Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase

Gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (CcO) is one of the challenges of modern biophysics. Despite promising mechanistic proposals, most works have not related the activation barriers of the different assumed steps to the protein structure, and there has not been a physically consistent model that reproduced the barriers needed to create a working pump. This work reevaluates the activation barriers for the primary proton transfer (PT) steps by calculations that reflect all relevant free energy contributions, including the electrostatic energies of the generated charges, the energies of water insertion, and large structural rearrangements of the donor and acceptor. The calculations have reproduced barriers that account for the directionality and sequence of events in the primary PT in CcO. It has also been found that the PT from Glu-286 (E) to the propionate of heme a(3) (Prd) provides a gate for an initial back leakage from the high pH side of the membrane. Interestingly, the rotation of E that brings it closer to Prd appears to provide a way for blocking competing pathways in the primary PT. Our study elucidates and quantifies the nature of the control of the directionality in the primary PT in CcO and provides instructive insight into the role of the water molecules in biological PT, showing that "bridges" of several water molecules in hydrophobic regions present a problem (rather than a solution) that is minimized in the primary PT.     

The proton donor for O-O bond scission by cytochrome c oxidase

Cytochrome c oxidase is the main catalyst of oxygen consumption in mitochondria and many aerobic bacteria. The key step in oxygen reduction is scission of the O-O bond and formation of an intermediate P(R) of the binuclear active site composed of heme a(3) and Cu(B). The donor of the proton required for this reaction has been suggested to be a unique tyrosine residue (Tyr-280) covalently cross-linked to one of the histidine ligands of Cu(B). To test this idea we used the Glu-278-Gln mutant enzyme from Paracoccus denitrificans, in which the reaction with oxygen stops at the P(R) intermediate. Three different time-resolved techniques were used. Optical spectroscopy showed fast (approximately 60 micros) appearance of the P(R) species along with full oxidation of heme a, and FTIR spectroscopy revealed a band at 1,308 cm(-1), which is characteristic for the deprotonated form of the cross-linked Tyr-280. The development of electric potential during formation of the P(R) species suggests transfer of a proton over a distance of approximately 4 A perpendicular to the membrane plane, which is close to the distance between the oxygen atom of the hydroxyl group of Tyr-280 and the bound oxygen. These results strongly support the hypothesis that the cross-linked tyrosine is the proton donor for O-O bond cleavage by cytochrome c oxidase and strengthens the view that this tyrosine also provides the fourth electron in O(2) reduction in conditions where heme a is oxidized.     

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.     

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase

Aerobic life is based on a molecular machinery that utilizes oxygen as a terminal electron sink. The membrane-bound cytochrome c oxidase (CcO) catalyzes the reduction of oxygen to water in mitochondria and many bacteria. The energy released in this reaction is conserved by pumping protons across the mitochondrial or bacterial membrane, creating an electrochemical proton gradient that drives production of ATP. A crucial question is how the protons pumped by CcO are prevented from flowing backwards during the process. Here, we show by molecular dynamics simulations that the conserved glutamic acid 242 near the active site of CcO undergoes a protonation state-dependent conformational change, which provides a valve in the pumping mechanism. The valve ensures that at any point in time, the proton pathway across the membrane is effectively discontinuous, thereby preventing thermodynamically favorable proton back-leakage while maintaining an overall high efficiency of proton translocation. Suppression of proton leakage is particularly important in mitochondria under physiological conditions, where production of ATP takes place in the presence of a high electrochemical proton gradient.     

Initiation of the proton pump of cytochrome c oxidase

Cytochrome c oxidase is the terminal enzyme of the respiratory chain that is responsible for biological energy conversion in mitochondria and aerobic bacteria. The membrane-bound enzyme converts free energy from oxygen reduction to an electrochemical proton gradient by functioning as a redox-coupled proton pump. Although the 3D structure and functional studies have revealed proton conducting pathways in the enzyme interior, the location of proton donor and acceptor groups are not fully identified. We show here by time-resolved optical and FTIR spectroscopy combined with time-resolved electrometry that some mutant enzymes incapable of proton pumping nevertheless initiate catalysis by proton transfer to a proton-loading site. A conserved tyrosine in the so-called D-channel is identified as a potential proton donor that determines the efficiency of this reaction.     

