Kinetic coupling between electron and proton transfer in cytochrome c oxidase: simultaneous measurements of conductance and absorbance changes

Stimulation of cytochrome c oxidase activity by detergents

Cytochrome c oxidase (CytcO) is an integral membrane protein, which catalyzes four-electron reduction of oxygen linked to proton uptake and pumping. Amphipathic molecules bind in sites near the so-called K proton pathway of CytcO to reversibly modulate its activity. However, purification of CytcO for mechanistic studies typically involves the use of detergents, which may interfere with binding of these regulatory molecules. Here, we investigated the CytcO enzymatic activity as well as intramolecular electron transfer linked to proton transfer upon addition of different detergents to bovine heart mitoplasts. The CytcO activity increased upon addition of alkyl glucosides (DDM and DM) and the steroid analog GDN. The maximum stimulating effect was observed for DDM and DM, and the half-stimulating effect correlated with their CMC values. With GDN the stimulation effect was smaller and occurred at a concentration higher than CMC. A kinetic analysis suggests that the stimulation of activity is due to removal of a ligand bound near the K proton pathway, which indicates that in the native membrane this site is occupied to yield a lower than maximal possible CytcO activity. Possible functional consequences are discussed.

The catalytic reaction of cytochrome c oxidase probed by in situ gas titrations and FTIR difference spectroscopy

Cytochrome c oxidase (CcO) is a transmembrane heme‑copper metalloenzyme that catalyzes the reduction of O2 to H2O at the reducing end of the respiratory electron transport chain. To understand this reaction, we followed the conversion of CcO from Rhodobacter sphaeroides between several active-ready and carbon monoxide-inhibited states via attenuated total reflection Fourier-transform infrared (ATR FTIR) difference spectroscopy. Utilizing a novel gas titration setup, we prepared the mixed-valence, CO-inhibited R2CO state as well as the fully-reduced R4 and R4CO states and induced the "active ready" oxidized state OH. These experiments are performed in the dark yielding FTIR difference spectra exclusively triggered by exposure to O2, the natural substrate of CcO. Our data demonstrate that the presence of CO at heme a3 does not impair the catalytic oxidation of CcO when the cycle starts from the fully-reduced states. Interestingly, when starting from the R2CO state, the release of the CO ligand upon purging with inert gas yield a product that is indistinguishable from photolysis-induced states. The observed changes at heme a3 in the catalytic binuclear center (BNC) result from the loss of CO and are unrelated to electronic excitation upon illumination. Based on our experiments, we re-evaluate the assignment of marker bands that appear in time-resolved photolysis and perfusion-induced experiments on CcO.

Proton transfer in uncoupled variants of cytochrome c oxidase

Cytochrome c oxidase is a membrane-bound redox-driven proton pump that harbors two proton-transfer pathways, D and K, which are used at different stages of the reaction cycle. Here, we address the question if a D pathway with a modified energy landscape for proton transfer could take over the role of the K pathway when the latter is blocked by a mutation. Our data indicate that structural alterations near the entrance of the D pathway modulate energy barriers that influence proton transfer to the proton-loading site. The data also suggest that during reduction of the catalytic site, its protonation has to occur via the K pathway and that this proton transfer to the catalytic site cannot take place through the D pathway.

Functions of the hydrophilic channels in protonmotive cytochrome c oxidase

The structures and functions of hydrophilic channels in electron-transferring membrane proteins are discussed. A distinction is made between proton channels that can conduct protons and dielectric channels that are non-conducting but can dielectrically polarize in response to the introduction of charge changes in buried functional centres. Functions of the K, D and H channels found in A1-type cytochrome c oxidases are reviewed in relation to these ideas. Possible control of function by dielectric channels and their evolutionary relation to proton channels is explored.

