Flash photolysis of the carbon monoxide compounds of wild-type and mutant variants of cytochrome bo from Escherichia coli

Construction of histidine-tagged yeast mitochondrial cytochrome c oxidase for facile purification of mutant forms

Yeast CcO (cytochrome c oxidase) has been developed as a facile system for the production and analysis of mutants of a mitochondrial form of CcO for mechanistic studies. First, a 6H tag (His6 tag) was fused to the C-terminus of a nuclear-encoded subunit of CcO from yeast Saccharomyces cerevisiae. This allowed efficient purification of a WT (wild-type) mitochondrial CcO, 6H-WT (yeast CcO with a 6H tag on the nuclear-encoded Cox13 subunit), with a recovery yield of 45%. Its catalytic-centre activity [≈180 e·s(-1) (electrons per s)], UV-visible signatures of oxidized and reduced states and ability to form the P(M) ['peroxy' (but actually a ferryl/radical state)] and F (ferryl) intermediates confirm normal functioning of the histidine-tagged protein. Point mutations were introduced into subunit I of the 6H-WT strain. All mutants were screened for their ability to assemble CcO and grow on respiratory substrate. One such mutant [6H-E243DI (the 6H-WT strain with an additional mutation of E243D in mitochondrial DNA-encoded subunit I)] was purified and showed ~50% of the 6H-WT catalytic-centre activity, consistent with the effects of the equivalent mutation in bacterial oxidases. Mutations in both the D and the H channels affect respiratory growth and these effects are discussed in terms of their putative roles in CcO mechanism.

B3LYP study on reduction mechanisms from O2 to H2O at the catalytic sites of fully reduced and mixed-valence bovine cytochrome c oxidases

Reduction mechanisms of oxygen molecule to water molecules in the fully reduced (FR) and mixed-valence (MV) bovine cytochrome c oxidases (CcO) have been systematically examined based on the B3LYP calculations. The catalytic cycle using four electrons and four protons has been also shown consistently. The MV CcO catalyses reduction to produce one water molecule, while the FR CcO catalyses to produce two water molecules. One water molecule is added into vacant space between His240 and His290 in the catalytic site. This water molecule constructs the network of hydrogen bonds of Tyr244, farnesyl ethyl, and Thr316 that is a terminal residue of the K-pathway. It plays crucial roles for the proton transfer to the dioxygen to produce the water molecules in both MV and FR CcOs. Tyr244 functions as a relay of the proton transfer from the K-pathway to the added water molecule, not as donors of a proton and an electron to the dioxygen. The reduction mechanisms of MV and FR CcOs are strictly distinguished. In the FR CcO, the Cu atom at the Cu(B) site maintains the reduced state Cu(I) during the process of formation of first water molecule and plays an electron storage. At the final stage of formation of first water molecule, the Cu(I) atom releases an electron to Fe-O. During the process of formation of second water molecule, the Cu atom maintains the oxidized state Cu(II). In contrast with experimental proposals, the K-pathway functions for formation of first water molecule, while the D-pathway functions for second water molecule. The intermediates, P(M), P(R), F, and O, obtained in this work are compared with those proposed experimentally.

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.

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).

Functional analogues of the dioxygen reduction site in cytochrome oxidase: mechanistic aspects and possible effects of Cu(B)

Catalytic reduction of O(2) and H(2)O(2) by new synthetic analogues of the heme/Cu site in cytochrome c and ubiquinol oxidases has been studied in aqueous buffers. Among the synthetic porphyrins yet reported, those employed in this study most faithfully mimic the immediate coordination environment of the Fe/Cu core. Under physiologically relevant conditions, these biomimetic catalysts reproduce key aspects of the O(2) and H(2)O(2) chemistry of the enzyme. When deposited on an electrode surface, they catalyze the selective reduction of O(2) to H(2)O at potentials comparable to the midpoint potential of cytochrome c. The pH dependence of the half-wave potentials and other data are consistent with O-O bond activation at these centers proceeding via a slow generation of a formally ferric-hydroperoxo intermediate, followed by its rapid reduction to the level of water. This kinetics is analogous to that proposed for the O-O reduction step at the heme/Cu site. It minimizes the steady-state concentration of the catalytic intermediate whose decomposition would release free H(2)O(2). The maximum catalytic rate constants of O(2) reduction by the ferrous catalyst and of H(2)O(2) reduction by both ferric and ferrous catalysts are comparable to those reported for cytochrome oxidase. The oxidized catalyst also displays catalase activity. Comparison of the catalytic properties of the biomimetic complexes in the FeCu and Cu-free forms indicates that, in the regime of rapid electron flux, Cu does not significantly affect the turnover frequency or the stability of the catalysts, but it suppresses superoxide-releasing autoxidation of an O(2)-catalyst adduct. The distal Cu also accelerates O(2) binding and minimizes O-O bond homolysis in the reduction of H(2)O(2).