Vectorial proton transfer coupled to reduction of O2 and NO by a heme-copper oxidase

The heme-copper oxidase (HCuO) superfamily consists of integral membrane proteins that catalyze the reduction of either oxygen or nitric oxide. The HCuOs that reduce O₂ to H₂O couple this reaction to the generation of a transmembrane proton gradient by using electrons and protons from opposite sides of the membrane and by pumping protons from inside the cell or organelle to the outside. The bacterial NO-reductases (NOR) reduce NO to N₂O (2NO + 2e⁻ + 2H⁺ → N₂O + H₂O), a reaction as exergonic as that with O₂. Yet, in NOR both electrons and protons are taken from the outside periplasmic solution, thus not conserving the free energy available. The cbb₃-type HCuOs catalyze reduction of both O₂ and NO. Here, we have investigated energy conservation in the Rhodobacter sphaeroides cbb₃ oxidase during reduction of either O₂ or NO. Whereas O₂ reduction is coupled to buildup of a substantial electrochemical gradient across the membrane, NO reduction is not. This means that although the cbb₃ oxidase has all of the structural elements for uptake of substrate protons from the inside, as well as for proton pumping, during NO reduction no pumping occurs and we suggest a scenario where substrate protons are derived from the outside solution. This would occur by a reversal of the proton pathway normally used for release of pumped protons. The consequences of our results for the general pumping mechanism in all HCuOs are discussed.     

Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase

Cytochrome c oxidases (Coxs) are the basic energy transducers in the respiratory chain of the majority of aerobic organisms. Coxs studied to date are redox-driven proton-pumping enzymes belonging to one of three subfamilies: A-, B-, and C-type oxidases. The C-type oxidases (cbb₃ cytochromes), which are widespread among pathogenic bacteria, are the least understood. In particular, the proton-pumping machinery of these Coxs has not yet been elucidated despite the availability of X-ray structure information. Here, we report the discovery of the first (to our knowledge) sodium-pumping Cox (Scox), a cbb₃ cytochrome from the extremely alkaliphilic bacterium Thioalkalivibrio versutus. This finding offers clues to the previously unknown structure of the ion-pumping channel in the C-type Coxs and provides insight into the functional properties of this enzyme.The known terminal oxidases according to the structure of their active centers and their phylogenetic relations are subdivided into two superfamilies (1). One is composed of numerous representatives containing a heme-copper binuclear active center (BNC). Oxidases belonging to the other superfamily have no copper. This superfamily includes bacterial oxidases of the bd type. The superfamily of representatives with heme-copper BNC is subdivided in turn into two groups, cytochrome c oxidases (Coxs) and quinol oxidases, depending upon the electron donor, which can be either cytochrome c or quinol. Quinol oxidases with a heme-copper BNC are found only in prokaryotes, whereas Coxs are widespread among living organisms of all domains: Eukarya (where they are found in mitochondria and chloroplasts), Bacteria, and Archaea. Although terminal oxidases with heme-copper BNC constitute a diverse group of multisubunit enzymes having from 2 to 13 subunits, conservatism and similar architecture are obviously inherent in their main (catalytic) subunit. The catalytic center of the main subunit always contains two hemes and copper as redox active prosthetic groups and a redox active tyrosine covalently bound to histidine in the polypeptide chain (2–5). Iron of one of the hemes and copper constitute the BNC. Coxs are the best-studied group of terminal oxidases. The basic mechanism of energy transduction by Coxs during respiration consists of the oxidation of cytochrome c by molecular oxygen (O₂) coupled to transmembrane pumping of protons (H⁺). This process results in reduction of O₂ to water by the BNC, where O₂ is bound. In Coxs, it requires four protons (“chemical” H⁺ for water production) taken from the inner side of the membrane and can be coupled to the translocation of another four protons (“pumped” H⁺) from the inner to the outer side of the membrane into the intermembrane or the periplasmic space of mitochondria or prokaryotic cells, respectively, according to the following equation (6–8):4cytc2++4Hin,chem++4Hin,chem++4Hin,pump++O2→4cytc3++4Hout,pump++2H2O.In A-type Coxs, two H⁺ pathways in the main subunit were identified, the so-called D channel, conducting all pumped and part of chemical H⁺, and the K channel, conducting most of chemical H⁺ (9). In C-type Coxs, only a K-channel analog was found (10). The described catalytic events are accomplished through generation of a transmembrane difference in H⁺ potentials (Δμ¯H+), which is used as a convertible membrane-linked biological currency. Microorganisms living in an alkaline environment maintain a nearly neutral cytoplasmic pH (11). This presents a problem for alkaliphiles because it gives rise to an inverted pH gradient that decreases the Δμ¯H+ (12, 13). Some alkaliphilic microorganisms solve this problem by using an Na⁺-pumping NADH-CoQ reductase (NQR) (14), and perhaps a Na⁺-pumping terminal oxidase, as was assumed (15). At present, NQR is the only respiratory chain enzyme for which Na⁺ pumping has been directly and undoubtedly established (16). However, NQR is absent in the extremely alkaliphilic bacterium Thioalkalivibrio versutus AL2, which inhabits an alkaline (∼pH 10) Siberian soda lake at saturating salt concentrations (17). T. versutus is a chemolithotroph that oxidizes sulfur compounds and employs Cox as a terminal component of its aerobic electron transport chain. Here we report that T. versutus uses a novel C-type Cox that (i) specifically requires Na⁺ for its activity and (ii) electrogenically exports Na⁺ from cells or right-side-out subcellular membrane vesicles, the process being coupled to oxidation of ascorbate by O₂.     

