Reaction of formate with the fast form of cytochrome oxidase: a model for the fast to slow conversion

A Resonance Raman Marker Band Characterizes the Slow and Fast Form of Cytochrome c Oxidase

Cytochrome c oxidase (CcO) in its as-isolated form is known to exist in a slow and fast form, which differ drastically in their ability to bind oxygen and other ligands. While preparation methods have been established that yield either the fast or the slow form of the protein, the underlying structural differences have not been identified yet. Here, we have performed surface enhanced resonance Raman (SERR) spectroscopy of CcO immobilized on electrodes in both forms. SERR spectra obtained in resonance with the heme a₃ metal-to-ligand charge transfer (MLCT) transition at 650 nm displayed a sharp vibrational band at 748 or 750 cm^-1 when the protein was in its slow or fast form, respectively. DFT calculations identified the band as a mode of the His-419 ligand that is sensitive to the oxygen ligand and the protonation state of Tyr-288 within the binuclear complex. Potential-dependent SERR spectroscopy showed a redox-induced change of this band around 525 mV versus Ag/AgCl exclusively for the fast form, which coincides with the redox potential of the Tyr-O/Tyr-O^- transition. Our data points to a peroxide ligand in the resting state of CcO for both forms. The observed frequencies and redox sensitivities of the Raman marker band suggest that a radical Tyr-288 is present in the fast form and a protonated Tyr-288 in the slow form.

Computational prediction and in vitro analysis of potential physiological ligands of the bile acid binding site in cytochrome c oxidase

A conserved bile acid site has been crystallographically defined in the membrane domain of mammalian and Rhodobacter sphaeroides cytochrome c oxidase (RsCcO). Diverse amphipathic ligands were shown previously to bind to this site and affect the electron transfer equilibrium between heme a and a3 cofactors by blocking the K proton uptake path. Current studies identify physiologically relevant ligands for the bile acid site using a novel three-pronged computational approach: ROCS comparison of ligand shape and electrostatics, SimSite3D comparison of ligand binding site features, and SLIDE screening of potential ligands by docking. Identified candidate ligands include steroids, nicotinamides, flavins, nucleotides, retinoic acid, and thyroid hormones, which are predicted to make key protein contacts with the residues involved in bile acid binding. In vitro oxygen consumption and ligand competition assays on RsCcO wildtype and its Glu101Ala mutant support regulatory activity and specificity of some of these ligands. An ATP analog and GDP inhibit RsCcO under low substrate conditions, while fusidic acid, cholesteryl hemisuccinate, retinoic acid, and T3 thyroid hormone are more potent inhibitors under both high and low substrate conditions. The sigmoidal kinetics of RsCcO inhibition in the presence of certain nucleotides is reminiscent of previously reported ATP inhibition of mammalian CcO, suggesting regulation involving the conserved core subunits of both mammalian and bacterial oxidases. Ligand binding to the bile acid site is noncompetitive with respect to cytochrome c and appears to arrest CcO in a semioxidized state with some resemblance to the "resting" state of the enzyme.

Cytochrome c oxidase: chemistry of a molecular machine

The plethora of proposed chemical models attempting to explain the proton pumping reactions catalyzed by the CcO complex, especially the number of recent models, makes it clear that the problem is far from solved. Although we have not discussed all of the models proposed to date, we have described some of the more detailed models in order to illustrate the theoretical concepts introduced at the beginning of this section on proton pumping as well as to illustrate the rich possibilities available for effecting proton pumping. It is clear that proton pumping is effected by conformational changes induced by oxidation/reduction of the various redox centers in the CcO complex. It is for this reason that the CcO complex is called a redox-linked proton pump. The conformational changes of the proton pump cycle are usually envisioned to be some sort of ligand-exchange reaction arising from unstable geometries upon oxidation/reduction of the various redox centers. However, simple geometrical rearrangements, as in the Babcock and Mitchell models are also possible. In any model, however, hydrogen bonds must be broken and reformed due to conformational changes that result from oxidation/reduction of the linkage site during enzyme turnover. Perhaps the most important point emphasized in this discussion, however, is the fact that proton pumping is a directed process and it is electron and proton gating mechanisms that drive the proton pump cycle in the forward direction. Since many of the models discussed above lack effective electron and/or proton gating, it is clear that the major difficulty in developing a viable chemical model is not formulating a cyclic set of protein conformational changes effecting proton pumping (redox linkage) but rather constructing the model with a set of physical constraints so that the proposed cycle proceeds efficiently as postulated. In our discussion of these models, we have not been too concerned about which electron of the catalytic cycle was entering the site of linkage, but merely whether an ET to the binuclear center played a role. However, redox linkage only occurs if ET to the activated binuclear center is coupled to the proton pump. Since all of the models of proton pumping presented here, with the exception of the Rousseau expanded model and the Wikström model, have a maximum stoichiometry of 1 H+/e-, they inadequately explain the 2 H+/e- ratio for the third and fourth electrons of the dioxygen reduction cycle (see Section V.B). One way of interpreting this shortfall of protons is that the remaining protons are pumped by an as yet undefined indirectly coupled mechanism. In this scenario, the site of linkage could be coupled to the pumping of one proton in a direct fashion and one proton in an indirect fashion for a given electron. For a long time, it was assumed that at least some elements of such an indirect mechanism reside in subunit III. While recent evidence argues against the involvement of subunit III in the proton pump, subunit III may still participate in a regulatory and/or structural capacity (Section II.E). Attention has now focused on subunits I and II in the search for residues intimately involved in the proton pump mechanism and/or as part of a proton channel. In particular, the role of some of the highly conserved residues of helix VIII of subunit I are currently being studied by site directed mutagenesis. In our opinion, any model that invokes heme alpha 3 or CuB as the site of linkage must propose a very effective means by which the presumedly fast uncoupling ET to the dioxygen intermediates is prevented. It is difficult to imagine that ET over the short distance from heme alpha 3 or CuB to the dioxygen intermediate requires more than 1 ns. In addition, we expect the conformational changes of the proton pump to require much more than 1 ns (see Section V.B).

