 NO molecule per cyt bo(3) functional unit. After this "rapid" NO binding phase, there was a slow, but significant rate of NO consumption ( approximately 0.3molNOmol bo(3)(-1)min(-1)), indicating that cyt bo(3) possesses a low level of NO reductase activity. The binding of NO to fast pulsed enzyme was also investigated. The results show that in the [NO] range used (1-14 microM) both fast and pulsed oxidised cyt bo(3) bind NO with a stoichiometry of 1:1 with an observed dissociation constant of K(d)=5.6+/-0.6 microM and that NO binding was inhibited by the presence of Cl(-). The binding of nitrite to the binuclear centre causes spectral changes similar to those observed upon NO binding to fast cyt bo(3). These results are discussed in relation to the model proposed by Wilson and co-workers [FEBS Lett. 414 (1997) 281] where the binding of NO to Cu(B)(II) results in the formation of the nitrosonium (Cu(B)(I)-NO(+)) complex. NO(+) then reacts with OH(-), a Cu(B) ligand, to form nitrite, which can bind at the binuclear centre. This work suggests for the first time that the binding of NO to oxidised cyt bo(3) does result in the reduction of Cu(B).

The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides

The structure of cytochrome c oxidase from Rhodobacter sphaeroides has been solved at 2.3/2.8A (anisotropic resolution). This high-resolution structure revealed atomic details of a bacterial terminal oxidase including water molecule positions and a potential oxygen pathway, which has not been reported in other oxidase structures. A comparative study of the wild-type and the EQ(I-286) mutant enzyme revealed structural rearrangements around E(I-286) that could be crucial for proton transfer in this enzyme. In the structure of the mutant enzyme, EQ(I-286), which cannot transfer protons during oxygen reduction, the side-chain of Q(I-286) does not have the hydrogen bond to the carbonyl oxygen of M(I-107) that is seen in the wild-type structure. Furthermore, the Q(I-286) mutant has a different arrangement of water molecules and residues in the vicinity of the Q side-chain. These differences between the structures could reflect conformational changes that take place upon deprotonation of E(I-286) during turnover of the wild-type enzyme, which could be part of the proton-pumping machinery of the enzyme.

MHYT, a new integral membrane sensor domain

MHYT, a new conserved protein domain with a likely signaling function, is described. This domain consists of six transmembrane segments, three of which contain conserved methionine, histidine, and tyrosine residues that are projected to lie near the outer face of the cytoplasmic membrane. In Synechocystis sp. PCC6803, this domain forms the N-terminus of the sensor histidine kinase Slr2098. In Pseudomonas aeruginosa and several other organisms, the MHYT domain forms the N-terminal part of a three-domain protein together with previously described GGDEF and EAL domains, both of which have been associated with signal transduction due to their presence in likely signaling proteins. In Bacillus subtilis YkoW protein, an additional PAS domain is found between the MHYT and GGDEF domains. A ykoW null mutant of B. subtilis did not exhibit any growth alterations, consistent with a non-essential, signaling role of this protein. A model of the membrane topology of the MHYT domain indicates that its conserved residues could coordinate one or two copper ions, suggesting a role in sensing oxygen, CO, or NO.

Structures and proton-pumping strategies of mitochondrial respiratory enzymes

Enzymes of the mitochondrial respiratory chain serve as proton pumps, using the energy made available from electron transfer reactions to transport protons across the inner mitochondrial membrane and create an electrochemical gradient used for the production of ATP. The ATP synthase enzyme is reversible and can also serve as a proton pump by coupling ATP hydrolysis to proton translocation. Each of the respiratory enzymes uses a different strategy for performing proton pumping. In this work, the strategies are described and the structural bases for the action of these proteins are discussed in light of recent crystal structures of several respiratory enzymes. The mechanisms and efficiency of proton translocation are also analyzed in terms of the thermodynamics of the substrate transformations catalyzed by these enzymes.

pH-dependent structural changes at the Heme-Copper binuclear center of cytochrome c oxidase