Kinetic gating of the proton pump in cytochrome c oxidase

Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain, reduces oxygen to water and uses the released energy to pump protons across a membrane. Here, we use kinetic master equations to explore the energetic and kinetic control of proton pumping in CcO. We construct models consistent with thermodynamic principles, the structure of CcO, experimentally known proton affinities, and equilibrium constants of intermediate reactions. The resulting models are found to capture key properties of CcO, including the midpoint redox potentials of the metal centers and the electron transfer rates. We find that coarse-grained models with two proton sites and one electron site can pump one proton per electron against membrane potentials exceeding 100 mV. The high pumping efficiency of these models requires strong electrostatic couplings between the proton loading (pump) site and the electron site (heme a), and kinetic gating of the internal proton transfer. Gating is achieved by enhancing the rate of proton transfer from the conserved Glu-242 to the pump site on reduction of heme a, consistent with the predictions of the water-gated model of proton pumping. The model also accounts for the phenotype of D-channel mutations associated with loss of pumping but retained turnover. The fundamental mechanism identified here for the efficient conversion of chemical energy into an electrochemical potential should prove relevant also for other molecular machines and novel fuel-cell designs.     

Electrostatics,hydration, and proton transfer dynamics in the membrane domain of respiratory complex I

Complex I serves as the primary electron entry point into the mitochondrial and bacterial respiratory chains. It catalyzes the reduction of quinones by electron transfer from NADH, and couples this exergonic reaction to the translocation of protons against an electrochemical proton gradient. The membrane domain of the enzyme extends ∼180 Å from the site of quinone reduction to the most distant proton pathway. To elucidate possible mechanisms of the long-range proton-coupled electron transfer process, we perform large-scale atomistic molecular dynamics simulations of the membrane domain of complex I from Escherichia coli. We observe spontaneous hydration of a putative proton entry channel at the NuoN/K interface, which is sensitive to the protonation state of buried glutamic acid residues. In hybrid quantum mechanics/classical mechanics simulations, we find that the observed water wires support rapid proton transfer from the protein surface to the center of the membrane domain. To explore the functional relevance of the pseudosymmetric inverted-repeat structures of the antiporter-like subunits NuoL/M/N, we constructed a symmetry-related structure of a possible alternate-access state. In molecular dynamics simulations, we find the resulting structural changes to be metastable and reversible at the protein backbone level. However, the increased hydration induced by the conformational change persists, with water molecules establishing enhanced lateral connectivity and pathways for proton transfer between conserved ionizable residues along the center of the membrane domain. Overall, the observed water-gated transitions establish conduits for the unidirectional proton translocation processes, and provide a possible coupling mechanism for the energy transduction in complex I.Complex I, or NADH:ubiquinone oxidoreductase, is an enzyme crucial for biological energy conversion. By transferring electrons from reduced NADH to quinone (Q), it functions as a primary entry point for electrons into the mitochondrial and bacterial respiratory chains (1, 2). Complex I couples the Q reduction to translocation of three to four protons across the mitochondrial or bacterial membrane (3, 4), thus contributing to the electrochemical proton-motive force subsequently used for synthesis of ATP by F_oF₁-ATPase and for active transport of solutes (5).Complex I is a large (550–980 kDa) L-shaped enzyme, which consists of a hydrophilic domain located in the mitochondrial matrix/bacterial cytoplasm, and a membrane domain, embedded in the mitochondrial inner membrane/bacterial cytoplasmic membrane (1, 2). Its 14 core subunits are evolutionarily conserved in bacteria and eukaryotes (1), with over 20 additional subunits in higher organisms (6). The hydrophilic domain provides an electron transfer chain from NADH via a flavine mononucleotide and eight to nine iron-sulfur centers to Q, located at the end of this chain (Fig. 1A) (7, 8). Leakage from this electron transfer pathway is a likely source of mitochondrial reactive oxygen species (9) associated with neurodegenerative diseases and aging.Open in a separate windowFig. 