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.

Proton NMR study of the heme environment in bacterial quinol oxidases

The heme environment and ligand binding properties of two relatively large membrane proteins containing multiple paramagnetic metal centers, cytochrome bo3 and bd quinol oxidases, have been studied by high field proton nuclear magnetic resonance (NMR) spectroscopy. The oxidized bo3 enzyme displays well-resolved hyperfine-shifted 1H NMR resonance assignable to the low-spin heme b center. The observed spectral changes induced by addition of cyanide to the protein were attributed to the structural perturbations on the low-spin heme (heme b) center by cyanide ligation to the nearby high-spin heme (heme o) of the protein. The oxidized hd oxidase shows extremely broad signals in the spectral region where protons near high-spin heme centers resonate. Addition of cyanide to the oxidized bd enzyme induced no detectable perturbations on the observed hyperfine signals, indicating the insensitive nature of this heme center toward cyanide. The proton signals near the low-spin heme b558 center are only observed in the presence of 20% formamide, consistent with a critical role of viscosity in detecting NMR signals of large membrane proteins. The reduced bd protein also displays hyperfine-shifted 1H NMR signals, indicating that the high-spin heme centers (hemes b595 and d) remain high-spin upon chemical reduction. The results presented here demonstrate that structural changes of one metal center can significantly influence the structural properties of other nearby metal center(s) in large membrane paramagnetic metalloproteins.

Direct Detection of Formate Ligation in Cytochrome c Oxidase by ATR-FTIR Spectroscopy

The IR signature of binding of formate to the heme a(3-)Cu(B) binuclear site of bovine cytochrome c oxidase has been obtained by perfusion ATR-FTIR spectroscopy. The data show unequivocally that formate binds in its anionic form despite its binding being electroneutral overall. The bound formate can be distinguished from free ligand by the binding-induced sharpening and downshifting of vibrational bands. Formate ligation also causes shifts of vibrational modes of heme a(3) and its substituents and perturbation of histidine residues. The association of the accompanying protonation change with a carboxylate or tyrosine can be ruled out and may involve a histidine metal ligand or, more likely, a simple displacement into the bulk phase of a hydroxide ligand to heme a(3) or CU(B), a reaction which would account for stoichiometric proton uptake and maintenance of net charge within the binuclear center domain.

Detergent modulation of electron and proton transfer reactions in bovine cytochrome c oxidase

The effect of detergents on electron and proton transfer in bovine cytochrome c oxidase was studied using steady-state and transient-state methods. Cytochrome c oxidase in lauryl maltoside has high maximal turnover (TN(max)=400 s(-1)), whereas activity is low (TN(max)=10 s(-1)) in Triton X-100. Single turnover studies of intramolecular electron transfer show similar rates in either detergent. Transient proton uptake experiments show the oxidase in lauryl maltoside consumes 1.8+/-0.3 H(+)/aa(3) during either partial reduction of the oxidase or reaction of fully reduced enzyme with O(2). However, the oxidase in Triton X-100 consumes 2.6+/-0.4 H(+)/aa(3) during partial reduction and 1.0+/-0.2 H(+)/aa(3) in the O(2) reaction. Absorption spectra recorded during turnover show that the enzyme undergoes activation in lauryl maltoside, but does not activate in Triton X-100. We propose that cytochrome c oxidase in different detergents allows access to different sites of protonation, which in turn influences steady-state 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.

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.

