Current issues in the chemistry of cytochrome c oxidase

Intermolecular Interactions and Intramolecular Couplings of Binuclear Porphyrin Models for Cytochrome c Oxidase

Cytochrome c oxidase (CcO) has a binuclear active site composed of a high-spin heme group and a tris-histidine-ligated copper ion (Cu_B). By using two different porphyrin models derived by Gunter (H₂TPyPP) and us (H₂TImPP), we have isolated several mono- and binuclear complexes including one carbonyl and three chloride derivatives which are determined by 100 K single-crystal X-ray. Low-temperature (4 K) EPR and multitemperature (295-25 K) Mössbauer investigations on the products not only confirmed the spin states of the two metal ions (S = 5/2 Fe³⁺ and S = 1/2 Cu²⁺) but also revealed the intermolecular interactions and intramolecular couplings which are in accordance with the crystal structural features.

Relative Propensities of Cytochrome c Oxidase and Cobalt Corrins for Reaction with Cyanide and Oxygen: Implications for Amelioration of Cyanide Toxicity

In aqueous media at neutral pH, the binding of two cyanide molecules per cobinamide can be described by two formation constants, K_f1 = 1.1 (±0.6) × 10⁵ M^-1 and K_f2 = 8.5 (±0.1) × 10⁴ M^-1, or an overall cyanide binding constant of ∼1 × 10¹⁰ M^-2. In comparison, the cyanide binding constants for cobalamin and a fully oxidized form of cytochrome c oxidase, each binding a single cyanide anion, were found to be 7.9 (±0.5) × 10⁴ M^-1 and 1.6 (±0.2) × 10⁷ M^-1, respectively. An examination of the cyanide-binding properties of cobinamide at neutral pH by stopped-flow spectrophotometry revealed two kinetic phases, rapid and slow, with apparent second-order rate constants of 3.2 (±0.5) × 10³ M^-1 s^-1 and 45 (±1) M^-1 s^-1, respectively. Under the same conditions, cobalamin exhibited a single slow cyanide-binding kinetic phase with a second-order rate constant of 35 (±1) M^-1 s^-1. All three of these processes are significantly slower than the rate at which cyanide is bound by complex IV during enzyme turnover (>10⁶ M^-1 s^-1). Overall, it can be understood from these findings why cobinamide is a measurably better cyanide scavenger than cobalamin, but it is unclear how either cobalt corrin can be antidotal toward cyanide intoxication as neither compound, by itself, appears able to out-compete cytochrome c oxidase for available cyanide. Furthermore, it has also been possible to unequivocally show in head-to-head comparison assays that the enzyme does indeed have greater affinity for cyanide than both cobalamin and cobinamide. A plausible resolution of the paradox that both cobalamin and cobinamide clearly are antidotal toward cyanide intoxication, involving the endogenous auxiliary agent nitric oxide, is suggested. Additionally, the catalytic consumption of oxygen by the cobalt corrins is demonstrated and, in the case of cobinamide, the involvement of cytochrome c when present. Particularly in the case of cobinamide, these oxygen-dependent reactions could potentially lead to erroneous assessment of the ability of the cyanide scavenger to restore the activity of cyanide-inhibited cytochrome c oxidase.

Transepithelial transport of macromolecular substances in IL-4 treated human intestinal T84 cell monolayers

The effect of interleukin-4 (IL-4), a cytokine associated with allergy and inflammation, on the permeability of the intestinal epithelium was investigated. IL-4 reduced transepithelial electrical resistance (TER) and increased permeation to horseradish peroxidase (HRP) and Lucifer Yellow (LY) of human intestinal T84 cell monolayers. The increased permeation due to IL-4 treatment was also observed at 4 degrees C. The permeability of T84 cell monolayers to beta-lactogulobulin (beta-Lg), ovalbumin (OVA), and fluorescein isothiocyanate (FITC)-dextran of various molecular sizes was also high in the IL-4-treated cell monolayers. Sodium azide (NaN(3)), which inhibits ATP synthesis of the cells, did not inhibit the increases in these substances. Even 150 kDa FITC-dextran significantly permeated the T84 cells when the monolayers were treated with IL-4. These results suggest that fairly large molecules are able to permeate intestinal epithelial monolayers via the energy-independent paracellular pathway when the monolayers are exposed to excessive IL-4.

