Crystalline cytochrome c oxidase of bovine heart mitochondrial membrane: composition and x-ray diffraction studies

Cholate Disrupts Regulatory Functions of Cytochrome c Oxidase

Cytochrome c oxidase (CytOx), the oxygen-accepting and rate-limiting enzyme of mitochondrial respiration, binds with 10 molecules of ADP, 7 of which are exchanged by ATP at high ATP/ADP-ratios. These bound ATP and ADP can be exchanged by cholate, which is generally used for the purification of CytOx. Many crystal structures of isolated CytOx were performed with the enzyme isolated from mitochondria using sodium cholate as a detergent. Cholate, however, dimerizes the enzyme isolated in non-ionic detergents and induces a structural change as evident from a spectral change. Consequently, it turns off the "allosteric ATP-inhibition of CytOx", which is reversibly switched on under relaxed conditions via cAMP-dependent phosphorylation and keeps the membrane potential and ROS formation in mitochondria at low levels. This cholate effect gives an insight into the structural-functional relationship of the enzyme with respect to ATP inhibition and its role in mitochondrial respiration and energy production.

The Interplay among Subunit Composition, Cardiolipin Content, and Aggregation State of Bovine Heart Cytochrome c Oxidase

Mitochondrial cytochrome c oxidase (CcO) is a multisubunit integral membrane complex consisting of 13 dissimilar subunits, as well as three to four tightly bound molecules of cardiolipin (CL). The monomeric unit of CcO is able to form a dimer and participate in the formation of supercomplexes in the inner mitochondrial membrane. The structural and functional integrity of the enzyme is crucially dependent on the full subunit complement and the presence of unperturbed bound CL. A direct consequence of subunit loss, CL removal, or its oxidative modification is the destabilization of the quaternary structure, loss of the activity, and the inability to dimerize. Thus, the intimate interplay between individual components of the complex is imperative for regulation of the CcO aggregation state. While it appears that the aggregation state of CcO might affect its conformational stability, the functional role of the aggregation remains unclear as both monomeric and dimeric forms of CcO seem to be fully active. Here, we review the current status of our knowledge with regard to the role of dimerization in the function and stability of CcO and factors, such as subunit composition, amphiphilic environment represented by phospholipids/detergents, and posttranslational modifications that play a role in the regulation of the CcO aggregation state.

The pore-lining regions in cytochrome c oxidases: A computational analysis of caveolin, cholesterol and transmembrane helix contributions to proton movement

Cytochrome c oxidase (CcO) is the terminal enzyme in the electron transfer chain. CcO catalyzes a four electron reduction of O2 to water at a catalytic site formed by high-spin heme (a3) and copper atoms (CuB). While it is recognized that proton movement is coupled to oxygen reduction, the proton channel(s) have not been well defined. Using computational methods developed to study protein topology, membrane channels and 3D packing arrangements within transmembrane (TM) helix arrays, we find that subunit-1 (COX-1), subunit-2 (COX-2) and subunit-3 (COX-3) contribute 139, 46 and 25 residues, respectively, to channel formation between the mitochondrial matrix and intermembrane space. Nine of 12 TM helices in COX-1, both helices in COX-2 and 5 of the 6 TM helices in COX-3 are pore-lining regions (possible channel formers). Heme a3 and the CuB sites (as well as the CuA center of COX-2) are located within the channel that includes TM-6, TM-7, TM-10 and TM-11 of COX-1 and are associated with multiple cholesterol and caveolin-binding (CB) motifs. Sequence analysis identifies five CB motifs within COX-1, two within COX-2 and four within COX-3; each caveolin containing a pore-lining helix C-terminal to a TM helix-turn-helix. Channel formation involves interaction between multiple pore-lining regions within protein subunits and/or dimers. PoreWalker analysis lends support to the D-channel model of proton translocation. Under physiological conditions, caveolins may introduce channel formers juxtaposed to those in COX-1, COX-2 and COX-3, which together with cholesterol may form channel(s) essential for proton translocation through the inner mitochondrial membrane.

A physical chemist's expedition to explore the world of membrane proteins

Despite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

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).

Structural genomics of membrane proteins

A program on the structural genomics of membrane proteins has started at the BIRC, AIST, involving other academic institutions and industrial companies. Emphasis is being put on the development of techniques for the structural determination of membrane proteins of biological importance and ligand-receptor interactions by means of electron microscopy, X-ray diffraction, NMR, and computer simulation. Most efforts at the present stage, however, are being directed to finding suitable expression and purification systems and crystallization conditions for such proteins. The program is expected to be linked with the human full-length cDNA project and should lead to medical and industrial uses.