Molecular Heme-Cyanide-Copper Bridged Assemblies: Linkage Isomerism, Trends in nu(CN) Values, and Relation to the Heme-a(3)/Cu(B) Site in Cyanide-Inhibited Heme-Copper Oxidases

Bovine heart cytochrome c oxidase and related heme copper oxidases are inhibited by cyanide, which binds at the binuclear heme-a(3)/Cu(B) site where dioxygen is reduced to water. To determine the mode of cyanide binding, heme-based binuclear complexes containing iron-cyanide-copper bridges in different oxidation states have been prepared by the reaction of [(py)(OEP)Fe(CN)] with Cu(II,I) precursors and structurally characterized by X-ray methods. Structures of two precursor complexes and two binuclear Cu(I)-CN-Cu(I) species are reported. The assembly [(py)(OEP)Fe-CN-Cu(Npy(3))](2+) has a nearly linear Fe(III)-CN-Cu(II) bridge containing low-spin Fe(III). The assemblies [(OEP)Fe-NC-Cu(MeNpy(2))](+) and [(OEP-CH(2)CN)Fe-NC-Cu(Npy(3))](+) exhibit the high-spin bridges Fe(III)-NC-Cu(I) and Fe(II)-NC-Cu(I), respectively. These are the first title bridges in these oxidation states. Bridge atom sequences are obtained from structural refinements of both linkage isomers; those for the reduced bridges are consistent with the soft-acid nature of Cu(I). Cyanide stretching frequencies respond to metal oxidation state and bridge geometry and, using data for solution and solid states, fall into the following ranges: Fe(III)-CN-Cu(II), 2120-2184 cm(-)(1) (11 examples); Fe(III)-NC-Cu(I), 2072-2100 cm(-)(1) (2 examples); Fe(II)-NC-Cu(I), 2099-2107 cm(-)(1) (1 example). These data are compared with nu(CN) values for the enzymes in different oxidation states. A nonlinear Fe(III)-CN-Cu(II) bridge (Cu-N-C = 150-160 degrees ) is consistent with the 2146-2152 cm(-)(1) range found for the fully oxidized enzymes. Bands that can be assigned with some certainty as Fe-CN vibrations in partially and fully reduced enzymes do not appear to correspond to Fe(III)-NC-Cu(I) and Fe(II)-NC-Cu(I) bridges but rather to Fe(II)-CN modes. The current work complements and extends our previous investigation (Scott and Holm, J. Am. Chem. Soc. 1994, 116, 11357) of linear and nonlinear Fe(III)-CN-Cu(II) bridges and is part of an investigation directed at providing a molecular basis of cyanide toxicity. (MeNpy(2) = bis(2-(2-pyridylethyl))methylamine; Npy(3) = tris(2-pyridylmethyl)amine; OEP = octaethylporphyrinate(2-), OEP-CH(2)CN = N-(cyanomethyl)octaethylporphyrinate(1-).)

Mössbauer and Magnetization Studies of Heme-Copper-Bridged Assemblies Pertinent to Cytochrome c Oxidase

In order to elucidate the structural and electronic properties of the dioxygen-reducing site of cytochrome oxidases, we have studied heme-based molecular assemblies containing the bridge unit Fe(III)-X-Cu(II) with X = O(2)(-), OH(-), and HCO(2)(-). Here we describe the results of Mössbauer and magnetization studies of [(OEP)Fe-O-Cu(Me(6)tren)](1+) (3), [(OEP)Fe-(OH)-Cu(Me(5)dien)(OClO(3))](1+) (4), [(OEP)Fe-(O(2)CH)-Cu(Me(5)dien)(OClO(3))](1+) (5), and [(OEP)Fe{(O(2)CH)Cu(Me(6)tren)}(2)](3+) (6). On the basis of magnetization studies, the oxidized binuclear enzyme site has been reported to be strongly coupled, with an S = 2 ground state. For 3 and 4 the Mössbauer data were analyzed for strong antiferromagnetic coupling between a high-spin Fe(III) (S(1) = (5)/(2)) and Cu(II) (S(2) = (1)/(2)), resulting in an S = 2 ground state. The exchange coupling of hydroxo-bridged 4 is substantial, J = 170 cm(-)(1) (H(ex) = JS(1).S(2)), but is smaller than J >/= 200 cm(-)(1) reported for oxo-bridged 3. The collective evidence for synthetic complexes and the oxidized enzymes indicates that the Fe(III)-(OH)-Cu(II) bridge unit is probable for the latter in the resting state. The similarity of properties of formate-inhibited and "slow" cytochrome oxidase has suggested a carboxylate bridge in the binuclear site. Formate-bridged 5 maintains an anti-anti carboxylate bridge conformation and has J = +18 cm(-)(1). While the bridge conformation of 5 might not apply to a putative carboxylate bridge in the binuclear enzyme site, the order-of-magnitude difference between the J values of 3, 4, and 5 suggests that no stereochemically possible &mgr;-eta(1):eta(1) carboxylate bridge conformation is likely to approach the strong coupling (J >/= 200 cm(-)(1)) of the formate-inhibited and "slow" enzyme forms. If carboxylate does bridge, the &mgr;-eta(2) mode appears more likely. Complex 6, which is not biologically pertinent, displays weak ferromagnetic coupling between a central high-spin Fe(III) and two Cu(II) sites, -0.50 cm(-)(1) < J < -0.10 cm(-)(1).