A spectroscopic investigation of a tridentate Cu-complex mimicking the tyrosine-histidine cross-link of cytochrome C oxidase

Heme-copper oxidases have a crucial role in the energy transduction mechanism, catalyzing the reduction of dioxygen to water. The reduction of dioxygen takes place at the binuclear center, which contains heme a3 and CuB. The X-ray crystal structures have revealed that the C6' of tyrosine 244 (bovine heart numbering) is cross-linked to a nitrogen of histidine 240, a ligand to CuB. The role of the cross-linked tyrosine at the active site still remains unclear. In order to provide insight into the function of the cross-linked tyrosine, we have investigated the spectroscopic and electrochemical properties of chemical analogues of the CuB-His-Tyr site. The analogues, a tridentate histidine-phenol cross-linked ether ligand and the corresponding Cu-containing complex, were previously synthesized in our laboratory (White, K.; et al. Chem. Commun. 2007, 3252-3254). Spectrophotometric titrations of the ligand and the Cu-complex indicate a pKa of the phenolic proton of 8.8 and 7.7, respectively. These results are consistent with the cross-linked tyrosine playing a proton delivery role at the cytochrome c oxidase active site. The presence of the phenoxyl radical was investigated at low temperature using electron paramagnetic resonance (EPR) and Fourier transform infrared (FT-IR) difference spectroscopy. UV photolysis of the ligand, without bound copper, generated a narrow g=2.0047 signal, attributed to the phenoxyl radial. EPR spectra recorded before and after UV photolysis of the Cu-complex showed a g=2 signal characteristic of oxidized copper, suggesting that the copper is not spin-coupled to the phenoxyl radical. An EPR signal from the phenoxyl radical was not observed in the Cu-complex, either due to spin relaxation of the two unpaired electrons or to masking of the narrow phenoxyl radical signal by the strong copper contribution. Stable isotope (13C) labeling of the phenol ring (C1') Cu-complex, combined with photoinduced difference FT-IR spectroscopy, revealed bands at 1485 and 1483 cm(-1) in the 12C-minus-13C-isotope-edited spectra of the ligand and Cu-complex, respectively. These bands are attributed to the radical v7a stretching frequency and are shifted to 1468 and 1472 cm(-1), respectively, with 13C1' labeling. These results show that a radical is generated in both the ligand and the Cu-complex and support the unambiguous assignment of a vibrational band to the phenoxyl radical v7a stretching mode. These data are discussed with respect to a possible role of the cross-linked tyrosine radical in cytochrome c oxidase.

Flavoprotein autofluorescence imaging in the cerebellar cortex in vivo

Autofluorescence optical imaging is rapidly becoming a widely used tool for mapping activity in the central nervous system function in vivo and investigating the coupling among neurons, glia, and metabolism. This paper provides a brief review of autofluorescence and of our recent work using flavoprotein imaging in the cerebellar cortex. Stimulation of the parallel fibers evokes an intrinsic fluorescence signal that is tightly coupled to neuronal activation and primarily generated postsynaptically. The signal originates from mitochondrial flavoproteins. The signal is biphasic, with the initial increase in fluorescence (light phase) resulting from the oxidation of flavoproteins and the subsequent decrease (dark phase) from the reduction of flavoproteins. The light phase is primarily neuronal, and the dark phase is primarily glial. Exploiting the spatial properties of molecular layer inhibition in the cerebellar cortex, we show that flavoprotein autofluorescence can monitor both excitatory and inhibitory activity in the cerebellar cortex. Furthermore, flavoprotein autofluorescence has revealed that molecular layer inhibition is organized into parasagittal domains that differentially modulate the spatial pattern of cerebellar cortical activity. The reduction in flavoprotein autofluorescence occurring in the inhibitory bands most likely reflects a decrease in intracellular Ca(2+) in the neurons inhibited by the molecular layer interneurons. Therefore, flavoprotein autofluorescence imaging is providing new insights into cerebellar cortical function and neurometabolic coupling.

Delivery of drugs and macromolecules to mitochondria

Mitochondria is where the bulk of the cell's ATP is produced. Mutations occur to genes coding for members of the complexes involved in energy production. Some are a result of damages to nuclear coded genes and others to mitochondrial coded genes. This review describes approaches to bring small molecules, proteins and RNA/DNA into mitochondria. The purpose is to repair damaged genes as well as to interrupt mitochondrial function including energy production, oxygen radical formation and the apoptotic pathway.