Control of mitochondrial membrane potential and ROS formation by reversible phosphorylation of cytochrome c oxidase

Phosphorylation of isolated cytochrome c oxidase from bovine kidney and heart, and of the reconstituted heart enzyme, with protein kinase A, cAMP and ATP turns on the allosteric ATP-inhibition at high ATP/ADP ratios. Also incubation of isolated bovine liver mitochondria only with cAMP andATP turns on, and subsequent incubation with Ca2+ turns off the allosteric ATP-inhibition of cytochrome c oxidase. In the bovine heart enzyme occur only three consensus sequences for cAMP-dependent phosphorylation (in subunits I, III and Vb). The evolutionary conservation of RRYS441 at the cytosolic side of subunit I, together with the above results, suggest that phosphorylation of Ser441 turns on the allosteric ATP-inhibition of cytochrome c oxidase. The results support the 'molecular-physiological hypothesis' [29], which proposes a low mitochondrial membrane potential through the allosteric ATP-inhibition. A hormone- or agonist-stimulated increase of cellular [Ca2+] is suggested to activate a mitochondrial protein phosphatase which dephosphorylates cytochrome c oxidase, turns off the allosteric ATP-inhibition and results in increase of mitochondrial membrane potential and ROS formation.

Membrane potential-controlled inhibition of cytochrome c oxidase by zinc

Like many voltage-sensitive ion pumps, cytochrome c oxidase is inhibited by zinc. Binding of zinc to the outside surface of Rhodobacter sphaeroides cytochrome c oxidase inhibits the enzyme with a K(I) of < or = 5 microm when the enzyme is reconstituted into phospholipid vesicles in the presence of a membrane potential. In the absence of a membrane potential and a pH gradient, millimolar concentrations of zinc are required to inhibit. This differential inhibition causes a dramatic increase in the respiratory control ratio from 6 to 40 for wild-type oxidase. The external zinc inhibition is removed by EDTA and is not competitive with cytochrome c binding but is competitive with protons. Only Cd(2+) of the many metals tested (Mg(2+), Mn(2+), Ca(2+), Ba(2+), Li(2+), Cs(2+), Hg(2+), Ni(2+), Co(2+), Cu(2+) Tb(3+), Tm(3+)) showed inhibitory effects similar to Zn(2+). Proton pumping is slower and less efficient with zinc. The results suggest that zinc inhibits proton movement through a proton exit path, which can allow proton back-leak at high membrane potentials. The physiological and mechanistic significance of proton movement in the exit pathway and its blockage by zinc is discussed in terms of regulation of the efficiency of energy transduction.

Control of mitochondrial membrane potential and ROS formation by reversible phosphorylation of cytochrome c oxidase

Phosphorylation of isolated cytochrome c oxidase from bovine kidney and heart, and of the reconstituted heart enzyme, with protein kinase A, cAMP and ATP turns on the allosteric ATP-inhibition at high ATP/ADP ratios. Also incubation of isolated bovine liver mitochondria only with cAMP andATP turns on, and subsequent incubation with Ca2+ turns off the allosteric ATP-inhibition of cytochrome c oxidase. In the bovine heart enzyme occur only three consensus sequences for cAMP-dependent phosphorylation (in subunits I, III and Vb). The evolutionary conservation of RRYS441 at the cytosolic side of subunit I, together with the above results, suggest that phosphorylation of Ser441 turns on the allosteric ATP-inhibition of cytochrome c oxidase. The results support the 'molecular-physiological hypothesis' [29], which proposes a low mitochondrial membrane potential through the allosteric ATP-inhibition. A hormone- or agonist-stimulated increase of cellular [Ca2+] is suggested to activate a mitochondrial protein phosphatase which dephosphorylates cytochrome c oxidase, turns off the allosteric ATP-inhibition and results in increase of mitochondrial membrane potential and ROS formation.

Three-dimensional structure of transporter associated with antigen processing (TAP) obtained by single Particle image analysis

The transporter associated with antigen processing (TAP) is an ATP binding cassette transporter responsible for peptide translocation into the lumen of the endoplasmic reticulum for assembly with major histocompatibility complex class I molecules. Immunoaffinity-purified TAP particles comprising TAP1 and TAP2 polypeptides, and TAP2 particles alone were characterized after detergent solubilization and studied by electron microscopy. Projection structures of TAP1+2 particles reveal a molecule approximately 10 nm across with a deeply staining central region, whereas TAP2 molecules are smaller in projection. A three-dimensional structure of TAP reveals it is isolated as a single heterodimeric complex, with the TAP1 and TAP2 subunits combining to create a central 3-nm-diameter pocket on the predicted endoplasmic reticulum-lumenal side. Its structural similarity to other ABC transporters demonstrates a common tertiary structure for this diverse family of membrane proteins.