Formate bound to cytochrome oxidase can be removed by cyanide and by reduction

Using 14C-radiolabeled formate we have found that the rapid form of oxidized cytochrome oxidase can bind up to 1 mol of formate. Treatment of this formate-ligated enzyme with excess cyanide releases 97% of the radiolabel while reduction of formate-labeled enzyme with NADH+ruthenium releases 80-85% of the radioactivity. These data are most simply interpreted by assuming that formate binds to the heme iron of cytochrome a3.

Molecular Assemblies Containing Unsupported [Fe(III)-(&mgr;(2):eta(2)-RCO(2))-Cu(II)] Bridges

Formate is an inhibitor of cytochrome oxidases and also effects conversion of the bovine heart enzyme from the "fast" to the "slow" cyanide-binding form. The molecular basis of these effects is unknown; one possibility is that formate inserts as a bridge into the binuclear heme a(3)-Cu(B) site, impeding the binding of dioxygen or cyanide. Consequently, Fe-Cu-carboxylate interactions are a matter of current interest. We have initiated an examination of such interactions by the synthesis of the first examples of [Fe(III)-(&mgr;(2):eta(2)-RCO(2))-Cu(II)] bridges, minimally represented by Fe(III)-L + Cu(II)-O(2)CR --> [Fe(III)-(RCO(2))-Cu(II)] + L. A series of Cu(II) precursor complexes and solvate forms have been prepared and their structures determined, including [Cu(Me(5)dien)(O(2)CH)](+) (3), [Cu(Me(5)dien)(O(2)CH)(MeOH)](+) (4), [Cu(Me(6)tren)(O(2)CH)](+) (5), and [Cu(Me(5)dien)(OAc)](+) (6). [4](ClO(4)) was obtained in monoclinic space group P2(1)/n with a = 8.166(3) Å, b = 15.119(5) Å, c = 15.070(4) Å, beta = 104.65(2) degrees, and Z = 4. [5](ClO(4))/[6](ClO(4)) crystallize in orthorhombic space groups Pnma/Pna2(1) with a = 16.788(2)/14.928(5) Å, b = 9.542(1)/9.341(4) Å, c = 12.911(1)/12.554(4) Å, and Z = 4/4. In all cases, the carboxylate ligand is terminal and is bound in a syn orientation. Also prepared for the purpose of structural comparison was [Fe(OEP)(O(2)CH)], which occurred in monoclinic space group P2(1)/c with a = 13.342(2) Å, b = 13.621(2) Å, c = 19.333(2) Å, beta = 106.12(2) degrees, and Z = 4. The desired bridges were stabilized in the assemblies [(OEP)Fe(O(2)CH)Cu(Me(5)dien)(OClO(3))](+) (9), [(OEP)Fe(OAc)Cu(Me(5)dien)](2+) (10), and {(OEP)Fe[(O(2)CH)Cu(Me(6)tren)](2)}(3+) (11), which were prepared by the reaction of 3, 6, and 5, respectively, with [Fe(OEP)(OClO(3))] in acetone or dichloromethane. [9](ClO(4))/[10](ClO(4))(2).CH(2)Cl(2) crystallize in triclinic space group P&onemacr; with a = 9.016(3)/13.777(3) Å, b = 15.377(5)/13.847(3) Å, c = 19.253(5)/17.608(4) Å, alpha = 78.12(3)/96.82(3) degrees, beta = 86.30(4)/108.06(3) degrees, gamma = 76.23(3)/114.32(3) degrees, and Z = 2/2. Each assembly contains a [Fe(III)-(RCO(2))-Cu(II)] bridge but with the differing orientations anti-anti (9) and syn-anti (10, 11). The compound [11](ClO(4))(2)(SbF(6)) occurs in orthorhombic space group Pbcn with a = 12.517(6) Å, b = 29.45(1) Å, c = 21.569(8) Å, and Z = 4. Complex 11 is trinuclear; the Fe(III) site has two axial formate ligands with bond distances indicative of a high-spin configuration. Structural features of 9-11 are discussed and are considered in relation to the possible insertion of formate into the binuclear sites of two oxidases whose structures were recently determined. The present results contribute to the series of molecular assemblies with the bridge groups [Fe(III)-X-Cu(II)], X = O(2)(-), OH(-), and RCO(2)(-), all with a common high-spin heme, thereby allowing an examination of electronic structure as dependent on the bridging atom or group and bridge structure. (Me(5)dien = 1,1,4,7,7-pentamethyldiethylenetriamine; Me(6)tren = tris(2-(dimethylamino)ethyl)amine; OEP = octaethylporphyrinate(2-).)