1.Structure and internal symmetry of complex I from E. coli. (A) Membrane (PDB ID: 3RKO) and hydrophilic domains (PDB ID: 2FUG) of complex I embedded in a lipid membrane. The antiporter-like subunits NuoN, NuoM, and NuoL are shown in yellow, blue, and red, respectively. (B) TM helix segments 4–8 (blue) and 9–13 (red) in NuoN/M/L structurally superimposed. TM helices 4–6 and 9–11 have high structural similarity, whereas TM helices 7–8, and 12–13 are in a different conformation. (C) Position of key residues in the membrane domain of complex I. The amphipathic HL helix (red) lies parallel to the membrane plane, and contacts all three antiporter-like subunits.The proton-translocating membrane domain of complex I comprises three antiporter-like subunits, NuoN, NuoM, and NuoL (Escherichia coli naming), which are connected to the hydrophilic domain by the NuoA/J/K/H subunits (10, 11). The antiporter-like subunits are homologous to each other as well as to, for example, Mrp (multiresistance and pH adaptation) Na⁺/H⁺-antiporters and certain hydrogenases (12). The antiporter-like subunits have an intrinsic sequence identity of ∼20%, but an even more evident structural homology: the transmembrane (TM) helices 4–8 and 9–13 can be structurally superimposed (Fig. 1B). These subunits also contain several crucial residues for the proton translocation process (Fig. 1C): a conserved Lys-Glu (or Asp in NuoL) ion pair in TM helices 5/7a, and one or two other conserved lysines, have been confirmed by site-directed mutagenesis experiments to be crucial for the proton translocation process (1, 2) (Table S1). During the completion of this study, a new X-ray structure of the intact complex I from Thermus thermophilus was released (13). The structure reveals that the NuoH subunit (Nqo8 in T. thermophilus) has structural resemblance to the TM helix segment 4–8 of the antiporter-like NuoN/M/L subunits (13), and may thus also be involved in the proton-pumping machinery. A detailed comparison of key regions of the Escherichia coli and T. thermophilus membrane domains is shown in Fig. S1.Interestingly, mutation of conserved residues in the NuoL subunit, ∼180 Å away from the hydrophilic domain, leads to loss of the Q-reductase activity (1, 2) (Table S1). Although expected for a fully reversible proton-coupled electron transfer machine, this tight coupling imposes severe mechanistic demands. Remarkably, after deletion of subunits equivalent to NuoL and NuoM, the apparent pumping stoichiometry was reduced by about one-half (14). The putative proton transfer pathways through the membrane domain are distant from the redox-active groups mediating electron transfer through the hydrophilic domain (10). As a consequence, the proton-coupled electron transfer in complex I is expected to differ mechanistically from that in other systems, such as ribonucleotide reductase, an enzyme involved in synthesis of DNA from RNA, where the proton and the electron are transferred concertedly along a pathway of conserved residues (15, 16). In contrast, in complex I the electron and proton transfers are separated both kinetically and spatially. To explain this long-range coupling, both “direct” (redox-driven) and “indirect” (conformational-driven) mechanisms have been suggested, but the molecular principles of these mechanisms remain elusive (1, 2, 4, 17–22).Complex I has been suggested to undergo conformational changes, which may drive the proton-translocation process (11, 23). Superimposing the TM helix segments of NuoN, NuoM, and NuoL suggests that TM helices 4–6/9–11 are structurally in a similar conformation, whereas the TM helices 7–8/12–13 have a different tilting angle relative to the membrane normal (Fig. 1B). In terms of its evolutionary homology to antiporters, this internal symmetry would suggest that the two segments are in different conformational states with connectivity to different sides of the membrane, in analogy to what has been observed for carrier-type transporters (24).To gain further insight into the long-range coupling mechanism, we study here the dynamics of the membrane domain of complex I from E. coli by large-scale atomistic molecular dynamics (MD) simulations, hybrid quantum mechanics/molecular mechanics (QM/MM) approaches, and continuum electrostatics calculations. Our simulations, both in the state of the crystal structure and in a putative alternate-access state with inverted symmetry established by harmonic restraints, give molecular insight into the structural dynamics and coupling of key residues involved in the proton translocation process. Instead of large-scale conformational changes associated with traditional transporter function, we show here that extensive changes in internal hydration establish the changes in protonic access required for pumping. With these hydration changes found to be strongly coupled to the charge states of conserved titratable residues, and their charge states in turn coupled to each other, internal water thus emerges as the key element in the redox-coupled proton translocation process that connects the extensive network of buried ionizable residues with each other and with the surfaces.     