Functional interactions between membrane-bound transporters and membranes

One key role of many cellular membranes is to hold a transmembrane electrochemical ion gradient that stores free energy, which is used, for example, to generate ATP or to drive transmembrane transport processes. In mitochondria and many bacteria, the gradient is maintained by proton-transport proteins that are part of the respiratory (electron-transport) chain. Even though our understanding of the structure and function of these proteins has increased significantly, very little is known about the specific role of functional protein-membrane and membrane-mediated protein-protein interactions. Here, we have investigated the effect of membrane incorporation on proton-transfer reactions within the membrane-bound proton pump cytochrome c oxidase. The results show that the membrane acts to accelerate proton transfer into the enzyme's catalytic site and indicate that the intramolecular proton pathway is wired via specific amino acid residues to the two-dimensional space defined by the membrane surface. We conclude that the membrane not only acts as a passive barrier insulating the interior of the cell from the exterior solution, but also as a component of the energy-conversion machinery.

Nanosecond electron tunneling between the hemes in cytochrome bo3

Biological electron transfer (eT) between redox-active cofactors is thought to occur by quantum-mechanical tunneling. However, in many cases the observed rate is limited by other reactions coupled to eT, such as proton transfer, conformational changes, or catalytic chemistry at an active site. A prominent example of this phenomenon is the eT between the heme groups of mitochondrial cytochrome c oxidase, which has been reported to take place in several different time domains. The question of whether pure eT tunneling in the nanosecond regime between the heme groups can be observed has been the subject of some experimental controversy. Here, we report direct observations of eT between the heme groups of the quinol oxidase cytochrome bo(3) from Escherichia coli, where the reaction is initiated by photolysis of carbon monoxide from heme o(3). eT from CO-dissociated ferrous heme o(3) to the low-spin ferric heme b takes place at a rate of (1.2 ns)(-1) at 20 degrees C as determined by optical spectroscopy. These results establish heme-heme electron tunneling in the bo(3) enzyme, a bacterial relative to the mitochondrial cytochrome c oxidase. The properties of eT between the closely lying heme groups in the heme-copper oxidases are discussed in terms of the reorganization energy for the process, and two methods for assessing the rate of electron tunneling are presented.

An IR study of protonation changes associated with heme-heme electron transfer in bovine cytochrome c oxidase

IR changes caused by photolysis of CO from the mixed valence form of bovine cytochrome c oxidase have been investigated over the pH/pD range 6-9.8. Band assignments were based on effects of H2O/D2O exchange and by comparisons with published IR data and crystallographic data. Changes arise both from CO photolysis and from subsequent reversed electron transfer from heme a3 to heme a. This reversed electron transfer is known to have pH-independent and, above pH 8, pH-dependent components. The pH-independent component is associated with a trough around the 1742 cm(-1) band attributable to one or more protonated carboxylic acids. Its peak position, but not extent, is pH-dependent, indicative of a titratable group with a pK of 8.2 whose acid form causes increased hydrogen bonding to the IR-detectable carboxylic group. A different protonatable group with pK above 9 controls the extent of the pH-dependent component. This phase is associated with perturbation of an arginine guanidinium that is most clearly observed as a trough at 1592 cm(-1) after H/D exchange. It is suggested that this group, probably Arg-438 that is in close contact with propionate groups of both hemes and already proposed to be of functional significance, lowers the energy of the transient charge-uncompensated electron-transfer intermediate by changing the charge distribution in response to heme-heme electron transfer. No other IR signature of a titratable group that controls the extent of the pH-dependent phase is present, and it most likely arises from a nonphysiological deprotonation of the proximal water ligand of ferric heme a3 at high pH that has been reported to exhibit a similar pK.