Kinetics and mechanism for the binding of HCN to cytochrome c oxidase

The kinetics of cyanide binding to cytochrome c oxidase were systematically studied as a function of [HCN], [oxidase], pH, ionic strength, temperature, type and concentration of solubilizing detergent, and monomer-dimer content of oxidase. On the basis of these results a minimum reaction mechanism is proposed in which the spectrally visible rapid and slow cyanide binding reactions are two consecutive first-order reactions, not parallel reactions with different conformers of cytochrome c oxidase. The fast reaction (k'obs) follows saturation type kinetics to form an HCN complex that subsequently undergoes a slow reaction (k'obs). The fast k'obs reaction is independent of ionic strength but is strongly dependent upon pH. Two pK values were evaluated from the bell-shaped rate versus pH profile; one is due to an ionizable group on the protein (pKa = 7.45), while the other is that of HCN (pKHCN = 9.15). Therefore, oxidase is reactive toward HCN only when the group on the protein is unprotonated. The slow k'obs reaction is not a reaction of oxidase with either CN- or HCN; in fact, the product formed by the fast k'obs reaction, the oxidase-HCN complex, still undergoes the slow k" process even if all of the excess KCN is removed. The apparent rate constant of the slower phase (k"obs) is independent of all the variations done in this study, and it probably corresponds to either a slow conformational change in the protein or a change in ligand coordination at one of the metal centers after HCN binds to the bimetallic center of oxidase. Based upon the bell-shaped pH dependence of the fast phase and the pH independence of the slow phase, the mechanism also predicts that a single conformer of cytochrome c oxidase can exhibit either monophasic or biphasic cyanide binding kinetics depending upon the pH. At either very low or very high pH, the two rates become comparable in magnitude, which makes the reaction appear to be monophasic even though both reactions still occur. The amount of monomeric or dimeric oxidase only slightly affects the magnitude of k'obs and k"obs values, and both processes are clearly present in both types of oxidase.

Integral cytochrome-c oxidase. Preparation and progress towards a three-dimensional crystallization

A new rapid procedure for the preparation of monodispersed highly active cytochrome-c oxidase from bovine heart is described. The crucial step is the separation of cytochrome-c oxidase from cytochrome-c reductase by selective solubilization in the non-ionic detergents Triton X-100 or lauryl beta-D-maltoside. The enzyme is purified by subsequent anion-exchange chromatography. The preparation is finished within two days yielding approximately 60% of the oxidase present in mitochondria. The enzyme has a heme alpha/protein ratio of 9.7 +/- 0.5 nmol/mg, approximately equal to the theoretical value of 9.77 nmol/mg based on a molecular mass of 204.696 kDa for the protein monomer. SDS/PAGE of the preparation reveals the presence of the well-known thirteen protein components. Quantitative Edman degradation of the enzyme exclusively releases the known ten N-terminal residues; three of the thirteen protein components are blocked at the N-terminus. The preparation is highly active with maximal turnover numbers of approximately 600 s-1, identical to the maximal activity found in the mitochondrial membrane under these conditions. No g = 12 signal and no adventitious copper signal are observed in the EPR spectrum. The enzyme exhibits a fast monophasic reaction with cyanide. Determination of the metal contents of the enzyme indicates the stoichiometric presence of three copper ions besides two iron, one magnesium and one zinc ion in relation to the 94 sulfur atoms of the protein monomer. Gel-filtration experiments show a monodispersed dimeric association to form a complex of approximately 500 kDa. The phosphorus content 44 +/- 6.8 atoms/dimer, results from 59% cardiolipin, 23% phosphatidylethanolamine and 18% phosphatidylcholine, indicating a stable lipid shell, different from other previously described preparations. Crystals have been obtained from these preparations and are investigated for their suitability for X-ray work.

Conformational change due to reduction of cytochrome-c oxidase in lauryl maltoside: picosecond time-resolved tryptophan fluorescence studies on the native and heat modified enzyme

Detailed fluorescence studies on bovine heart cytochrome-c oxidase (CcO) has been carried out in lauryl maltoside solution. Steady-state fluorescence of the tryptophan residues of the enzyme showed that the fluorophores are embedded deep inside the hydrophobic protein cavity. Time resolved studies of tryptophan fluorescence of native and heat treated CcO have been carried out in both reduced and oxidised forms using synchronously pumped pulsed picosecond dye laser and single photon counting technique. Decay of the tryptophan fluorescence have been fitted using discrete four exponential model. Amplitude distribution of lifetimes also showed four distinct regions in the analysis of the decay profiles by maximum entropy method (MEM). The results indicate that controlled heat treatment of CcO affects the conformation of the enzyme near the active centers which makes it incapable of active proton pumping while the electron transfer property is still conserved. Reduction of the native CcO is associated with a large conformation change in lauryl maltoside near the active centers which is not observed in case of CcO encapsulated in vesicles. Reduction of the heat treated enzyme was found to have a conformation different from the reduced native CcO.