Palmitate decreases proton pumping of liver-type cytochrome c oxidase

The H+/e- stoichiometry of reconstituted cytochrome c oxidase from bovine kidney, containing subunit VIaL (liver type), is 0.5 under standard conditions but 1.0 on addition of 1% cardiolipin to the lipid mixture (asolectin). Low concentrations of palmitate (half-maximal effect at 0.5 microm), but not laurate, myristate, stearate, oleate, 1-hexadecanol, palmitoyl glycerol and palmitoyl CoA, decreased the H+/e- ratio in the presence of cardiolipin from 1.0 to 0.5, accompanied by an increase of coupled, but not of uncoupled respiration of proteoliposomes. Cardiolipin and palmitate did not influence the H+/e- stoichiometry and respiration of reconstituted cytochrome c oxidase from bovine heart, containing subunit VIaH (heart-type). The H+/e- stoichiometry of the heart enzyme, however, is decreased from 1.0 to 0.5 by 5 mm intraliposomal ATP (instead of 5 mm ADP). It is assumed that palmitate binds to subunit VIaL. The partial uncoupling of proton pumping in cytochrome c oxidase is suggested to participate in mammalian thermogenesis.

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

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

The allosteric ATP-inhibition of cytochrome c oxidase activity is reversibly switched on by cAMP-dependent phosphorylation

In previous studies the allosteric inhibition of cytochrome c oxidase at high intramitochondrial ATP/ADP-ratios via binding of the nucleotides to the matrix domain of subunit IV was demonstrated. Here we show that the allosteric ATP-inhibition of the isolated bovine heart enzyme is switched on by cAMP-dependent phosphorylation with protein kinase A of subunits II (and/or III) and Vb, and switched off by subsequent incubation with protein phosphatase 1. It is suggested that after cAMP-dependent phosphorylation of cytochrome c oxidase mitochondrial respiration is controlled by the ATP/ADP-ratio keeping the proton motive force Deltap low, and the efficiency of energy transduction high. After Ca(2+)-induced dephosphorylation this control is lost, accompanied by increase of Deltap, slip of proton pumping (decreased H(+)/e(-) stoichiometry), and increase of the rate of respiration and ATP-synthesis at a decreased efficiency of energy transduction.

Cell respiration is controlled by ATP, an allosteric inhibitor of cytochrome-c oxidase

The activity of cytochrome-c oxidase, the terminal enzyme of the mitochondrial respiratory chain, is known to be regulated by the substrate pressure, i.e. the ferro-/ferricytochrome c ratio, by the oxygen concentration, and by the electrochemical proton gradient delta muH+ across the inner mitochondrial membrane. Here we describe a further mechanism of 'respiratory control' via allosteric inhibition of cytochrome-c oxidase by ATP, which binds to the matrix domain, of subunit IV. The cooperativity between cytochrome-c-binding sites in the dimeric enzyme complex is mediated by cardiolipin, which is essential for cooperativity of the enzyme within the lipid membrane.

ATP and ADP bind to cytochrome c oxidase and regulate its activity

By equilibrium dialysis of cytochrome c oxidase from bovine heart with [35S]ATPalphaS and [35S]ADPalphaS, seven binding sites for ATP and ten for ADP were determined per monomer of the isolated enzyme. The binding of ATP occurs in a time-dependent manner, as shown by a filtration method, which is apparently due to slow exchange of bound cholate. In the crystallized enzyme 10 mol of cholate were determined and partly identified in the high resolution crystal structure. Binding of ADP leads to conformational changes of the Tween 20-solubilized enzyme, as shown by a 12% decrease of the gamma-band. The conformational change is specific for ADP, since CDP, GDP and UDP showed no effects. The spectral changes are not obtained with the dodecylmaltoside solubilized enzyme. The polarographically measured activity of cytochrome c oxidase is lower after preincubation with high ATP/ADP-ratios than with low, in the presence of Tween 20. This effect of nucleotides is due to interaction with subunit IV, because preincubation of the enzyme with a monoclonal antibody to subunit IV released the inhibition by ATP. In the presence of dodecylmaltoside the enzyme had a 2 to 3-fold higher total activity, but this activity was not influenced by preincubation with ATP or ADP.