Filling the catalytic site of cytochrome c oxidase with electrons. Reduced CuB facilitates internal electron transfer to heme a3

In the reductive phase of its catalytic cycle, cytochrome c oxidase receives electrons from external electron donors. Two electrons have to be transferred into the catalytic center, composed of heme a(3) and Cu(B), before reaction with oxygen takes place. In addition, this phase of catalysis appears to be involved in proton translocation. Here, we report for the first time the kinetics of electron transfer to both heme a(3) and Cu(B) during the transition from the oxidized to the fully reduced state. The state of reduction of both heme a(3) and Cu(B) was monitored by a combination of EPR spectroscopy, the rapid freeze procedure, and the stopped-flow method. The kinetics of cytochrome c oxidase reduction by hexaamineruthenium under anaerobic conditions revealed that the rate-limiting step is the initial electron transfer to the catalytic site that proceeds with apparently identical rates to both heme a(3) and Cu(B). After Cu(B) is reduced, electron transfer to oxidized heme a(3) is enhanced relative to the rate of entry of the first electron.

The mechanism of proton transfer between adjacent sites on the molecular surface

The surface of a protein, or a membrane, is spotted with a multitude of proton binding sites, some of which are only few A apart. When a proton is released from one site, it propagates through the water by a random walk under the bias of the local electrostatic potential determined by the distribution of the charges on the protein. Eventually, the released protons are dispersed in the bulk, but during the first few nanoseconds after the dissociation, the protons can be trapped by encounter with nearby acceptor sites. While the study of this reaction on the surface of a protein suffers from experimental and theoretical difficulties, it can be investigated with simple model compounds like derivatives of fluorescein. In the present study, we evaluate the mechanism of proton transfer reactions that proceed, preferentially, inside the Coulomb cage of the dye molecules. Kinetic analysis of the measured dynamics reveals the role of the dimension of the Coulomb cage on the efficiency of the reaction and how the ordering of the water molecules by the dye affects the kinetic isotope effect.

Analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection

In a recent work from this group (Popovic, D. M.; Stuchebrukhov A. A. FEBS Lett. 2004, 566, 126), a model of proton pumping by cytochrome c oxidase (CcO) was proposed. The key element of the model is His291 (bovine notation), a histidine ligand to enzyme's CuB redox center, which plays the role of the pump element. The model assumes that upon electron transfer between heme a and the binuclear catalytic center of the enzyme, two sequential proton transfers occur: First, a proton from Glu242 is transferred to an unprotonated His291, then a second proton, after reprotonation of Glu242 from the negative side of the membrane, is transferred to a hydroxyl group in the binuclear center, a water molecule is formed, and the first proton, due to proton-proton repulsion, is expelled from His291 to the positive side of the membrane, resulting in a pumping event. In the process the free energy of water formation (i.e., reduction of oxygen) is transformed into a proton gradient across the membrane. The model possesses specific kinetic features. It assumes, for example, that upon electron transfer the first proton is transferred to the proton-loading site of the pump, His291, and not to the catalytic center of the enzyme. Here, we analyze the kinetic properties of the proposed model, and calculate the time dependence of the membrane potential generated by CcO upon a single electron injection into the enzyme. These data are directly compared with recent experimental measurements of the membrane potential generated by CcO. Specifically, F to O, and O to E transitions will be discussed. Several enzymes from different organisms (bovine, two bacterial enzymes, and several mutants) are compared and discussed in detail. The kinetic description, however, is phenomenological, and does not include explicitly the nature of the groups involved in proton translocation, except in terms of their position depth within the membrane; thus, the kinetic equations developed here are in fact describe a generic model, similar, e.g., to that proposed earlier by Peter Rich (P.R. Rich, Towards an understanding of the chemistry of oxygen reduction and proton translocation in the iron-copper respiratory oxidases. Aust. J. Plant Physiol. 22 (1995) 479-486), and which is based on the idea of displacement of the pumped protons by the chemical ones.