'CO2-ligated' cytochrome c oxidase: characterization and comparison with the Cl- -ligated enzyme

A form of fully oxidized bovine heart cytochrome c oxidase that is induced by CO2/HCO3- is described. The ligand-binding properties of this form are similar to those of Cl(-)-ligated oxidase [Moody, Cooper and Rich (1991) Biochim. Biophys. Acta 1059, 189-207]. Both bind cyanide at a rate (0.2 M-1.s-1 at pH 6.5) intermediate between the rate of binding to the fast and slow forms of the enzyme, and binding of formate to both is almost undetectable. They are also similar in showing poor reactivity with H2O2, or with CO in the presence of O2, which, with fast oxidase, induce the formation of the 'ferryl' and 'peroxy' states respectively. However, there is a clear difference in the near-u.v./visible absorption spectra of the two forms; that induced by CO2/HCO3- has a Soret maximum at 427 nm whereas Cl(-)-ligated oxidase has a Soret maximum similar to that of fast oxidase at about 424 nm. It appears that both CO2/HCO3- and Cl- are members of a class of ligands that lowers the reactivity of the binuclear centre but does not impede intramolecular electron transfer from haem a to the binuclear centre, unlike the putative endogenous ligand responsible for slow oxidase.

Kinetic and structural model for the binding of formate to the rapid form of cytochrome c oxidase

The binding of formate to the rapid form of cytochrome c oxidase from bovine heart has been examined at pH 8.8 and high ionic strength. The optical changes included (1) a transient decrease at 414 nm, followed by a biphasic increase, and (2) an isosbestic wavelength. The apparent blue shift in the Soret envelope, following the transient, was consistent with a 430-->414 transition in cytochrome a3, described previously for acid jump conditions in the absence of formate [Papadopoulos, P. G., Walter, S. A., Li, J., & Baker, G. M. (1991) Biochemistry 30, 840-850]. A two-step binding mechanism was implied by the biphasic increase, but the k(obs) values for each phase, when plotted against formate concentration, were unable to statistically discriminate two rival kinetic models. Both models postulated a rapid 430 + L<-->414.L step (where L = HCOOH + HCOO-), but they differed in whether the slower step depended on L. The equilibrium dissociation constant, KDapp, for the overall binding reaction was 0.3 mM. An analysis of the rival mechanisms indicated this value to be consistent with a step that was independent of L. A slow 414.L<-->414'.L conversion was therefore postulated, and the Keq for this step was found to be approximately 9. The analysis to this point assumed that cytochrome alpha 3 was entirely in the 430 state at the time of formate addition. Modeling of the transient could not be achieved, however, unless cytochrome a3 was present as a rapid equilibrium mixture of 414 and 430 states. The 414, 414.L, and 414'.L states were assumed to be electronically identical to account for the isosbestic wavelength.(ABSTRACT TRUNCATED AT 250 WORDS)

A comparison of three preparations of cytochrome c oxidase. Optical absorbance spectra, EPR spectra and reaction towards ligands

Three preparations of cytochrome c oxidase, the preparation as traditionally prepared in our laboratory as described by Van Buuren (1992; PhD Thesis, University of Amsterdam), a preparation according to Volpe and Caughey (Biochem. Biophys. Res. Commun. 61 (1974) 502-509) and a preparation of 'fast' cytochrome c oxidase (Brandt, U., Schägger, H. and Von Jagow, G. (1989) Eur. J. Biochem. 182, 705-711), are compared in their reaction with cyanide and carbon monoxide. The reaction with cyanide is nearly as fast for the Van Buuren preparation as for the 'fast' preparation, but much slower for the Volpe-Caughey preparation. Mixed-valence cytochrome c oxidase (cytochrome a3 and CuB reduced with carbon monoxide bound and cytochrome a and CuA oxidized) is prepared by anaerobic incubation with carbon monoxide. With the Van Buuren preparation complete formation of the species takes 4 h, whereas with the Volpe-Caughey preparation it takes 20 h. Longer incubation under CO results in partial reduction of cytochrome a and CuA. With the 'fast' preparation mixed-valence cytochrome c oxidase is formed after more than one day of incubation with CO, but it is stable for at least 3 days. The presence of oxidized cytochrome c did enhance the reactivity towards cyanide and towards carbon monoxide in cytochrome c oxidase of all three preparations. Furthermore, optical and EPR spectra of the preparations of cytochrome c oxidase are compared. The Volpe-Caughey preparation has an intense g' = 12 EPR-signal, the Van Buuren preparation has hardly any g' = 12 signal and the 'fast' preparation has no g' = 12 signal. In the 'fast' preparation the low-spin heme signal is shifted (from g = 3.00 to g = 2.97). The absorbance spectra of the three preparations in the Soret region are similar with a maximum at 424 nm. Only the 'fast' preparation as isolated was completely oxidized, whereas the other preparations were partially reduced. It was concluded that differences in the reaction of cytochrome c oxidase with ligands are determined by the internal or external ligand bound to the cytochrome a3-CuB couple.