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.

Electron transfer at the low-spin heme b of cytochrome bo(3) induces an environmental change of the catalytic enhancer glutamic acid-286

Intramolecular proton transfer of heme-copper oxidases is performed via the K- and the transmembrane D-channels. A carboxyl group conserved in a subgroup of heme-copper oxidases, located within the D-channel close to the binuclear center (=glutamic acid-286 in cytochrome bo(3) from Escherichia coli) is essential for proton pumping. Upon electron transfer to the fully oxidized (FO) enzyme, this amino acid has been shown to undergo a cyanide-independent environmental change. The redox-induced environmental transition of glutamic acid-286 is preserved in the site-directed mutant Y288F, which has lost its Cu(B) binding capacity. Furthermore, the mixed-valence (MV) redox state of cytochrome bo(3) (in which Cu(B) and high-spin heme are reduced, whereas the low-spin heme stays oxidized) was prepared by anaerobic exposure of the protein to carbon monoxide. This complex was converted (i) to the FO state by reaction with the caged dioxygen donor mu-peroxo) (mu-hydroxo) bis [bis (bipyridyl) cobalt (III)] and (ii) to the fully reduced (FR) state via caged electron donors; the environmental change of glutamic acid-286 could be observed only upon reduction. Taken together, these results from two different lines of evidence clearly show that the redox transition of the low-spin heme b center alone triggers the change in the chemical environment of this acidic side chain. It is suggested that glutamic acid-286 is a kinetic enhancer of proton translocation, which is energetically favoured in mesophilic oxidases.

Transient formation of ubisemiquinone radical and subsequent electron transfer process in the Escherichia coli cytochrome bo

To elucidate a unique mechanism for the quinol oxidation in the Escherichia coli cytochrome bo, we applied pulse radiolysis technique to the wild-type enzyme with or without a single bound ubiquinone-8 at the high-affinity quinone binding site (Q(H)), using N-methylnicotinamide (NMA) as an electron mediator. With the ubiquinone bound enzyme, the reduction of the oxidase occurred in two phases as judged from kinetic difference spectra. In the faster phase, the transient species with an absorption maximum at 440 nm, a characteristic of the formation of ubisemiquinone anion radical, appeared within 10 micros after pulse radiolysis. In the slower phase, a decrease of absorption at 440 nm was accompanied by an increase of absorption at 428 and 561 nm, characteristic of the reduced form. In contrast, with the bound ubiquinone-8-free wild-type enzyme, NMA radicals directly reduced hemes b and o, though the reduction yield was low. These results indicate that a pathway for an intramolecular electron transfer from ubisemiquinone anion radical at the Q(H) site to heme b exists in cytochrome bo. The first-order rate constant of this process was calculated to be 1.5 x 10(3) s(-1) and is comparable to a turnover rate for ubiquinol-1. The rate constant for the intramolecular electron transfer decreased considerably with increasing pH, though the yields of the formation of ubisemiquinone anion radical and the subsequent reduction of the hemes were not affected. The pH profile was tightly linked to the stability of the bound ubisemiquinone in cytochrome bo [Ingledew, W. J., Ohnishi, T., and Salerno, J. C. (1995) Eur. J. Biochem. 227, 903-908], indicating that electron transfer from the bound ubisemiquinone at the Q(H) site to the hemes slows down at the alkaline pH where the bound ubisemiquinone can be stabilized. These findings are consistent with our previous proposal that the bound ubiquinone at the Q(H) site mediates electron transfer from the low-affinity quinol oxidation site in subunit II to low-spin heme b in subunit I.