Copper A of cytochrome c oxidase, a novel, long-embattled, biological electron-transfer site

This review traces the history of understanding of the CuA site in cytochrome c oxidase (COX) from the beginnings, when few believed that there was any significant Cu in COX, to the verification of three atoms Cu/monomer and to the final identification of the site as a dinuclear, Cys-bridged average valence Cu1.5+ ... Cu1.5+ structure through spectroscopy, recombinant DNA techniques, and crystallography. The critical steps forward in understanding the nature of the CuA site are recounted and the present state (as of the end of 1996) of our knowledge of the molecular and electronic structure is discussed in some detail. The contributions made through the years by the development of methodology and concepts for solving the enigma of CuA are emphasized and impediments, often rooted in contemporary preconceptions and attitudes rather than solid data, are mentioned, which discouraged the exploitation of early valuable clues. Finally, analogies in construction principles of polynuclear Cu-S and Fe-S proteins are pointed out.

Infrared and EPR studies on cyanide binding to the heme-copper binuclear center of cytochrome bo-type ubiquinol oxidase from Escherichia coli. Release of a CuB-cyano complex in the partially reduced state

Cyanide-binding to the heme-copper binuclear center of bo-type ubiquinol oxidase from Escherichia coli was investigated with Fourier transform-infrared and EPR spectroscopies. Upon treatment of the air-oxidized CN-inhibited enzyme with excess sodium dithionite, a 12C-14N stretching vibration at 2146 cm-1 characteristic of the FeO3+ C=N CuB2+ bridging structure was quickly replaced with another stretching mode at 2034.5 cm-1 derived from the FeO2+ C=N moiety. The presence of ubiquinone-8 or ubiquinone-1 caused a gradual autoreduction of the metal center(s) of the air-oxidized CN-inhibited enzyme and a concomitant appearance of a strong cyanide stretching band at 2169 cm-1. This 2169 cm-1 species could not be retained with a membrane filter (molecular weight cutoff = 10,000) and showed unusual cyanide isotope shifts and a D2O shift. These observations together with metal content analyses indicate that the 2169 cm-1 band is due to a CuB.CN complex released from the enzyme. The same species could be produced by anaerobic partial reduction of the CN-inhibited ubiquinol oxidase and, furthermore, of the CN-inhibited cytochrome c oxidase; but not at all from the fully reduced CN-inhibited enzymes. These findings suggest that there is a common intermediate structure at the binuclear center of heme-copper respiratory enzymes in the partially reduced state from which the CuB center can be easily released upon cyanide-binding.

Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome c oxidase

Crystallization of membrane proteins, a prerequisite for their X-ray crystallographic analysis, remains difficult. Here, we demonstrate that the crystallization of the cytochrome c oxidase from Paracoccus denitrificans can be mediated by co-crystallization with an antibody Fv fragment. The crystals obtained contain all four subunits of this membrane protein complex and the Fv fragment. The approach of co-crystallizing membrane proteins with antibody fragments should be useful in obtaining well-ordered crystals of membrane proteins in general.

Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A

The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.

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.

The superfamily of heme-copper respiratory oxidases

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Hydrazine and hydroxylamine as probes for O2-reduction site of mitochondrial cytochrome c oxidase

Reactions of hydrazine and hydroxylamine with bovine heart cytochrome c oxidase in the fully reduced state were investigated under anaerobic conditions following the visible-Soret spectral change. Hydrazine gave a sharp band at 575 nm with 20% decrease in the alpha band at 603 nm, and hydroxylamine induced a 2 nm blue-shift for the alpha band without any clear splitting. The Soret band at 443 nm was decreased significantly in intensity, with the concomitant appearance of a shoulder with hydrazine or a peak with hydroxylamine, both near 430 nm. The dependence on pH of the affinity of these reagents for the enzyme indicates that only the deprotonated forms of these reagents bind to the enzyme, suggesting a highly hydrophobic environment of the haem ligand-biding site. These spectral changes were largely removed by addition of cyanide or CO. However, detailed analysis of these spectral changes indicates that hydrazine perturbs the shape of the spectral change induced by cyanide and hydroxylamine perturbs that induced by CO. These results suggest that these aldehyde reagents bind to haem a3 iron as well as to a second site which is most likely to be the formyl group on the haem periphery, and that these two sites bind these reagents anti-cooperatively with each other.