Strong-field and integral spin-ligand complexes of the cytochrome bo quinol oxidase in Escherichia coli membrane preparations

The cytochrome bo-type terminal oxidase of Escherichia coli is an analogue of mammalian aa3-type cytochrome c oxidase. The catalytic core of both enzymes is a binuclear site containing a penta-coordinate heme (heme o or a3) and copper (CuB). Herein we report on UV-visible and magnetic properties of ligand complexes of the binuclear site of cytochrome bo. Cyanide, sulfide, and azide react with the Fe(3+)-Cu+ center to give EPR-detectable low-spin complexes, analogous to those formed by cytochrome aa3. Analyses of the ligand fields of these complexes indicate that heme o has a single axial histidine ligand. Cyanide and azide react with the Fe(3+)-Cu2+ center to yield forms observable via UV-visible spectroscopy but not EPR. With formate and fluoride, cytochrome bo forms integral spin complexes similar to those of cytochrome aa3. These complexes have UV-visible characteristics of high-spin species, but EPR spectra show features which appear to correspond to transitions within an integral spin multiplet. Cytochrome bo forms another integral spin complex with azide and NO which is nearly identical to the azide-NO species in cytochrome aa3. This suggests that the binuclear centers of the two enzymes are quite similar.

Slow ('resting') forms of mitochondrial cytochrome c oxidase consist of two kinetically distinct conformations of the binuclear CuB/a3 centre--relevance to the mechanism of proton translocation

We have purified slow ('resting') cytochrome oxidase from bovine heart, free of contamination with fast ('pulsed') enzyme. This form of the enzyme shows two kinetic phases of reduction of haem a3 by dithionite (k = 0.020 +/- 0.005 s-1 and k = 0.005 +/- 0.002 s-1). The presence of ligands that bind to the oxidized or reduced binuclear centre (formate or carbon monoxide respectively) has no effect on these rates. Varying the dithionite concentration also has no effect on either phase, although at low dithionite concentrations a lag phase is observed as the rate of haem a reduction is slower. The results are consistent with a model for reduction of the slow enzyme where the rate of electron transfer to the binuclear centre is the limiting step, rather than an equilibrium model where the haem a3 redox potential is low. Increasing the pH decreases the rate of the slower phase of dithionite reduction, but has no effect on the faster phase. EPR studies show that the slow phase (only) correlates with the disappearance of the g' = 12/g' = 2.95 signals, with the same pH dependence; again the presence of formate has no effect on these results. Deconvolution of the oxidized optical spectra shows that the enzyme reduced in the slow phase has a blue-shifted Soret band, relative to that reduced in the faster phase. Incubation of the oxidized enzyme at high pH causes a line-broadening of both the g' = 12 and g' = 2.95 EPR signals with no obvious effect on the amount of signal. The results are interpreted in a model where the presence of a carboxylate bridge between haem a3 and CuB defines the slow enzyme. It is suggested that the two rates of dithionite reduction are the result of different ligation to CuB--where water is the ligand the binuclear centre is FeIV/CuI (EPR-silent) and where hydroxide is the ligand the binuclear centre is FeIII/CuII (g' = 12/g' = 2.95 EPR signals).

Structure of the heme-copper binuclear center of the cytochrome bo complex of Escherichia coli: EPR and Fourier transform infrared spectroscopic studies

The cytochrome bo complex is a terminal quinol oxidase in the aerobic respiratory chain of Escherichia coli and functions as a redox-coupled proton pump. To clarify the structural differences of the binuclear reaction center between the cytochrome bo complex and the mitochondrial cytochrome c oxidase, a combined study using EPR and Fourier transform infrared spectroscopies was carried out. The EPR spectrum of the highly purified cytochrome bo complex in the air-oxidized state showed a broad EPR signal (peak g* = 3.7) from an integer spin system. This confirms the existence of the spin-spin exchange-coupled binuclear site, in which the Feo3+ and CuB2+ centers were bridged by an unknown ligand (X). Binding of azide at the binuclear site as an ionic modulator weakened the strength of the spin-spin exchange coupling and thus caused a narrowing of the broad EPR signal. Binding of another modulator, formate, at the binuclear site caused the formation of EPR signals at g' = 12 and 2.7, which are very similar to those observed for cytochrome c oxidase. Cyanide replaced the bridging ligand (X) to form an Feo(3+)-C-N-CuB2+ structure in which strong spin-spin exchange coupling is expected, leading to a complete EPR-invisible state. Infrared evidence (a 2146 cm-1 C-N stretching band for the cyanide complex and a 2041 cm-1 azide antisymmetric stretching band for the azide complex) supported the theory that these ligands form bridging structures at the binuclear center, as previously observed for cytochrome c oxidase.(ABSTRACT TRUNCATED AT 250 WORDS)

Stoichiometry and redox behaviour of metals in cytochrome-c oxidase

The early observation of extra copper in preparations of cytochrome-c oxidase has recently lead to a renewed interest in its stoichiometry and possible redox function. In various, pure preparations (heme A contents close to the theoretical value of 9.79 nmol/mg protein for the 13-subunit bovine enzyme) protein-related metal stoichiometries of 3 Cu, 2 Fe, 1 Zn, 1 Mg/monomer with M(r) 204266 were determined. Despite the presence of five potential redox metal ions, reductive and reoxidative titrations indicate the presence of only four one-electron-accepting/donating species in the ligand-free enzyme. Participation of two copper ions in a binuclear copper site acting as one-electron acceptor may explain both the observed copper stoichiometry and the redox behaviour. The homology of the C-terminal sequence of subunit II with one of the copper-binding sites in nitrous-oxide reductases provides possible ligands for complexing two copper ions in a binuclear center.