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 and Chemical Changes of the PMIntermediate ofParacoccus denitrificansCytochromecOxidase Revealed by IR Spectroscopy with Labeled Tyrosines and Histidine†

Structural and chemical changes in the P(M) intermediate of Paracoccus denitrificans cytochrome c oxidase have been investigated by attenuated total reflection-Fourier transform infrared spectroscopy. Prior studies of P(M) minus oxidized (O) IR difference spectra of unlabeled, universally (15)N-labeled and ring-d(4)-tyrosine-labeled proteins (Iwaki, M., Puustinen, A., Wikström, M., and Rich, P. R. (2004) Biochemistry 43, 14370-14378). provided a basis for band assignments to changes in metal centers and the covalently linked His-Tyr ligand of Cu(B) and highlighted a structural alteration of the protonated Glu278 in the P(M) intermediate. This work has been extended to equivalent measurements on enzymes with (13)C(9)(15)N-labeled and ring-(13)C(6)-labeled tyrosine and with (13)C(6)(15)N(3)-labeled histidine. Histidine labeling allows the assignment of troughs at 1104 and 973 cm(-1) in reduced minus O spectra to histidine changes, whereas tyrosine labeling moves otherwise obscured tyrosine bandshifts to 1454-1437 and 1287-1284 cm(-1). P(M) minus O spectra reveal bands at 1506, 1311, and 1094 cm(-1) in the oxidized state that are replaced by a band at 1519 cm(-1) in P(M). These bands shift with both tyrosine- and histidine-labeling, providing evidence for their assignment to the covalent His-Tyr and for its chemical change in P(M). Comparisons of isotope effects on the amide I regions in P(M) minus O spectra demonstrate that amide carbonyl bonds of tyrosine and histidine are major contributors. This suggests a structural alteration in P(M) that is centered on the His276-Pro277-Glu278-Val279-Tyr280 pentapeptide formed by the His-Tyr covalent linkage. This structural change is proposed to mediate the perturbation of the IR band of the protonated Glu278 headgroup.

Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism

The transcriptional regulation of several dozen genes in response to low oxygen tension is mediated by hypoxia-inducible factor 1 (HIF-1), a heterodimeric protein composed of two subunits, HIF-1alpha and HIF-1beta. In the HIF-1alpha-deficient human leukemic cell line, Z-33, exposed to mild (8% O(2)) or severe (1% O(2)) hypoxia, we found significant upregulation of two related heterogenous nuclear ribonucleoproteins, RNA-binding motif protein 3 (RBM3) and cold inducible RNA-binding protein (CIRP), which are highly conserved cold stress proteins with RNA-binding properties. Hypoxia also induced upregulation of RBM3 and CIRP in the murine HIF-1beta-deficient cell line, Hepa-1 c4. In various HIF-1 competent cells, RBM3 and CIRP were induced by moderate hypothermia (32 degrees C) but hypothermia was ineffective in increasing HIF-1alpha or vascular endothelial growth factor (VEGF), a known HIF-1 target. In contrast, iron chelators induced VEGF but not RBM3 or CIRP. The RBM3 and CIRP mRNA increase after hypoxia was inhibited by actinomycin-D, and in vitro nuclear run-on assays demonstrated specific increases in RBM3 and CIRP mRNA after hypoxia, which suggests that regulation takes place at the level of gene transcription. Hypoxia-induced RBM3 or CIRP transcription was inhibited by the respiratory chain inhibitors NaN(3) and cyanide in a dose-dependent fashion. However, cells depleted of mitochondria were still able to upregulate RBM3 and CIRP in response to hypoxia. Thus, RBM3 and CIRP are adaptatively expressed in response to hypoxia by a mechanism that involves neither HIF-1 nor mitochondria.

Flavoprotein autofluorescence imaging of neuronal activation in the cerebellar cortex in vivo