Probing heart cytochrome c oxidase structure and function by infrared spectroscopy

IR spectra directly probe specific vibrators in bovine heart cytochrome c oxidase, yielding quantitative as well as qualitative information on structures and reactions at these vibrators. C-O IR spectra reveal that CO binds to Fe2+ a3 as two conformers each in isolated immobile environments sensitive to Fea and/or CuA oxidation state but remarkably insensitive to pH, medium, anesthetics, and other factors that affect activity. C-N IR spectra reveal that the one CN- that binds to fully and partially oxidized enzyme can be in three different structures. These structures vary in relative amounts with redox level, thereby reflecting dynamic electron exchange among Fea, CuA, and CuB with associated changes in protein conformation of likely significance in O2 reduction and H(+)-pumping. Azide IR spectra also reflect redox-dependent long-range effects. The amide I IR bands, due to C-O vibrators of peptide linkages and composed of multiple bands derived from different secondary structures, reveal high levels of alpha-helix (approximately 60%) and subtle changes with redox level and exposure to anesthetics. N2O IR spectra reveal that these anesthetic molecules at clinically relevant levels occupy three sites of different polarity within the enzyme as the enzyme is reversibly, but only partially, inhibited.

Effects of crystallization on the heme-carbon monoxide moiety of bovine heart cytochrome c oxidase carbonyl

Cytochrome c oxidase isolated from bovine heart was crystallized in the fully reduced carbon monoxide (CO)-bound form. To evaluate the structure of the O2 reaction site in crystals and in solution, the bound C-O stretch infrared band in protein crystals was compared with the band for protein solution. In solution, the C-O stretch band could be deconvoluted into two extremely narrow bands, one at 1963.6 cm-1 with delta v1/2 = 3.4 cm-1 of 60% Gaussian/40% Lorentzian character represented 86% of the total band area and the other at 1960.3 cm-1 with delta v1/2 = 3.0 cm-1 of 47% Gaussian/53% Lorentzian character represented 14% of the total band area. The crystals exhibited two deconvoluted C-O infrared bands having very similar band parameters with those in solution. These findings support the presence of two structurally similar conformers in both crystals and solution. Thus crystallization of this enzyme does not affect the structure at the CO-binding site to as great extent as has been noted for myoglobin and hemoglobin carbonyls, indicating that the active (CO- or O2-binding) site of cytochrome c oxidase must be conformationally very stable and highly ordered compared to other hemoproteins such as hemoglobin.

A high-resolution solid-state 13C-NMR study on crystalline bovine heart cytochrome-c oxidase and lysozyme. Dynamic behavior of protein and detergent in the complex

We have recorded 100.6-MHz high-resolution solid-state 13C-NMR spectra of crystalline cytochrome-c oxidase from bovine heart muscle and hen egg-white lysozyme, to compare conformation and dynamics of a typical membrane-protein complex with those of lysozyme. The absence of severe interference with the solid-state 13C-NMR spectra, from both the line broadenings from paramagnetic centers and overlapping of intense detergent signals, provided spectral resolution of 13C-NMR feature of cytochrome-c oxidase crystals comparable to that of lysozyme crystal and better than that of dissolved or lyophilized samples. In fact, the observed peak intensities of the polar heads of the detergents BL8SY and Brij 35 were only about 10% and 3% of the anticipated values, respectively. The dynamic behavior of the backbone and side chains of cytochrome-c oxidase was compared with that of lysozyme on the basis of the 13C spin-lattice relaxation times (T1): the backbone of the cytochrome-c oxidase turned out to be more flexible than that of lysozyme. Molecular motions of the detergent molecules attached to the proteins are found to be highly heterogeneous. Detergent molecules undergo rapid tumbling motions in the crystals in about 10 ns as detected by T1. In addition to rapid motions, slow motions were detected by 1H spin-lattice relaxation time in the rotating frame (TH1 rho) and cross-polarization time (TCH), together with data from static spectra, indicating that the aliphatic portion of the detergent interacts more strongly with hydrophobic protein surfaces than do the polar heads.

Cloning, sequencing and deletion from the chromosome of the gene encoding subunit I of the aa3-type cytochrome c oxidase of Rhodobacter sphaeroides

The ctaD gene encoding subunit I of the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides has been cloned. The gene encodes a polypeptide of 565 residues which is highly homologous to the sequences of subunit I from other prokaryotic and eukaryotic sources, e.g. 51% identity with that from bovine, and 75% identity with that from Paracoccus denitrificans. The ctaD gene was deleted from the chromosome of R. sphaeroides, resulting in a strain that spectroscopically lacks cytochrome a. This strain maintains about 50% of the cytochrome c oxidase activity of the wild-type strain owing to the presence of an alternate o-type cytochrome c oxidase. The aa3-type oxidase was restored by complementing the chromosomal deletion with a plasmid-borne copy of the ctaD gene. This system is well suited for site-directed mutagenesis probing of the structure and function of cytochrome c oxidase.