Current issues in the chemistry of cytochrome c oxidase

Some contemporary issues relevant to the chemistry of mammalian cytochrome c oxidase are discussed. These include the optical properties of heme A and the spectroscopic consequences of the differences in side-chain substitution compared to heme B; a common fallacy concerning the electrostatic exchange interaction between cytochrome a3 and CuB; the question of the number and location of the copper components of the enzyme; and the mode of binding of ligands such as cyanide and azide.

Distinct forms of the haem o-Cu binuclear site of oxidised cytochrome bo from Escherichia coli. Evidence from optical and EPR spectroscopy

Oxidised, formate-bound and fluoride-bound forms of E. coli cytochrome bo give rise to an electronic absorption band near 630 nm, diagnostic of high-spin ferric haem o, whose position is sensitive to the nature of the bound anion. In all three forms, haem o remains spin-coupled to Cu(B)(II), resulting in distinct broad X-band EPR signals. Those of formate-bound cytochrome bo are similar to the signals seen in slow cytochrome aa3 but cannot be induced by incubation at acid pH suggesting that the endogenous carboxylate believed to be important in slow cytochrome aa3 is not present in cytochrome bo. The oxidised form gives rise to novel EPR signals at g = 3.74 and g = 3.08 which have not been detected in cytochrome aa3 and may arise from a weak magnetic coupling between high-spin haem o, S = 5/2, and Cu(B)(II), S = 1/2.

Ligand-binding properties and heterogeneity of cytochrome bo from Escherichia coli

Cyanide and formate induce spectral changes in E. coli cytochrome bo which are similar to those induced in bovine heart cytochrome-c oxidase (cytochrome aa3). Cyanide induces a red shift of 6 nm in the Soret band, whereas formate induces a blue shift of 2 nm. Cytochrome bo as purified shows multiphasic cyanide-binding kinetics. At least three phases can be seen with rate constants of 16, 1 and 0.1 M-1 s-1, respectively, at pH 7 and 20 degrees C. The enzyme after redox cycling ('pulsing') or in situ in E. coli membranes shows essentially monophasic binding with a rate constant of 15 M-1 s-1. Further evidence of heterogeneity in the enzyme as prepared comes from formate binding, which also shows at least three phases (rate constants of 1.4, 0.2 and 0.01 M-1 s-1, respectively, at pH 5 and 20 degrees C). The fast phase of cyanide binding is eliminated in less than 2 min by incubation with 40 mM formate, but the intermediate phase is unaffected by incubation for 3.5 h with 40 mM formate. Thus, the subpopulation that causes the fast phase of cyanide binding also causes the fast phase of formate binding. Formate-ligated cytochrome bo has similar cyanide-binding kinetics to the subpopulation that causes the slow phase of cyanide binding in cytochrome bo as prepared. It appears, from all this, that the subpopulations responsible for the fast and slow phase of cyanide binding are analogous to the 'fast' and 'slow' forms, respectively, of cytochrome aa3.(ABSTRACT TRUNCATED AT 250 WORDS)

The formate complex of the cytochrome bo quinol oxidase of Escherichia coli exhibits a 'g = 12' EPR feature analogous to that of 'slow' cytochrome oxidase

The cytochrome bo quinol oxidase of Escherichia coli is homologous in sequence and in structure to cytochrome aa3 type cytochrome oxidase in subunit I, which contains the catalytic core. The cytochrome bo enzyme forms a formate complex which exhibits 'g = 12' and 'g = 2.9' EPR signals at X band; similar signals have previously been observed only in association with the 'slow' and formate-ligand states of cytochrome oxidase. These signals arise from transitions within integral spin multiples identified with the homologous heme-copper binuclear catalytic centers in both enzymes.

Single electron reduction of 'slow' and 'fast' cytochrome-c oxidase

Evidence is presented that single electron reduction is sufficient for rapid electron transfer (k greater than 20 s-1 at pH 8.0 in 0.43 M potassium EDTA) between haem a/CuA and the binuclear centre in 'fast' oxidase, whereas in 'slow' oxidase intramolecular electron transfer is slow even when both CuA and haem a are reduced (k congruent to 0.01 s-1). However, while a single electron can equilibrate rapidly between CuA, haem a and CuB in 'fast' oxidase, it seems that equilibration with haem a3 is relatively slow (k congruent to 2 s-1). Electron transfer between cytochrome c and CuA/haem a is similar for both types of enzyme (k congruent to 2.4 x 10(5) M-1.s-1).