The Mechanism of Proton Transfer between Adjacent Sites Exposed to Water

The surface of a protein, or a membrane, is spotted with a multitude of proton-binding sites, some of which are only a few angstroms apart. When a proton is released from one site, it propagates through the water by a random walk under the bias of the local electrostatic potential determined by the distribution of the charges on the protein. Some of the released protons disperse into the bulk, but during the first few nanoseconds, the released protons can be trapped by encounter with nearby acceptor sites. This process resembles a scenario which corresponds with the time-dependent Debye-Smoluchowski equation. In the present study, we investigated the mechanism of proton transfer between sites that are only a few angstroms apart, using as a model the proton exchange between sites on a small molecule, fluorescein, having two, spectrally distinguishable, proton-binding sites. The first site is the oxyanion on the chromophore ring structure. The second site is the carboxylate moiety on the benzene ring of the molecule. Through our experiments, we were able to reconstruct the state of protonation at each site and the velocity of proton transfer between them. The fluorescein was protonated by a few nanosecond long proton pulse under specific conditions that ensured that the dye molecules would be protonated only by a single proton. The dynamics of the protonation of the chromophore were measured under varying initial conditions (temperature, ionic strength, and different solvents (H(2)O or D(2)O)), and the velocity of the proton transfer between the two sites was extracted from the overall global analysis of the signals. The dynamics of the proton transfer between the two proton-binding sites of the fluorescein indicated that the efficiency of the site-to-site proton transfer is very sensitive to the presence of the screening electrolyte and has a very high kinetic isotope effect (KIE = 55). These two parameters clearly distinguish the mechanism from proton diffusion in bulk water. The activation energy of the reaction (E(a) = 11 kcal mol(-1)) is also significantly higher than the activation energy for proton dissociation in bulk water (E(a) approximately 2.5 kcal mol(-1)). These observations are discussed with respect to the effect of the solute on the water molecules located within the solvation layer.

FTIR studies of internal proton transfer reactions linked to inter-heme electron transfer in bovine cytochrome c oxidase

FTIR difference spectroscopy is used to reveal changes in the internal structure and amino acid protonation states of bovine cytochrome c oxidase (CcO) that occur upon photolysis of the CO adduct of the two-electron reduced (mixed valence, MV) and four-electron reduced (fully reduced, FR) forms of the enzyme. FTIR difference spectra were obtained in D(2)O (pH 6-9.3) between the MV-CO adduct (heme a(3) and Cu(B) reduced; heme a and Cu(A) oxidized) and a photostationary state in which the MV-CO enzyme is photodissociated under constant illumination. In the photostationary state, part of the enzyme population has heme a(3) oxidized and heme a reduced. In MV-CO, the frequency of the stretch mode of CO bound to ferrous heme a(3) decreases from 1965.3 cm(-1) at pH* </=7 to 1963.7 cm(-1) at pH* 9.3. In the CO adduct of the fully reduced enzyme (FR-CO), the CO stretching frequency is observed at 1963.46+/-0.05 cm(-1), independent of pH. This indicates that in MV-CO there is a group proximal to heme a that deprotonates with a pK(a) of about 8.3, but that remains protonated over the entire pH* range 6-9.3 in FR-CO. The pK(a) of this group is therefore strongly coupled to the redox state of heme a. Following photodissociation of CO from heme a(3) in MV oxidases, the extent of electron transfer from heme a(3) to heme a shows a pH-dependent phase between pH 7 and 9, and a pH-independent phase at all pH's. The FTIR difference spectrum resulting from photolysis of MV-CO exhibits vibrational features of the protein backbone and side chains associated with (1) the loss of CO by the a(3) heme in the absence of electron transfer, (2) the pH-independent phase of the electron transfer, and (3) the pH-dependent phase of the electron transfer. Many infrared features change intensity or frequency during both electron transfer phases and thus appear as positive or negative features in the difference spectra. In particular, a negative band at 1735 cm(-1) and a positive band at 1412 cm(-1) are consistent with the deprotonation of the acidic residue E242. Positive features at 1552 and 1661 cm(-1) are due to amide backbone modes. Other positive and negative features between 1600 and 1700 cm(-1) are consistent with redox-induced shifts in heme formyl vibrations, and the redox-linked protonation of an arginine residue, accompanying electron transfer from heme a(3) to heme a. An arginine could be the residue responsible for the pH-dependent shift in the carbonyl frequency of MV-CO. Specific possibilities as to the functional significance of these observations are discussed.