Autofluorescence has been used as an indirect measure of neuronal activity in isolated cell cultures and brain slices, but only to a limited extent in vivo. Intrinsic fluorescence signals reflect the coupling between neuronal activity and mitochondrial metabolism, and are caused by the oxidation/reduction of flavoproteins or nicotinamide adenine dinucleotide (NADH). The present study evaluated the existence and properties of these autofluorescence signals in the cerebellar cortex of the ketamine/xylazine anesthetized mouse in vivo. Surface stimulation of the unstained cerebellar cortex evoked a narrow, transverse beam of optical activity consisting of a large amplitude, short latency increase in fluorescence followed by a longer duration decrease. The optimal wavelengths for this autofluorescence signal were 420-490 nm for excitation and 515-570 nm for emission, consistent with a flavoprotein origin. The amplitude of the optical signal was linearly related to stimulation amplitude and frequency, and its duration was linearly related to the duration of stimulation. Blocking synaptic transmission demonstrated that a majority of the autofluorescence signal is attributed to activating the postsynaptic targets of the parallel fibers. Hypothesized to be the result of oxidation and subsequent reduction of flavoproteins, blocking mitochondrial respiration with sodium cyanide or inactivation of flavoproteins with diphenyleneiodonium substantially reduced the optical signal. This reduction in the autofluorescence signal was accomplished without altering the presynaptic and postsynaptic components of the electrophysiological response. Results from reflectance imaging and blocking nitric oxide synthase demonstrated that the epifluorescence signal is not the result of changes in hemoglobin oxygenation or blood flow. This flavoprotein autofluorescence signal thus provides a powerful tool to monitor neuronal activity in vivo and its relationship to mitochondrial metabolism.

Redox-linked conformational changes in bovine heart cytochrome c oxidase: picosecond time-resolved fluorescence studies of cyanide complex

Picosecond time-resolved fluorescence studies are carried out on cyanide-inhibited and heat-modified cytochrome c oxidase in aqueous lauryl maltoside surfactant solution, as well as in an aqueous vesicle, to understand the conformational changes associated with electron transfer and proton pumping activity of the enzyme. The tryptophan fluorescence decay profiles follow a four exponential model, which also matches the lifetime maxima obtained in a maximum entropy method analysis. The fast lifetime components are highly affected by the reduction and chemical modification of the enzyme. Changes in these lifetime components are related to the conformational changes in the vicinity of the heme centers of the enzyme. The cyanide-inhibited enzyme in the oxidized form shows a fluorescence decay profile similar to that of the native oxidized form, indicating that the conformational changes due to cyanide binding are very small. However, reduction of the cyanide-inhibited enzyme that leaves cyanide bound heme alpha3 oxidized causes a large increase in the fluorescence lifetimes, which indicates very significant conformational changes due to electron transfer to the dinuclear Cu(A) and heme alpha centers. A comparison of the tryptophan fluorescence decay of various other modified forms of the enzyme leads us to propose that the possible site of conformational coupling is located near heme alpha instead of the binuclear heme alpha3-Cu(B) center.

Nature of the inhibition of horseradish peroxidase and mitochondrial cytochrome c oxidase by cyanyl radical

Previous studies established that the cyanyl radical ((*)CN), detected as 5,5-dimethyl-1-pyrroline N-oxide (DMPO)/(*)CN by the electron spin resonance (ESR) spin-trapping technique, can be generated by horseradish peroxidase (HRP) in the presence of hydrogen peroxide (H(2)O(2)) and by mitochondrial cytochrome c oxidase (CcO) in the absence of H(2)O(2). To investigate the mechanism of inhibition by cyanyl radical, we isolated and characterized the iron protoporphyrin IX and heme a from the reactions of CN(-) with HRP and CcO, respectively. The purified heme from the reaction mixture of HRP/H(2)O(2)/KCN was unambiguously identified as cyanoheme by the observation of the protonated molecule, (M + H)(+), of m/z = 642.9 in the matrix-assisted laser desorption/ionization (MALDI) mass spectrum. The proton NMR spectrum of the bipyridyl ferrous cyanoheme complex revealed that one of the four meso protons was missing and had been replaced with a cyanyl group, indicating that the single, heme-derived product was meso-cyanoheme. The holoenzyme of HRP from the reconstitution of meso-cyanoheme with the apoenzyme of HRP (apoHRP) showed no detectable catalytic activity. The Soret peak of cyanoheme-reconstituted apoHRP was shifted to 411 nm from the 403 nm peak of native HRP. In contrast, the heme a isolated from partially or fully inhibited CcO did not show any change in the structure of the protoporphyrin IX as indicated by its MALDI mass spectrum, which showed an (M + H)(+) of m/z = 853.6, and by its pyridine hemochromogen spectrum. However, a protein-centered radical on the CcO can be detected in the reaction of CcO with cyanide and was identified as the thiyl radical(s) based on inhibition of its formation by N-ethylmaleimide pretreatment, suggesting that the protein matrix rather than protoporphyrin IX was attacked by the cyanyl radical. In addition to the difference in heme structures between HRP and CcO, the available crystallographic data also suggested that the distinct heme environments may contribute to the different inhibition mechanisms of HRP and CcO by cyanyl radical.