The resonance Raman spectra of the aa3 cytochrome c oxidase from Rhodobacter sphaeroides reveal pH-dependent structural changes in the binuclear site at room temperature. The binuclear site, which is the catalytic center of the enzyme, possesses two conformations at neutral pH, assessed from their distinctly different Fe-CO stretching modes in the resonance Raman spectra of the CO complex of the fully reduced enzyme. The two conformations (alpha and beta) interconvert reversibly in the pH 6-9 range with a pKa of 7.4, consistent with Fourier transform infrared spectroscopy measurements done at cryogenic temperatures (D.M. Mitchell, J.P. Sapleigh, A.M.Archer, J.O. Alben, and R.B.Gennis, 1996, Biochemistry 35:9446-9450). It is postulated that the different structures result from a change in the position of the Cu(B) atom with respect to the CO due to the presence of one or more ionizable groups in the vicinity of the binuclear center. The conserved tyrosine residue (Tyr-288 in R. sphaeroides, Tyr-244 in the bovine enzyme) that is adjacent to the oxygen-binding pocket or one of the histidines that coordinate Cu(B) are possible candidates. The existence of an equilibrium between the two conformers at physiological pH and room temperature suggests that the conformers may be functionally involved in enzymatic activity.

Probing molecular structure of dioxygen reduction site of bacterial quinol oxidases through ligand binding to the redox metal centers

Cytochromes bo and bd are structurally unrelated terminal ubiquinol oxidases in the aerobic respiratory chain of Escherichia coli. The high-spin heme o-CuB binuclear center serves as the dioxygen reduction site for cytochrome bo, and the heme b595-heme d binuclear center for cytochrome bd. CuB coordinates three histidine ligands and serves as a transient ligand binding site en route to high-spin heme o one-electron donor to the oxy intermediate, and a binding site for bridging ligands like cyanide. In addition, it can protect the dioxygen reduction site through binding of a peroxide ion in the resting state, and connects directly or indirectly Tyr288 and Glu286 to carry out redox-driven proton pumping in the catalytic cycle. Contrary, heme b595 of cytochrome bd participate a similar role to CuB in ligand binding and dioxygen reduction but cannot perform such versatile roles because of its rigid structure.

Redox-linked conformational changes in bovine heart cytochrome c oxidase: picosecond time-resolved fluorescence studies of cyanide complex

Picosecond time-resolved fluorescence studies are carried out on cyanide-inhibited and heat-modified cytochrome c oxidase in aqueous lauryl maltoside surfactant solution, as well as in an aqueous vesicle, to understand the conformational changes associated with electron transfer and proton pumping activity of the enzyme. The tryptophan fluorescence decay profiles follow a four exponential model, which also matches the lifetime maxima obtained in a maximum entropy method analysis. The fast lifetime components are highly affected by the reduction and chemical modification of the enzyme. Changes in these lifetime components are related to the conformational changes in the vicinity of the heme centers of the enzyme. The cyanide-inhibited enzyme in the oxidized form shows a fluorescence decay profile similar to that of the native oxidized form, indicating that the conformational changes due to cyanide binding are very small. However, reduction of the cyanide-inhibited enzyme that leaves cyanide bound heme alpha3 oxidized causes a large increase in the fluorescence lifetimes, which indicates very significant conformational changes due to electron transfer to the dinuclear Cu(A) and heme alpha centers. A comparison of the tryptophan fluorescence decay of various other modified forms of the enzyme leads us to propose that the possible site of conformational coupling is located near heme alpha instead of the binuclear heme alpha3-Cu(B) center.

The cytochrome c oxidase from Paracoccus denitrificans does not change the metal center ligation upon reduction

Cytochrome c oxidase catalyzes the reduction of oxygen to water. This process is accompanied by the vectorial transport of protons across the mitochondrial or bacterial membrane ("proton pumping"). The mechanism of proton pumping is still a matter of debate. Many proposed mechanisms require structural changes during the reaction cycle of cytochrome c oxidase. Therefore, the structure of the cytochrome c oxidase was determined in the completely oxidized and in the completely reduced states at a temperature of 100 K. No ligand exchanges or other major structural changes upon reduction of the cytochrome c oxidase from Paracoccus denitrificans were observed. The three histidine Cu(B) ligands are well defined in the oxidized and in the reduced states. These results are hardly compatible with the "histidine cycle" mechanisms formulated previously.