Angular dependences of perpendicular and parallel mode electron paramagnetic resonance of oxidized beef heart cytochrome c oxidase

Cytochrome c oxidase catalyzes the reduction of oxygen to water with a concomitant conservation of energy in the form of a transmembrane proton gradient. The enzyme has a catalytic site consisting of a binuclear center of a copper ion and a heme group. The spectroscopic parameters of this center are unusual. The origin of broad electron paramagnetic resonance (EPR) signals in the oxidized state at rather low resonant field, the so-called g' = 12 signal, has been a matter of debate for over 30 years. We have studied the angular dependence of this resonance in both parallel and perpendicular mode X-band EPR in oriented multilayers containing cytochrome c oxidase to resolve the assignment. The "slow" form and compounds formed by the addition of formate and fluoride to the oxidized enzyme display these resonances, which result from transitions between states of an integer-spin multiplet arising from magnetic exchange coupling between the five unpaired electrons of high spin Fe(III) heme a(3) and the single unpaired electron of Cu(B). The first successful simulation of similar signals observed in both perpendicular and parallel mode X-band EPR spectra in frozen aqueous solution of the fluoride compound of the closely related enzyme, quinol oxidase or cytochrome bo(3), has been reported recently (Oganesyan et al., 1998, J. Am. Chem. Soc. 120:4232-4233). This suggested that the exchange interaction between the two metal ions of the binuclear center is very weak (|J| approximately 1 cm(-1)), with the axial zero-field splitting (D approximately 5 cm(-1)) of the high-spin heme dominating the form of the ground state. We show that this model accounts well for the angular dependences of the X-band EPR spectra in both perpendicular and parallel modes of oriented multilayers of cytochrome c oxidase derivatives and that the experimental results are inconsistent with earlier schemes that use exchange coupling parameters of several hundred wavenumbers.

Role of copper during carbon monoxide binding to terminal oxidases

Under fully reduced conditions, reassociation kinetics of CO were studied in several terminal oxidases containing copper in their binuclear center. The purified Paracoccus denitrificans ba3-type quinol oxidase was found to recombine with CO monophasically (tau 25-30 ms) like oxidases of the bo type from Escherichia coli, the caa3 type from Bacillus halodurans FTU, and the bo type from Methylobacillus flagellatum KT. Oxidase of the aa3 type from bovine heart recombined with CO monophasically at a higher rate (tau 16-19 ms) than the studied copper-containing bacterial oxidases. After prolonged incubation in the presence of CO, oxidases of the ba3 and aa3 types changed their CO-binding properties. The contribution of the slow component was diminished while new fast components arose. Measurement of the metal content in the oxidases indicated that during the incubation, the enzymes lost their copper, the process being accompanied by the appearance of a fast CO recombination rate resembling that of the non-copper oxidases of the bd type from E. coli and the bb type from Bacillus halodurans FTU. This points to a role of copper in CO binding by terminal oxidases.

Angular dependence of electron paramagnetic resonances of an azide-NO complex of cytochrome c oxidase: orientation of the haem-copper axis in cytochrome aa3 from ox heart

The orientation dependence of the EPR signals arising from the azide-nitric oxide complex of cytochrome oxidase was investigated using oriented multilayers of mitochondrial membranes from ox heart. Variations in line shape of the DeltaMS=1 signal of the triplet state were apparent, whilst the DeltaMS=2 transitions between g=4.7 and 3.9 varied in intensity as the angle of the applied magnetic field was varied. These half-field signals were maximal with the field parallel to the membrane plane. A model of the bi-liganded azide-nitric oxide complex has been constructed, in which the nitric oxide is bound to the high-spin haem in a bent configuration, with the Fe-N=O plane at 60-90 degrees to the membrane plane and the azide bound to the copper, distal from the haem. In addition, angular variations of the signals at g'=11 and g' around 3.5, derived from an integer-spin complex, were also observed.