The peroxynitrite reductase activity of cytochrome c oxidase involves a two-electron redox reaction at the heme a(3)-Cu(B) site

Fully and partially reduced forms of isolated bovine cytochrome c oxidase undergo a two-electron oxidation-reduction process with added peroxynitrite, leading to catalytic oxidation of ferrocytochrome c to ferricytochrome c. The other major reaction product is nitrite ion, 86% of the added peroxynitrite being measurably converted to this species. The reaction is inhibited in the presence of cyanide, implicating the heme a(3)-Cu(B) binuclear pair as the active site. Moreover, provided peroxynitrite is not added to excess, the reductase activity of the enzyme toward this oxidant efficiently protects other protein and detergent molecules in vitro from nitration of tyrosine residues and oxidative damage. If the enzyme is exposed to approximately 10(2)-fold excesses of peroxynitrite, then significant irreversible loss of electron transfer activity results, and the heme a(3)-Cu(B) binuclear pair no longer undergo a characteristic carbon monoxide-driven reduction. The accompanying rather small changes in the observed electronic absorption spectrum are suggestive of a modification in the vicinity of one or both hemes but probably not to the cofactors themselves.

Electron spin resonance investigation of the cyanyl and azidyl radical formation by cytochrome c oxidase

Cyanide (CN(-)) is a frequently used inhibitor of mitochondrial respiration due to its binding to the ferric heme a(3) of cytochrome c oxidase (CcO). As-isolated CcO oxidized cyanide to the cyanyl radical ((.)CN) that was detected, using the ESR spin-trapping technique, as the 5,5-dimethyl-1-pyrroline N-oxide (DMPO)/(.)CN radical adduct. The enzymatic conversion of cyanide to the cyanyl radical by CcO was time-dependent but not affected by azide (N(3)(-)). The small but variable amounts of compound P present in the as-isolated CcO accounted for this one-electron oxidation of cyanide to the cyanyl radical. In contrast, as-isolated CcO exhibited little ability to catalyze the oxidation of azide, presumably because of azide's lower affinity for the CcO. However, the DMPO/(.)N(3) radical adduct was readily detected when H(2)O(2) was included in the system. The results presented here indicate the need to re-evaluate oxidative stress in mitochondria "chemical hypoxia" induced by cyanide or azide to account for the presence of highly reactive free radicals.

Primary and secondary mechanisms of action of visible to near-IR radiation on cells

Cytochrome c oxidase is discussed as a possible photoacceptor when cells are irradiated with monochromatic red to near-IR radiation. Four primary action mechanisms are reviewed: changes in the redox properties of the respiratory chain components following photoexcitation of their electronic states, generation of singlet oxygen, localized transient heating of absorbing chromophores, and increased superoxide anion production with subsequent increase in concentration of the product of its dismutation, H2O2. A cascade of reactions connected with alteration in cellular homeostasis parameters (pHi, [Cai], cAMP, Eh, [ATP] and some others) is considered as a photosignal transduction and amplification chain in a cell (secondary mechanisms).

The post-translational modification in cytochrome c oxidase is required to establish a functional environment of the catalytic site

Mutation of tyrosine-288 to a phenylalanine in cytochrome c oxidase from Rhodobacter sphaeroides drastically alters its properties. Tyr-288 lies in the CuB-cytochrome a3 binuclear catalytic site and forms a hydrogen bond with the hydroxy group on the farnesyl side chain of the heme. In addition, through a post-translational modification, Y288 is covalently linked to one of the histidine ligands that is coordinated to CuB. In the Y288F mutant enzyme, the "as-isolated" preparation is a mixture of reduced cytochrome a and oxidized cytochrome a3. The cytochrome a3 heme, which is largely six-coordinate low-spin in both oxidation states of the mutant, cannot be reduced by cytochrome c, but only by dithionite, possibly due to a large decrease in its reduction potential. It is postulated that the Y288F mutation prevents the post-translational modification from occurring. As a consequence, the catalytic site becomes disrupted. Thus, one role of the post-translational modification is to stabilize the functional catalytic site by maintaining the correct ligands on CuB, thereby preventing nonfunctional ligands from coordinating to the heme.