FTIR detection of protonation/deprotonation of key carboxyl side chains caused by redox change of the Cu(A)-heme a moiety and ligand dissociation from the heme a3-Cu(B) center of bovine heart cytochrome c oxidase

FTIR spectral changes of bovine cytochrome c oxidase (CcO) upon ligand dissociation from heme a(3)() and redox change of the Cu(A)-heme a moiety (Cu(A)Fe(a)()) were investigated. In a photosteady state under CW laser illumination at 590 nm to carbonmonoxy CcO (CcO-CO), the C-O stretching bands due to Fe(a3)()(2+)CO and Cu(B)(1+)CO were identified at 1963 and 2063 cm(-)(1), respectively, for the fully reduced (FR) state [(Cu(A)Fe(a)())(3+)Fe(a3)()(2+)Cu(B)(1+)] and at 1965 and 2061 cm(-)(1) for the mixed valence (MV) state [(Cu(A)Fe(a)())(5+)Fe(a3)()(2+)Cu(B)(1+)] in H(2)O as well as in D(2)O. For the MV state, however, another band due to Cu(B)(1+)CO was found at 2040 cm(-)(1), which was distinct from the alpha/beta conformers in the spectral behaviors, and therefore was assigned to the (Cu(A)Fe(a)())(4+)Fe(a3)()(3+)Cu(B)(1+)CO generated by back electron transfer. The FR-minus-oxidized difference spectrum in the carboxyl stretching region provided two negative bands at 1749 and 1737 cm(-)(1) in H(2)O, which were apparently merged into a single band with a band center at 1741 cm(-)(1) in D(2)O. Comparison of these spectra with those of bacterial enzymes suggests that the 1749 and 1737 cm(-)(1) bands are due to COOH groups of Glu242 and Asp51, respectively. A similar difference spectrum of the carboxyl stretching region was also obtained between (Cu(A)Fe(a)())(3+)Fe(a3)()(2+)Cu(B)(1+)CO and (Cu(A)Fe(a)())(5+)Fe(a3)()(2+)Cu(B)(1+)CO. The results indicate that an oxidation state of the (Cu(A)Fe(a)()) moiety determines the carboxyl stretching spectra. On the other hand, CO-dissociated minus CO-bound difference spectra in the FR state gave rise to a positive and a negative peaks at 1749 and 1741 cm(-)(1), respectively, in H(2)O, but mainly a negative peak at 1735 cm(-)(1) in D(2)O. It was confirmed that the absence of a positive peak is not caused by slow deuteration of protein. The corresponding difference spectrum in the MV state showed a significantly weaker positive peak at 1749 cm(-)(1) and an intense negative peak at 1741 cm(-)(1) (1737 cm(-)(1) in D(2)O). The spectral difference between the FR and MV states is explained satisfactorily by the spectral change induced by the electron back flow upon CO dissociation as described above. Thus, the changes of carboxyl stretching bands induced both by oxidation of (Cu(A)Fe(a)()) and dissociation of CO appear at similar frequencies ( approximately 1749 cm(-)(1)) but are ascribed to different carboxyl side chains.

Ligand binding reveals protonation events at the active site of cytochrome c oxidase; is the K-pathway used for the transfer of H(+) or OH(-)?