Cytochrome oxidase as a proton pump

The general structure of cytochrome oxidase is reviewed and evidence that the enzyme acts as a redox-linked proton pump outlined. The overall H+/e- stoichiometry of the pump is discussed and results [Wikström (1989), Nature 338, 293] which suggest that only the final two electrons which reduce the peroxide adduct to water are coupled to protein translocated are considered in terms of the restrictions they place on pump mechanisms. "Direct" and "indirect" mechanisms for proton translocation are discussed in the context of evidence for redox-linked conformational changes in the enzyme, the role of subunit III, and the nature of the CuA site.

Cytochrome c oxidase metal centers: location and function

Cytochrome c oxidase of Paracoccus denitrificans is spectroscopically and functionally very similar to the mammalian enzyme. However, it has a very much simpler quaternary structure, consisting of only three subunits instead of the 13 of the bovine enzyme. The known primary structure of the Paracoccus denitrificans subunits, the knowledge of a large number of sequences from other species, and data on the controlled proteolytic digestion of the enzyme allow structural restrictions to be placed on the models describing the binding of the active metal centers to the polypeptide structure.

Characterization of two low Em forms of cytochrome a3 and their carbon monoxide complexes in mammalian cytochrome c oxidase

Evidence is presented for the existence of two forms of low-potential cytochrome a3. One appears to be similar to the low-spin form reported by Nicholls, P., and V. Hildebrandt (1978 Biochem. J. 173:65-72) and Wrigglesworth, J. M., J. Elsden, A. Chapman, N. Van der Water, and M. F. Grahn (1988. Biochim. Biophys. Acta. 936:452-464). It has a reduced Soret peak near 428 nm and a prominent alpha peak near 602 nm. This form is seen when the enzyme is either supplemented with lipoprotein or incorporated into a liposomal membrane, preexposed to a voltage greater than 400 mV for at least 30 min, and titrated in the presence of approximately 1 mM K3Fe(CN)6. The other form has a reduced Soret peak near 446 nm, and no prominent alpha peak. The 428-nm form has an Em near 175 mV and forms a CO complex with an Em near 225 mV. The 446-nm form has an Em near 200 mV and forms a CO complex with an Em near 335 mV.

Studies on cytochrome-c oxidase, XIV. The amino-acid sequence of subunit I--proteinchemical methods for the analysis of a large hydrophobic membrane protein

The amino-acid sequence of bovine heart cytochrome-c oxidase subunit I, previously deduced from mtDNA was corroborated by proteinchemical methods. The protein consists of 514 amino acids, the Mr is 57,060 including the N-terminal formyl group, which is positively identified. The study describes methods for the purification of the hydrophobic polypeptide by BioGel-chromatography in 3% SDS and/or HPLC and the sequence analysis via complete peptide maps obtained either by chymotryptic or cyanogenbromide cleavage in the presence of residual amounts of SDS. The methods may be used either for a stand alone sequencing of large integral membrane proteins or for obtaining probes to find the gene and provide the necessary complement for DNA sequencing. The results present the only protein-derived evidence for a family of about 20 DNA-deduced sequences of the catalytic subunit of cytochrome oxidases from bacteria to man.

A new high potential redox transition for cytochrome aa3

Using cyano-complexes of iron, tungsten, and molybdenum and a platinum working electrode, we have been able to attain and hold voltages in the range of 400 to 900 mV (vs. standard hydrogen electrode) in an aqueous medium. With this system we have obtained additional information in support of an earlier conclusion that cytochrome a3 has a high Em transition (i.e. greater than 460 mV) in addition to its Em in the 180-200 mV range (Hendler, R. W., K. V. S. Reddy, R. I. Shrager, and W. S. Caughey. 1986. Biophys. J. 49:717-729; Reddy, K. V. S., and R. W. Hendler. 1986. Biophys. J. 49:693-703). The proposed new transition has an Em near 770 mV and an n value greater than 1. The reduced form of the high-potential species of cytochrome a3 does not bind CO, in contrast to the reduced form of the low-potential species which does. A possible reaction scheme for cytochrome aa3 which incorporates the new information is presented.