Exploring the proton pump mechanism of cytochrome c oxidase in real time

Cytochrome c oxidase catalyzes most of the biological oxygen consumption on Earth, a process responsible for energy supply in aerobic organisms. This remarkable membrane-bound enzyme also converts free energy from O(2) reduction to an electrochemical proton gradient by functioning as a redox-linked proton pump. Although the structures of several oxidases are known, the molecular mechanism of redox-linked proton translocation has remained elusive. Here, correlated internal electron and proton transfer reactions were tracked in real time by spectroscopic and electrometric techniques after laser-activated electron injection into the oxidized enzyme. The observed kinetics establish the long-sought reaction sequence of the proton pump mechanism and describe some of its thermodynamic properties. The 10-micros electron transfer to heme a raises the pK(a) of a "pump site," which is loaded by a proton from the inside of the membrane in 150 micros. This loading increases the redox potentials of both hemes a and a(3), which allows electron equilibration between them at the same rate. Then, in 0.8 ms, another proton is transferred from the inside to the heme a(3)/Cu(B) center, and the electron is transferred to Cu(B). Finally, in 2.6 ms, the preloaded proton is released from the pump site to the opposite side of the membrane.     

Role of aspartate 132 at the orifice of a proton pathway in cytochrome c oxidase

Proton transfer across biological membranes underpins central processes in biological systems, such as energy conservation and transport of ions and molecules. In the membrane proteins involved in these processes, proton transfer takes place through specific pathways connecting the two sides of the membrane via control elements within the protein. It is commonly believed that acidic residues are required near the orifice of such proton pathways to facilitate proton uptake. In cytochrome c oxidase, one such pathway starts near a conserved Asp-132 residue. Results from earlier studies have shown that replacement of Asp-132 by, e.g., Asn, slows proton uptake by a factor of ∼5,000. Here, we show that proton uptake at full speed (∼10⁴ s⁻¹) can be restored in the Asp-132–Asn oxidase upon introduction of a second structural modification further inside the pathway (Asn-139–Thr) without compensating for the loss of the negative charge. This proton-uptake rate was insensitive to Zn²⁺ addition, which in the wild-type cytochrome c oxidase slows the reaction, indicating that Asp-132 is required for Zn²⁺ binding. Furthermore, in the absence of Asp-132 and with Thr at position 139, at high pH (>9), proton uptake was significantly accelerated. Thus, the data indicate that Asp-132 is not strictly required for maintaining rapid proton uptake. Furthermore, despite the rapid proton uptake in the Asn-139–Thr/Asp-132–Asn mutant cytochrome c oxidase, proton pumping was impaired, which indicates that the segment around these residues is functionally linked to pumping.     

Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase

The membrane-bound enzyme cytochrome c oxidase is responsible for cell respiration in aerobic organisms and conserves free energy from O2 reduction into an electrochemical proton gradient by coupling the redox reaction to proton-pumping across the membrane. O2 reduction produces water at the bimetallic heme a3/CuB active site next to a hydrophobic cavity deep within the membrane. Water molecules in this cavity have been suggested to play an important role in the proton-pumping mechanism. Here, we show by molecular dynamics simulations that the conserved arginine/heme a3 delta-propionate ion pair provides a gate, which exhibits reversible thermal opening that is governed by the redox state and the water molecules in the cavity. An important role of this gate in the proton-pumping mechanism is supported by site-directed mutagenesis experiments. Transport of the product water out of the enzyme must be rigidly controlled to prevent water-mediated proton leaks that could compromise the proton-pumping function. Exit of product water is observed through the same arginine/propionate gate, which provides an explanation for the observed extraordinary spatial specificity of water expulsion from the enzyme.     

Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway

Proton translocation in the D-pathway of cytochrome c oxidase has been studied by a combination of classical molecular dynamics and the multistate empirical valence bond methodology. This approach allows for explicit Grotthuss proton hopping between water molecules. According to mutagenesis experiments, the role of proton donor/acceptor along the D-pathway is carried by the highly conserved residue Glu-242. The present multistate empirical valence bond simulations indicate that the protonation/deprotonation state of Glu-242 is strongly coupled to the distance of proton propagation in the D-pathway. The proton was seen to travel the full length of the D-pathway when Glu-242 was deprotonated; however, it was trapped halfway along the path when Glu-242 was protonated. Further investigation in terms of both proton dynamical properties and free energy calculations for the pathway of proton transport provides evidence for a two-step proton transport mechanism in the D-pathway.     

CO impedes superfast O2 binding in ba3 cytochrome oxidase from Thermus thermophilus

Kinetic studies of heme-copper terminal oxidases using the CO flow-flash method are potentially compromised by the fate of the photodissociated CO. In this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by ba(3) cytochrome c oxidase from Thermus thermophilus in the absence and presence of CO using a photolabile O(2)-carrier. A novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the O(2)-carrier with a 355 nm laser pulse and the fully reduced CO-bound ba(3) simultaneously with a second 532-nm laser pulse. A kinetic analysis reveals a sequential mechanism in which O(2) binding to heme a(3) at 90 μM O(2) occurs with lifetimes of 9.3 and 110 μs in the absence and presence of CO, respectively, followed by a faster cleavage of the dioxygen bond (4.8 μs), which generates the P intermediate with the concomitant oxidation of heme b. The second-order rate constant of 1 × 10(9) M(-1) s(-1) for O(2) binding to ba(3) in the absence of CO is 10 times greater than observed in the presence of CO as well as for the bovine heart enzyme. The O(2) bond cleavage in ba(3) of 4.8 μs is also approximately 10 times faster than in the bovine enzyme. These results suggest important structural differences between the accessibility of O(2) to the active site in ba(3) and the bovine enzyme, and they demonstrate that the photodissociated CO impedes access of dioxygen to the heme a(3) site in ba(3), making the CO flow-flash method inapplicable.     