We have investigated the CO-recombination kinetics after flash photolysis of CO from the "half-reduced" cytochrome c oxidase as a function of pH. In addition, the reaction was investigated in mutant enzymes in which Lys(I-362) and Ser(I-299), located approximately in the middle of the K-pathway and near the enzyme surface, respectively, were modified. Laser-flash induced dissociation of CO is followed by rapid internal electron transfer from heme a(3) to a. At pH>7 this electron transfer is associated with proton release to the bulk solution (tau congruent with 1 ms at pH 8). Thus, the CO-recombination kinetics reflects protonation events at the catalytic site. In the wild-type enzyme, below pH approximately 7, the main component in the CO-recombination displayed a rate of approximately 20 s(-1). Above pH approximately 7, a slow CO-recombination component developed with a rate that decreased from approximately 8 s(-1) at pH 8 to approximately 1 s(-1) at pH 10. This slow component was not observed with KM(I-362), while with the SD(I-299)/SG(I-299) mutant enzymes at each pH it was slower than with the wild-type enzyme. The results are interpreted in terms of proton release from H(2)O in the catalytic site after CO dissociation, followed by OH(-) binding to the oxidized heme a(3). The CO-recombination kinetics is proposed to be determined by the protonation rate of OH(-) and not dissociation of OH(-), i.e. the K-pathway transfers protons and not OH(-). With the KM(I-362) mutant enzyme the proton is not released, i.e. OH(-) is not formed. With the SD(I-299)/SG(I-299) mutant enzymes the proton is released, but both the release and uptake are slowed by the mutations. During reaction of the reduced enzyme with O(2), the H(2)O at the binuclear center is most likely involved as a proton donor in the O-O cleavage reaction.

Photochemically induced electron transfer

Biochemical reactions involving electron transfer between substrates or enzyme cofactors are both common and physiologically important; they have been studied by means of a variety of techniques. In this paper we review the application of photochemical methods to the study of intramolecular electron transfer in hemoproteins, thus selecting a small, well-defined sector of this otherwise enormous field. Photoexcitation of the heme populates short-lived excited states which decay by thermal conversion and do not usually transfer electrons, even when a suitable electron acceptor is readily available, e.g., in the form of a second oxidized heme group in the same protein; because of this, the experimental setup demands some manipulation of the hemoprotein. In this paper we review three approaches that have been studied in detail: (i) the covalent conjugation to the protein moiety of an organic ruthenium complex, which serves as the photoexcitable electron donor (in this case the heme acts as the electron acceptor); (ii) the replacement of the heme group with a phosphorescent metal-substituted porphyrin, which on photoexcitation populates long-lived excited states, capable of acting as electron donors (clearly the protein must contain some other cofactor acting as the electron acceptor, most often a second heme group in the oxidized state); (iii) the combination of the reduced heme with CO (the photochemical breakdown of the iron-CO bond yields transiently the ground-state reduced heme which is able to transfer one electron (or a fraction of it) to an oxidized electron acceptor in the protein; this method uses a "mixed-valence hybrid" state of the redox active hemoprotein and has the great advantage of populating on photoexcitation an electron donor at physiological redox potential).

On the role of the K-proton transfer pathway in cytochrome c oxidase

Cytochrome c oxidase is a membrane-bound enzyme that catalyzes the four-electron reduction of oxygen to water. This highly exergonic reaction drives proton pumping across the membrane. One of the key questions associated with the function of cytochrome c oxidase is how the transfer of electrons and protons is coupled and how proton transfer is controlled by the enzyme. In this study we focus on the function of one of the proton transfer pathways of the R. sphaeroides enzyme, the so-called K-proton transfer pathway (containing a highly conserved Lys(I-362) residue), leading from the protein surface to the catalytic site. We have investigated the kinetics of the reaction of the reduced enzyme with oxygen in mutants of the enzyme in which a residue [Ser(I-299)] near the entry point of the pathway was modified with the use of site-directed mutagenesis. The results show that during the initial steps of oxygen reduction, electron transfer to the catalytic site (to form the "peroxy" state, P(r)) requires charge compensation through the proton pathway, but no proton uptake from the bulk solution. The charge compensation is proposed to involve a movement of the K(I-362) side chain toward the binuclear center. Thus, in contrast to what has been assumed previously, the results indicate that the K-pathway is used during oxygen reduction and that K(I-362) is charged at pH approximately 7.5. The movement of the Lys is proposed to regulate proton transfer by "shutting off" the protonic connectivity through the K-pathway after initiation of the O(2) reduction chemistry. This "shutoff" prevents a short-circuit of the proton-pumping machinery of the enzyme during the subsequent reaction steps.