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

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

Complexation of type 2 copper by cytochrome c oxidase: probing of metal-specific binding sites by electron paramagnetic resonance

Cytochrome c oxidase, CcO, contains at least four, probably five type 2 copper binding sites per monomer in addition to the mixed valence [CuA(1.5+)CuA(1.5+)], S = 1/2 center and the EPR-silent CuB. Electron paramagnetic resonance (EPR) parameters for these site are g parallel = 2.22 and A parallel = 195 G. Nitrogen superhyperfine structure is observed in the g perpendicular region, with A perpendicular N of around 15 G. The EPR parameters for Cu(2+) bound to a synthetic peptide, AHGSVVKSEDYALPS, are similar to the parameters for the type 2 sites in CcO. The lines in the EPR spectrum of the type 2 site in the synthetic peptide are better resolved at low microwave frequency (3.4 GHz). Resolved lines in the expansion of the MI = -1/2 line in the g parallel region of the low frequency spectrum are attributed to superhyperfine structure from three almost equivalent nitrogen donor atoms bound to Cu(2+) in a square planar configuration. The MI = -1/2 line in the g parallel region for excess Cu(2+) bound to CcO is not as well resolved as for the synthetic peptide, presumably because the four or five binding sites per monomer are similar, but not exactly equivalent. These binding sites are proposed to be at the N-terminus of subunits of CcO, for example, at subunit IV where the sequence is AHGS-. Nitrogen donor atoms from the alpha-amino group of the amino terminal residue, the imidazole group of histidine, and a peptide nitrogen are predicted to comprise the binding site.

The vesicle transport protein Vps33p is an ATP-binding protein that localizes to the cytosol in an energy-dependent manner

Molecular mechanisms of vesicle transport between the prevacuolar compartment and the vacuole in yeast or the lysosome in mammalian cells are poorly understood. To learn more about the specificity of this intercompartmental step, we have examined the subcellular localization of a SEC1 homologue, Vps33p, a protein implicated to function in transport between the prevacuolar compartment and the vacuole. Following short pulses, 80-90% of newly synthesized Vps33p cofractionated with a cytosolic enzyme marker after making permeabilized yeast cells. However, during a chase, 20-40% of Vps33p fractionated with permeabilized cell membranes in a time-dependent fashion with a half-time of approximately 40 min. Depletion of cellular ATP increased the association rate to a half-time of approximately 4 min and caused 80-90% of newly synthesized Vps33p to be associated with permeabilized cell membranes. The association of Vps33p with permeabilized cell membranes was reversible after restoring cells with glucose before permeabilization. The N-ethylmaleimide-sensitive fusion protein homologue, Sec18p, a protein with known ATP binding and hydrolysis activity, displayed the same reversible energy-dependent sedimentation characteristics as Vps33p. We determined that the photosensitive analog, 8-azido-[alpha-32P]ATP, could bind directly to Vps33p with low affinity. Interestingly, excess unlabeled ATP could enhance photoaffinity labeling of 8-azido-[alpha-32P]ATP to Vps33p, suggesting cooperative binding, which was not observed with excess GTP. Importantly, we did not detect significant photolabeling after deleting amino acid regions in Vps33p that show similarity to ATP interaction motifs. We visualized these events in living yeast cells after fusing the jellyfish green fluorescent protein (GFP) to the C terminus of full-length Vps33p. In metabolically active cells, the fully functional Vps33p-GFP fusion protein appeared to stain throughout the cytoplasm with one or two very bright fluorescent spots near the vacuole. After depleting cellular ATP, Vps33p-GFP appeared to localize with a punctate morphology, which was also reversible upon restoring cells with glucose. Overall, these data support a model where Vps33p cycles between soluble and particulate forms in an ATP-dependent manner, which may facilitate the specificity of transport vesicle docking or targeting to the yeast lysosome/vacuole.

Structure-function studies of iron-sulfur clusters and semiquinones in the NADH-Q oxidoreductase segment of the respiratory chain

Our recent experimental data on iron-sulfur clusters and semiquinones in the complex I segment of the respiratory chain is presented, focusing on the Paracoccus (P.) denitrificans and bovine heart studies. The iron-sulfur cluster N2 has attracted the attention of investigators in the research field of complex I, since the mid-point redox potential of this cluster is the highest among all clusters in complex I, and is pH dependent (60 mV/pH). It is known that this cluster is located either in the NQO6 (NuoB in E. coli/PSST in bovine heart nomenclature) or in the NQO9 (NuoI/TYKY) subunit in the amphipathic domain of complex I. Our preliminary data indicate that the cluster N2 is located in the NuoB rather than the long-advocated NuoI subunit, and may have a unique ligand structure. We previously reported spin-spin interactions between cluster N2 and two distinct species of semiquinone (designated SQNf and SQNs) associated with complex I. A parallel intensity change was observed between the SQNf (g = 2.00) signal and the N2 split g parallel signal, further supporting our proposed interaction between SQNf and N2 spins.