Mapping protein dynamics in catalytic intermediates of the redox-driven proton pump cytochrome c oxidase

Redox-driven proton pumps such as cytochrome c oxidase (CcO) are fundamental elements of the energy transduction machinery in biological systems. CcO is an integral membrane protein that acts as the terminal electron acceptor in respiratory chains of aerobic organisms, catalyzing the four-electron reduction of O2 to H2O. This reduction also requires four protons taken from the cytosolic or negative side of the membrane, with an additional uptake of four protons that are pumped across the membrane. Therefore, the proton pump must embody a "gate," which provides alternating access of protons to one or the other side of the membrane but never both sides simultaneously. However, the exact mechanism of proton translocation through CcO remains unknown at the molecular level. Understanding pump function requires knowledge of the nature and location of these structural changes that is often difficult to access with crystallography or NMR spectroscopy. In this paper, we demonstrate, with amide hydrogen/deuterium exchange MS, that transitions between catalytic intermediates in CcO are orchestrated with opening and closing of specific proton pathways, providing an alternating access for protons to the two sides of the membrane. An analysis of these results in the framework of the 3D structure of CcO indicate the spatial location of a gate, which controls the unidirectional proton flux through the enzyme and points to a mechanism by which CcO energetically couples electron transfer to proton translocation.     

Respiration triggers heme transfer from cytochrome c peroxidase to catalase in yeast mitochondria

In exponentially growing yeast, the heme enzyme, cytochrome c peroxidase (Ccp1) is targeted to the mitochondrial intermembrane space. When the fermentable source (glucose) is depleted, cells switch to respiration and mitochondrial H₂O₂ levels rise. It has long been assumed that CCP activity detoxifies mitochondrial H₂O₂ because of the efficiency of this activity in vitro. However, we find that a large pool of Ccp1 exits the mitochondria of respiring cells. We detect no extramitochondrial CCP activity because Ccp1 crosses the outer mitochondrial membrane as the heme-free protein. In parallel with apoCcp1 export, cells exhibit increased activity of catalase A (Cta1), the mitochondrial and peroxisomal catalase isoform in yeast. This identifies Cta1 as a likely recipient of Ccp1 heme, which is supported by low Cta1 activity in ccp1Δ cells and the accumulation of holoCcp1 in cta1Δ mitochondria. We hypothesized that Ccp1’s heme is labilized by hyperoxidation of the protein during the burst in H₂O₂ production as cells begin to respire. To test this hypothesis, recombinant Ccp1 was hyperoxidized with excess H₂O₂ in vitro, which accelerated heme transfer to apomyoglobin added as a surrogate heme acceptor. Furthermore, the proximal heme Fe ligand, His175, was found to be ∼85% oxidized to oxo-histidine in extramitochondrial Ccp1 isolated from 7-d cells, indicating that heme labilization results from oxidation of this ligand. We conclude that Ccp1 responds to respiration-derived H₂O₂ via a previously unidentified mechanism involving H₂O₂-activated heme transfer to apoCta1. Subsequently, the catalase activity of Cta1, not CCP activity, contributes to mitochondrial H₂O₂ detoxification.Cytochrome c peroxidase (Ccp1) is a monomeric nuclear encoded protein with a 68-residue N-terminal mitochondrial targeting sequence (1). This presequence crosses the inner mitochondrial membrane and is cleaved by matrix proteases (2, 3). Mature heme-loaded Ccp1 is found in the mitochondrial intermembrane space (IMS) in exponentially growing yeast (2, 3) but the point of insertion of its single b-type heme is unknown. Under strict anaerobic conditions, Ccp1 is present in mitochondria as the heme-free form or apoform (4). Once cells are exposed to O₂ and heme biosynthesis is turned on, apoCcp1 converts rapidly to the mature holoenzyme by noncovalently binding heme (5).It is well established that mature Ccp1 functions as an efficient H₂O₂ scavenger in vitro (6). Its catalytic cycle involves the reaction of ferric Ccp1 with H₂O₂ (Eq. 1) to form compound I (CpdI) with a ferryl (Fe^IV) heme and a cationic indole radical localized on Trp191 (W191^+•). CpdI is one-electron reduced by the ferrous heme of cytochrome c (Cyc1) to compound II (CpdII) with ferryl heme (Eq. 2), and electron donation by a second ferrous Cyc1 returns CpdII to the resting Ccp1^III form (Eq. 3):Ccp1^III + H₂O₂ → CpdI(Fe^IV, W191^+?) + H₂O[1]CpdI(Fe^IV, W191^+?) + Cyc1^II → CpdII(Fe^IV) + Cyc1^III[2]CpdII(Fe^IV) + Cyc1^II → Ccp1^III + Cyc1^III + H₂O.