Mechanisms for regulating electron transfer in multi-centre redox proteins

Protein-mediated electron transfer is a key process in nature. Many of the proteins involved in such electron transfers are complex and contain a number of redox-active cofactors. The very complexity of these multi-centre redox proteins has made it difficult to fully understand the various electron transfer events they catalyse. This is sometimes because the electron transfer steps themselves are gated or coupled to other processes such as proton transfer. However, with the molecular structures of many of these proteins now available it is possible to probe these electron transfer reactions at the molecular level. It is becoming apparent that many of these multi-centre redox proteins have rather subtle and elegant ways for regulating electron transfer. The purpose of this article is to illustrate how nature has used different approaches to control electron transfer in a number of different systems. Illustrative examples include: thermodynamic control of electron transfer in flavocytochromes b(2) and P450 BM3; a novel control mechanism involving calmodulin-binding-dependent electron transfer in neuronal nitric oxide synthase; the probable gating of electron transfer by ATP hydrolysis in nitrogenase; conformational gating of electron transfer in cytochrome cd(1); the regulation of electron transfer by protein dynamics in the cytochrome bc(1) complex; and finally the coupling of electron transfer to proton transfer in cytochrome c oxidase.

The proton collecting function of the inner surface of cytochrome c oxidase from Rhodobacter sphaeroides

The experiments presented in this study address the problem of how the cytoplasmic surface (proton-input side) of cytochrome c oxidase interacts with protons in the bulk. For this purpose, the cytoplasmic surface of the enzyme was labeled with a fluorescein (Flu) molecule covalently bound to Cys223 of subunit III. Using the Flu as a proton-sensitive marker on the surface and phiOH as a soluble excited-state proton emitter, the dynamics of the acid-base equilibration between the surface and the bulk was measured in the time-resolved domain. The results were analyzed by using a rigorous kinetic analysis that is based on numeric integration of coupled nonliner differential rate equations in which the rate constants are used as adjustable parameters. The analysis of 11 independent measurements, carried out under various initial conditions, indicated that the protonation of the Flu proceeds through multiple pathways involving diffusion-controlled reactions and proton exchange among surface groups. The surface of the protein carries an efficient system made of carboxylate and histidine moieties that are sufficiently close to each other as to form a proton-collecting antenna. It is the passage of protons among these sites that endows cytochrome c oxidase with the capacity to pick up protons from the buffered cytoplasmic matrix within a time frame compatible with the physiological turnover of the enzyme.

Cytochrome c oxidase: structure and spectroscopy

Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen, reducing the latter to water. Electron transfer is coupled to proton translocation across the membrane, resulting in a proton and charge gradient that is then employed by the F0F1-ATPase to synthesize ATP. Over the last years, substantial progress has been made in our understanding of the structure and function of this enzyme. Spectroscopic techniques such as EPR, absorbance and resonance Raman spectroscopy, in combination with site-directed mutagenesis work, have been successfully applied to elucidate the nature of the cofactors and their ligands, to identify key residues involved in proton transfer, and to gain insight into the catalytic cycle and the structures of its intermediates. Recently, the crystal structures of a bacterial and a mitochondrial cytochrome c oxidase have been determined. In this review, we provide an overview of the crystal structures, summarize recent spectroscopic work, and combine structural and spectroscopic data in discussing mechanistic aspects of the enzyme. For the latter, we focus on the structure of the oxygen intermediates, proton-transfer pathways, and the much-debated issue of how electron transfer in the enzyme might be coupled to proton translocation.