A functional model related to cytochrome c oxidase and its electrocatalytic four-electron reduction of O2

A cytochrome c oxidase model that consists of a cobalt(II) porphyrin with a copper(I) triazacyclononane macrocycle fastened on the distal face and an imidazole covalently attached to the proximal face has been synthesized and characterized. Redox titrations with molecular oxygen (O2) and cobaltocene were carried out, and O2 was found to bind irreversibly in a 1:1 ratio to the model compound. This O2 adduct (a bridged peroxide) can be fully reduced to the deoxygenated form with four equivalents of cobaltocene. The model compound was adsorbed on an edge-plane graphite electrode, and rotating ring-disk voltammetry was used to monitor the electrocatalytic reduction of O2. Four-electron reduction of O2 was observed at physiological pH.

Vibrational Analysis of a Molecular Heme-Copper Assembly with a Nearly Linear Fe(III)-CN-Cu(II) Bridge: Insight into Cyanide Binding to Fully Oxidized Cytochrome c Oxidase

The complete vibrational analysis of [(1-MeIm)Fe(OEP)-CN-Cu(Me(6)tren)](2+) (1), which has been constructed as a model for the cyanide-ligated binuclear center in the respiratory protein cytochrome c oxidase, has been carried out. The resonance Raman spectra (lambda(exc) = 647 nm) and the mid-infrared spectra display three cyanide isotope-dependent vibrational modes. Two vibrations showed monotonic decreases with increasing mass of the cyanide ligand (2182-2137-2146-2101 cm(-)(1) and 535-526-526-520 cm(-)(1), respectively, for the (12)C(14)N-(13)C(14)N-(12)C(15)N-(13)C(15)N isotopomers), and could thus be assigned to the C&tbd1;N and Fe-CN-Cu stretching vibrations, respectively. The third vibration, detected with resonance Raman, showed a zigzag-type behavior (495-487-493-485 cm(-)(1) with the set of isotopomers above) with the frequency being more sensitive to (13)C labeling of the cyanide ligand than with (15)N labeling. This pattern of isotopic dependence is characteristic of a bending vibration. Additionally, with the same laser excitation frequency, the C&tbd1;N stretching mode was observed, which is the first time that this vibration has been detected in the resonance Raman spectrum of a synthetic heme-cyanide complex. The normal coordinate analysis showed marked differences between bridged and unbridged heme-cyanide complexes. Internal coordinates that are orthogonal in unbridged systems are significantly mixed in the bridged model, despite the overall linearity of the Fe-CN-Cu moiety. These measurements strengthen the proposal that cyanide bridges the two metal atoms in the cyanide-ligated, oxidized binuclear center of cytochrome c oxidase. A quantitative consideration of the vibrational characteristics of cyanide bound to the resting enzyme, in light of our model compound results, strongly suggests that the binuclear center is flexible and can undergo structural rearrangement to accommodate exogenous ligands. This is likely to be of mechanistic importance in both dioxygen reduction and proton translocation.

Multiple-Edge XAS Studies of Synthetic Iron-Copper Bridged Molecular Assemblies Relevant to Cytochrome c Oxidase. Structure Determination Using Multiple-Scattering Analysis with Statistical Evaluation of Errors