[3]Because Ccp1 production is not under O₂/heme control (4, 5), CCP activity is assumed to be the frontline defense in the mitochondria, a major source of reactive oxygen species (ROS) in respiring cells (7). Contrary to the time-honored assumption that Ccp1 catalytically consumes the H₂O₂ produced during aerobic respiration (8), recent studies in our group reveal that the peroxidase behaves more like a mitochondrial H₂O₂ sensor than a catalytic H₂O₂ detoxifier (9–11). Notably, Ccp1 competes with complex IV for reducing equivalents from Cyc1, which shuttles electrons from complex III (ubiquinol cytochrome c reductase) to complex IV (cytochrome c oxidase) in the electron transport chain (12).Because CCP activity in the IMS siphons electrons from energy production, an H₂O₂ sensor role for Ccp1 should be energetically more favorable for the cell. Key evidence for a noncatalytic role for Ccp1 in H₂O₂ removal is that the isogenic strain producing the catalytically inactive Ccp1^W191F protein accumulates less H₂O₂ than wild-type cells (10). In fact, this mutant strain exhibits approximately threefold higher catalase A (Cta1) activity than wild-type cells (10) whereas CCP1 deletion results in a strain (ccp1Δ) with negligible Cta1 activity and high H₂O₂ levels (5). Unlike Cta1, which is the peroxisomal and mitochondrial catalase isoform in yeast (13), the cytosolic catalase Ctt1 (14) exhibits comparable activity in the wild-type, Ccp1^W191F, and ccp1Δ strains (10). Given that both Ccp1 and Cta1 are targeted to mitochondria, we hypothesized that Ccp1 may transfer its heme to apoCta1 in respiring cells.Cta1 is nuclear encoded with embedded mitochondrial and peroxisomal targeting sequences (15). Like Ccp1, each monomer noncovalently binds a b-type heme and mature Cta1 is active as a homotetramer. Synthesis of the Cta1 monomer is under O₂/heme control such that the apoenzyme begins to accumulate only during the logarithmic phase of aerobic growth (16). Hence, its O₂/heme independent production (4, 5) allows apoCcp1 to acquire heme while cells are synthesizing apoCta1. This, combined with our observation that Cta1 activity increases in respiring cells producing Ccp1 or Ccp1^W191F but not in ccp1Δ cells (10), led us to speculate that respiration-derived H₂O₂ triggers heme donation from Ccp1 to apoCta1 within mitochondria.What experimental evidence would support heme donation by Ccp1? It has been demonstrated that mutation of the proximal heme Fe ligand, His175, to a residue with weak or no Fe-coordinating ability produces Ccp1 variants (H175P, H175L, H175R, and H175M) that undergo mitochondrial processing but do not accumulate in isolated yeast mitochondria (17). Presumably, reduced heme affinity allows the Ccp1 variants to unfold and cross the outer mitochondrial membrane (17). Hence, we argued that if wild-type Ccp1 donated its heme, the apoprotein would likewise exit mitochondria. Consequently, we examine here age-dependent Ccp1–green fluorescent protein (Ccp1-GFP) localization in live cells chromosomally expressing Ccp1 C-terminally fused to GFP as well as the distribution of wild-type Ccp1 between subcellular fractions. Because weakening or removal of the proximal Fe ligand on His175 mutation reduces heme affinity (17), His175 oxidation in wild-type Ccp1 should have a similar effect, which we investigate here. We further speculated that in the absence of apoCta1 as an acceptor for its heme, more Ccp1 would remain trapped in the IMS so we compare mitochondrial Ccp1 levels in wild-type and cta1∆ cells. Our combined results support triggering of heme donation from Ccp1 to apoCta1 by respiration-derived H₂O₂. Such H₂O₂-activated heme transfer between proteins has not been reported to date and its implications in H₂O₂ signaling are discussed.     

Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase

Molecular oxygen acts as the terminal electron sink in the respiratory chains of aerobic organisms. Cytochrome c oxidase in the inner membrane of mitochondria and the plasma membrane of bacteria catalyzes the reduction of oxygen to water, and couples the free energy of the reaction to proton pumping across the membrane. The proton-pumping activity contributes to the proton electrochemical gradient, which drives the synthesis of ATP. Based on kinetic experiments on the O–O bond splitting transition of the catalytic cycle (A → P_R), it has been proposed that the electron transfer to the binuclear iron–copper center of O₂ reduction initiates the proton pump mechanism. This key electron transfer event is coupled to an internal proton transfer from a conserved glutamic acid to the proton-loading site of the pump. However, the proton may instead be transferred to the binuclear center to complete the oxygen reduction chemistry, which would constitute a short-circuit. Based on atomistic molecular dynamics simulations of cytochrome c oxidase in an explicit membrane–solvent environment, complemented by related free-energy calculations, we propose that this short-circuit is effectively prevented by a redox-state–dependent organization of water molecules within the protein structure that gates the proton transfer pathway.Life on Earth is supported by a constant supply of energy in the form of ATP. Cytochrome c oxidase (CcO) in the respiratory chains of mitochondria and bacteria catalyzes the exergonic reduction of molecular oxygen (O₂) to water and uses the free energy of the reaction to pump protons across the membrane (1–3). The oxygen reduction reaction takes place at a highly conserved active site formed by two metal sites, heme a₃ and Cu_B (Fig. 1 A and B), called the binuclear center (BNC). The electrons donated by the mobile electron carrier cytochrome c reach the BNC via two other conserved metal centers, Cu_A and heme a (Fig. 1A). The protons required for the chemistry of O₂ reduction to water, and for proton pumping, are transported with the assistance of side chains of polar amino acids and conserved water molecules in the protein interior (4–6) (Fig. 1A). Two such proton transfer pathways have been described in the mitochondrial and bacterial A-type oxidases (to distinguish between different types of oxidases, see ref. 7), namely, the D and K channels (8, 9), the names of which are based on the conserved amino acid residues Asp91 and Lys319, respectively (Fig. 1A, amino acid numbering based on the bovine heart CcO). The D channel is responsible for the translocation of all of the pumped protons, and for the transfer of at least two of the four protons required for oxygen reduction chemistry, whereas the K channel supplies one or two protons to the BNC during the reductive phase of the catalytic cycle (8, 9). The D channel terminates at a highly conserved glutamic acid residue, Glu242, from where the protons are either transferred to the BNC for consumption, or to the proton-loading site (PLS) for pumping across the membrane (Fig. 1A). In 2003, Wikström et al. postulated a molecular mechanism in which water molecules in the nonpolar cavity above Glu242 would form proton-transferring chains, the orientation of which depends upon the redox state of the enzyme (10). They proposed that the reduction of the low-spin heme would result in transfer of a proton via a preorganized water chain from Glu242 to the d-propionate (Dprp) of the high-spin heme, whereas in the case when the electron has moved to the BNC, the water chain would reorientate and conduct protons from Glu242 to the BNC (Fig. 1A, and see below). Even though there is little direct experimental support available for such a water-gated mechanism, a recent FTIR study indeed suggests changes in water organization upon changes in the redox state of the enzyme (11). Many of the elementary steps that were postulated in the water-gated mechanism have gained support from experiments in the recent past (12, 13).Open in a separate windowFig. 1.(A) A three-subunit (SU) CcO. SU I (blue), II (red), and III (orange) are displayed as transparent ribbons. The D and K channels of proton transfer are marked with blue arrows. Crystallographic water molecules present in these proton channels are shown in purple. Electron transfer (red arrow) takes place from Cu_A (orange) via heme a (yellow) to the binuclear center comprising heme a₃ (yellow)–Cu_B (orange). Protons are transferred from Glu242 (E242) either to the PLS or to the binuclear center (black arrows). Lipid bilayer (silver lines), water (gray dots), and sodium (light yellow) and chloride (cyan) ions are also displayed. (B) The catalytic cycle of CcO. The states of heme a₃, Cu_B, and the cross-linked tyrosine are displayed. Each light orange rectangle corresponds to a state of the BNC, the name of which is displayed in red (Upper Right). Pumped protons are shown in blue, black H⁺ indicates uptake of a proton for water formation, and e⁻ indicates transfer of an electron from the low-spin heme a. Catalysis of O₂ reduction occurs clockwise.It is generally thought that the proton pump of CcO operates via the same mechanism in each of the 4 one-electron reduction steps of the catalytic cycle (Fig. 1B). However, kinetic data on two different transitions (A → P_R and O_H → E_H) have suggested dissimilarities in some of the elementary steps (12, 13). Fully reduced enzyme reacts with oxygen and forms an oxygenated adduct A in ca. 10 µs, followed by splitting of the O–O bond leading to formation of the P_R intermediate (in ∼25 μs) that is linked to loading of the PLS with a proton (3, 12). O–O bond splitting from state A in the absence of electrons in heme a or Cu_A yields the stable state P_M without proton transfer to the PLS (3, 12). Therefore, it is the electron transfer from heme a into the BNC accompanying O–O bond scission during A → P_R that is linked to the proton transfer to the PLS. The structure of the P_R intermediate is well characterized with ferryl heme a₃, cupric hydroxide, and tyrosinate (3, 14). In P_M the tyrosine is almost certainly in the form of a neutral radical (3, 14), so the reaction P_M → P_R is a proton-coupled electron transfer reaction (PCET) that initiates the reactions of the proton pump (3, 12). Note that in the state P_R the proton at the PLS partially neutralizes the electron in the BNC (3) in accordance with the charge-neutralization principle of the BNC (15). However, an important question arises: how can proton transfer from Glu242 to the BNC be prevented, which would short-circuit one step of proton pumping and form the next stable intermediate F? In the O_H → E_H transition of the catalytic cycle this short-circuit is minimized because reduction of the low-spin heme is thought to raise the pK_a of the PLS sufficiently to lead to its protonation before transfer of the electron to the BNC (3, 10, 13, 16–18), and uncompensated proton transfer to the BNC is endergonic in nature (refs. 13,16,17; cf. ref. 19). In contrast, the likelihood of a proton leak in the A → P_R transition increases manifold because the electron transfer from heme a to the BNC is required for loading of the PLS with a proton (3, 12). This facet is analyzed in the current work, and it is proposed that it is the orientation of the water molecules in the nonpolar cavity above Glu242 that effectively gates the pump and minimizes such a short-circuit.