Structural and functional analysis of deficient mutants in subunit I of cytochrome c oxidase from Saccharomyces cerevisiae

Four point mutations in subunit I of cytochrome c oxidase from Saccharomyces cerevisiae that had been selected for respiratory incompetence but still contained spectrally detectable haem aa3 were analysed. The isolated mutant enzymes exhibited minor band shifts in their optical spectra and contained all eleven subunits. However, steady state activities were only a few percent compared to wild type enzyme. Using a comprehensive experimental approach, we first checked the integrity of the enzyme preparations and then identified the specific functional defect. The results are discussed using information from the recently solved structures of cytochrome c oxidase at 2.8 A. Mutation 167N is positioned between haem a and a conserved glutamate residue (E243). It caused a distortion of the EPR signal of haem a and shifted its midpoint potential by 54 mV to the negative. The high-resolution structure suggests that the primary reason for the low activity of the mutant enzyme could be that asparagine in position 67 might form a stable hydrogen bond to E243, which is part of a proposed proton channel. Cytochrome c oxidase isolated from mutant T316K did not meet our criteria for homogeneity and was therefore omitted from further analysis. Mutants G352V and V380M exhibited an impairment of electron transfer from haem a to a3 and ligand binding to the binuclear centre was affected. In mutant V380M also the midpoint potential of CuB was shifted by 65 mV to the positive. The results indicated for these two mutants changes primarily associated with the binuclear centre, possibly associated with an interference in the routes and/or sites of protonation which are required for stable formation of the catalytic intermediates. This interpretation is discussed in the light of the high resolution structure.

Comparison of the ligand-binding properties of native and copper-less cytochromes bo from Escherichia coli

The binding of four anionic ligands, cyanide, fluoride, azide and formate, to cytochrome bo purified from Escherichia coli cells grown with a copper supplement (+Cu cyt.bo) is described. Membrane-bound cytochrome bo that lacks the copper component, CuB, of its active site can be prepared from cells grown under conditions where the availability of copper is limited by the presence of a CuI chelator, 2,2'-bicinchinonic acid. The ligand-binding properties of this copper-less enzyme (-Cu cyt.bo) are compared with those of +Cu cyt. bo. As judged from near-UV/visible spectroscopic changes, cyanide forms a low-spin complex with +Cu cyt.bo, whereas azide, fluoride and formate form high-spin complexes. The pH-dependences of binding suggest that for all four of these anionic ligands, both the rates of binding and the binding affinities are primarily dependent on the concentration of their protonated forms. -Cu cyt.bo, which shows less than 15% of the duroquinol oxidase activity of +Cu cyt.bo, binds cyanide, azide and fluoride, but with greatly decreased affinity (<1/30, 1/2000 and 1/2500 respectively at pH5.5 compared with +Cu cyt.bo). The complex of azide with -Cu cyt.bo still seems to be high-spin and azide binding to -Cu cyt.bo is still pH-dependent, although less so than azide binding to +Cu cyt.bo.

The topology of CuA in relation to the other metal centres in cytochrome-c oxidase of Saccharomyces cerevisiae as determined by analysis of second-site reversions

Second-site revertants were selected from a respiratory-deficient mutant carrying the mutation D369N located in a loop between helices IX and X close to H376 and H378, the proposed ligands of haem a3 and haem a, respectively. A reversion was observed in subunit II, in the vicinity of the CuA ligands. This same reversion compensates the subunit I deficiency mutation, S140L, assumed to be near H62, the second putative histidine ligand to haem a. These data enable us to propose a three-dimensional topology in which CuA in subunit II is located on top of the Positive-side of subunit I and in proximity to all three of its metal centres.

Mechanistic and phenomenological features of proton pumps in the respiratory chain of mitochondria

Various direct, indirect (kinetic and thermodynamic), and combined mechanisms have been proposed to explain the conversion of redox energy into a transmembrane protonmotive force (delta p) by enzymatic complexes of respiratory chains. The conceptual evolution of these models is examined. The characteristics of thermodynamic coupling between redox transitions of electron carriers and scalar proton transfer in cytochrome c oxidase and its possible involvement in proton pumping is discussed. Other aspects dealt with in this paper are: (i) variability of <--H+/e- stoichiometries, in cytochrome c oxidase and cytochrome c reductase and its mechanistic implications; (ii) possible models by which the reduction of dioxygen to water at the binuclear heme-copper center of protonmotive oxidases can be directly involved in proton pumping. Finally a unifying concept for proton pumping by the redox complexes of respiratory chain is presented.