The generation of proton electrochemical potential gradient by cytochrome c oxidase

Cytochrome c oxidase, the terminal oxidase of mitochondria and some bacteria, catalyzes the four electron reduction of oxygen, and generates a proton electrochemical potential gradient (Delta microH). The recently determined structures of the bacterial and the bovine enzymes, together with studies of site directed mutants of a bacterial cytochrome c oxidase and a closely related ubiquinol oxidase, have greatly advanced our understanding of the mechanism by which oxygen reduction is coupled to the generation of Delta microH. Two different mechanisms contribute to the generation of Delta microH: protons that are consumed by the reduction of oxygen, are taken exclusively from the mitochondrial matrix ('consumed' protons), while other protons are translocated by the enzyme across the membrane ('pumped' protons). It is suggested that both proton consumption and proton pumping are driven by the electrostatic charging of the enzyme reaction center by the reducing electrons. Proton consumption is suggested to result from the electrostatically driven ejection of hydroxyls into the matrix that is catalyzed by a tyrosine residue in the reaction center. Proton pumping is suggested to result from the electrostatically driven translocation of a glutamate residue near the reaction center, and is assisted by secondary acceptors that release the translocated protons.

The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase

We have calculated the electrostatic potential and interaction energies of ionizable groups and analyzed the response of the protein environment to redox changes in Paracoccus denitrificans cytochrome c oxidase by using a continuum dielectric model and finite difference technique. Subsequent Monte Carlo sampling of protonation states enabled us to calculate the titration curves of all protonatable groups in the enzyme complex. Inclusion of a model membrane allowed us to restrict the calculations to the functionally essential subunits I and II. Some residues were calculated to have complex titration curves, as a result of strong electrostatic coupling, desolvation, and dipolar interactions. Around the heme a3-CuB binuclear center, we have identified a cluster of 18 strongly interacting residues that account for most of the proton uptake linked to electron transfer. This was calculated to be between 0.7 and 1.1 H+ per electron, depending on the redox transition considered. A hydroxide ion bound to CuB was determined to become protonated to form water upon transfer of the first electron to the binuclear site. The bulk of the protonation changes linked to further reduction of the heme a3-CuB center was calculated to be due to proton uptake by the interacting cluster and Glu(II-78). Upon formation of the three-electron reduced state (P1), His325, modeled in an alternative orientation away from CuB, was determined to become protonated. The agreement of these results with experiment and their relevance in the light of possible mechanisms of redox-coupled proton transfer are discussed.

Pathways of proton transfer in cytochrome c oxidase

During the last few years our knowledge of the structure and function of heme copper oxidases has greatly profited from the use of site-directed mutagenesis in combination with biophysical techniques. This, together with the recently-determined crystal structures of cytochrome c oxidase, has now made it possible to design experiments aimed at targeting specific pump mechanisms. Here, we summarize results from our recent kinetic studies of electron and proton-transfer reactions in wild-type and mutant forms of cytochrome c oxidase from Rhodobacter sphaeroides. These studies have made it possible to identify amino acid residues involved in proton transfer during specific reaction steps and provide a basis for discussion of mechanisms of electron and proton transfer in terminal oxidases. The results indicate that the pathway through K(I-362)/T(I-359), but not through D(I-132)/E(I-286), is used for proton transfer to a protonatable group interacting electrostatically with heme a3, i.e., upon reduction of the binuclear center. The pathway through D(I-132)/E(I-286) is used for uptake of pumped and substrate protons during the pumping steps during O2 reduction.

The role of electrostatic interactions for cytochrome c oxidase function

In recent years, the enormous increase in high-resolution three-dimensional structures of proteins together with the development of powerful theoretical techniques have provided the basis for a more detailed examination of the role of electrostatics in determining the midpoint potentials of redox-active metal centers and in influencing the protonation behavior of titratable groups in proteins. Based on the coordinates of the Paracoccus denitrificans cytochrome c oxidase, we have determined the electrostatic potential in and around the protein, calculated the titration curves for all ionizable residues in the protein, and analyzed the response of the protein environment to redox changes at the metal centers. The results of this study provide insight into how charged groups can be stabilized within a low-dielectric environment and how the range of their electrostatic effects can be modulated by the protein. A cluster of 18 titratable groups around the heme a3-CuB binuclear center, including a hydroxide ion bound to the copper, was identified that accounts for most of the proton uptake associated with redox changes at the binuclear site. Predicted changes in net protonation were in reasonable agreement with experimentally determined values. The relevance of these findings in the light of possible mechanisms of redox-coupled proton movement is discussed.