The reaction of hydrogen peroxide with pulsed cytochrome bo from Escherichia coli

The reaction of hydrogen peroxide (H2O2) with pulsed cytochrome bo leads to characteristic spectral changes in the enzyme. The difference spectrum shows minima at 401, 494 and 628 nm, and maxima at 420, approximately 468, 526 and 556 nm. delta epsilon 420-epsilon 401 is in the range 73-86 mM-1.cm-1 and delta epsilon 556-epsilon 628 is 7.7-9.6 mM-1.cm-1 (taking delta epsilon 560-epsilon 580 for the reduced minus oxidised spectrum to be 20.5 mM-1.cm-1). The stoichiometry of the reaction, determined by titration of the spectral changes, is 1:1. The second order rate constant for the reaction, which is 1.0-1.5 x 10(3) M-1.s-1 at 20 degrees C, is independent of pH over the range 6.5-8.0. The product of the reaction decays with a first-order rate constant in the range 1-4 x 10(-4) s-1, so the Kd value is apparently in the range 0.05-0.40 microM. The spectral changes observed immediately after quinol-induced turnover, or during steady-state turnover induced by hydrazine or by carbon monoxide, are qualitatively the same as those induced by H2O2 though of lower amplitude. H2O2 addition perturbs the hydrazine-induced or CO-induced steady states by increasing the amplitude of the spectral changes, but there is no qualitative change. From this observation, and the 1:1 stoichiometry of the reaction, we conclude that the intermediate induced by H2O2, which we term F., requires donation of only two electrons to the enzyme from an external source.

Facilitated intramolecular electron transfer in cytochrome bo-type ubiquinol oxidase initiated upon reaction of the fully reduced enzyme with dioxygen

Flow-flash and double-flash studies of the reaction of fully reduced bo-type quinol oxidase with oxygen have revealed that a single turnover of the enzyme proceeds much faster than mammalian cytochrome c oxidase. Facilitated intramolecular electron transfer in the bo-type oxidase with k > 5 x 10(4) s-1 at pH 7.4 and 20 degrees C is responsible for this fast turnover. The kinetics of this reaction indicates that the oxygen reduction does not require electron exchange between quinol oxidase molecules, each having three metal centers. Thus, a bound quinol in the fully reduced enzyme is suggested to be an electron source for complete reduction of dioxygen into water supplementing electrons provided by the metal centers. A single turnover of the quinol oxidase yields a novel spectral species with a Soret maximum at 415 nm corresponding to a 'pulsed' state of mammalian cytochrome c oxidase.

Time-resolved optical absorption studies of intramolecular electron transfer in cytochrome c oxidase

Intramolecular electron transfer and conformational changes in cytochrome c oxidase were studied at room temperature following the photodissociation of CO bound to mixed-valence enzyme (cytochrome a3(2+)-CO CuB+ cytochrome a3+ CuA2+) and fully reduced enzyme. Time-resolved optical absorption difference spectra were collected in the Soret region on time scales of nanoseconds to milliseconds using a gated optical spectrometric multichannel analyzer. A global exponential fitting procedure combined with a singular value decomposition method was used to analyze the transient difference spectra at various times following CO photolysis. The analysis shows that at least two processes, with apparent lifetimes of 1.4 microseconds and 11.1 ms, are present following the photodissociation of CO bound to the fully reduced enzyme. These are attributed to a conformational change and CO recombination at the cytochrome a3 site, respectively. Global analysis of the mixed-valence CO complex transient difference spectra showed the presence of five intermediates with apparent lifetimes of 1.0 microseconds, 5.2 microseconds, 83.7 microseconds, 10.5 ms, and 25.3 ms. The data on a microsecond time scale are consistent with a mechanism involving a conformational change at cytochrome a3, followed by electron transfer from cytochrome a3 to cytochrome a with subsequent electron transfer to CuA. One of the two processes on a millisecond time scale is attributed to CO recombination and the other to a structural rearrangement or heme-heme electron transfer. On the basis of this mechanism, the kinetics and the absorption spectra of the intermediates involved in the conformational and electron transfer dynamics of the mixed-valence enzyme were determined.

The cytochrome oxidase superfamily of redox-driven proton pumps

Most respiratory oxidases of eukaryotic and prokaryotic organisms are members of a superfamily of enzymes that couple the redox energy available from the reduction of molecular oxygen to the mechanism of pumping protons across the membrane. The recent applications of site-directed mutagenesis and of a variety of spectroscopic techniques have allowed major advances in our understanding of the structure and function of these proteins.