An X-ray absorption spectroscopy study has been carried out at the Fe and Cu K-edges for two bridged molecular assemblies, both of which contain an Fe-X-Cu (X = O(2)(-), OH(-)) bridge unit, some of whose features are relevant to the binuclear site of cytochrome c oxidase. The two complexes [(OEP)Fe-O-Cu(Me(6)tren)](1+) and [(OEP)Fe-(OH)-Cu(Me(5)tren)(OClO(3))](1+) have similar structural fragments around the metal centers except that they differ significantly in the bridge structure (the former contains a linear oxo bridge while the latter has a bent hydroxo bridge). We report a comparative study of these complexes using multiple-scattering (MS) EXAFS analysis and the program package GNXAS. It is found that there is a dramatic increase in the amplitude of the Fe-X-Cu MS pathway as the bridge unit approaches linearity. Full EXAFS MS analysis enables accurate quantitation of bridge metrical details and geometry for both complexes. These studies were done with an expanded version of GNXAS, which allows for simultaneous multiple-edge fitting. Such multiple-edge analysis (using both Fe and Cu edge data) allows common pathways (in this case involving the Fe-X-Cu bridge) to be constrained to be the same, thus improving the observation/variable ratio and enhancing sensitivity for determination of the bridge structure. The accuracy of the structural determination for the bridge units is evaluated by a statistical analysis methodology in which correlations among fitting parameters are identified and contour plots are used to determine random error. The overall error in the EXAFS structural determination is found by establishing the variance with the crystallographically determined values: for the EXAFS-determined parameters at distances below 4 Å, distances and angles deviated on average from crystallographic values by 0.014 Å and 1.5 degrees, respectively. It is also established that structural features in the Fe absorption preedge are diagnostic of oxo vs hydroxo ligation. The relevance of this study to the structural definition of binuclear bridged sites in cytochrome c oxidase and other metalloenzymes is considered.

A carbon monoxide irreducible form of cytochrome c oxidase and other unusual properties of the "monomeric" shark enzyme

Contrary to previous reports, the functional and spectral properties of "monomeric" shark cytochrome c oxidases are not entirely similar to those of the "dimeric" beef enzyme. Most significantly, unlike the behavior of beef oxidase, the fully oxidized shark enzyme is not reducible by carbon monoxide. Also, preparations of the shark enzyme, isolated at pH 7.8-8.0, lead to more than 60% of the sample always being obtained in a resting form, whereas similarly prepared beef oxidase is very often obtained, both by ourselves and others, exclusively in the pulsed form. Although the electronic absorption, magnetic circular dichroism and electron paramagnetic resonance (EPR) spectra of cytochrome c oxidase obtained from several shark species are similar to those of the beef enzyme, there are some significant differences. In particular, the Soret maximum is at 422 nm in the case of the fully oxidized resting shark oxidases at physiological pH and not 418 nm as commonly found for the beef enzyme. Moreover, the resting shark oxidases do not necessarily exhibit a "g = 12" signal in their EPR spectra. The turnover numbers of recent preparations of the shark enzyme are higher than previously reported and, interestingly, do not differ within experimental uncertainty from those documented for several beef isoenzymes assayed under comparable conditions.

The site of the redox-linked proton pump in eukaryotic cytochrome c oxidases

The electronic spectra of fully oxidized derivatives of some cytochrome c oxidase preparations are distinctly pH dependent. In general, the observed spectral shifts are greater in the case of pulsed derivatives compared to resting preparations and also, greater for preparations of the enzyme from shark skeletal muscle compared to beef heart. The low temperature near-infrared magnetic circular dichroism spectrum of the fully oxidized shark enzyme is not pH dependent in the experimental range, indicating the sensitivity of the visible region electronic spectrum to variation in pH to be due principally to changes at the heme a3-CuB chromophore. The results are discussed in relation to proposed mechanisms of proton translocation in cytochrome c oxidase.

Interconversion of fast and slow forms of cytochrome bo from Escherichia coli

The fully oxidized fast form of cytochrome bo from Escherichia coli is shown to convert spontaneously to a slow form when stored at -20 degrees C in 50 mM potassium borate, pH 8.5, containing 0.5 mM potassium EDTA. Evidence for the conversion, and that the form produced is analogous to the slow form of bovine heart cytochrome c oxidase, comes from (a) decreases in the extents of fast (k = 1-2 x 10(3) M-1 s-1) H2O2 binding and fast (k = 20-30 M-1 s-1) cyanide binding; (b) changes in the optical spectrum that are like those induced by formate, i.e., a blue shift in the Soret absorption band, loss of absorbance in the alpha and beta bands, and a red shift in the "630 nm" charge-transfer band; (c) changes in the EPR spectrum that are like those induced by formate, i.e., disappearance of signals at g = 8.6 and g = 3.71, and appearance of signals at g approximately 13, g = 3.14, and g = 2.58; and (d) appearance of a slow phase of reduction of heme o by dithionite. The mutant enzyme E286Q also converts to a slow form under the same conditions, as shown by (a) a decrease in the extent of fast H2O2 binding; (b) changes in the optical spectrum like those seen with wild-type enzyme; and (c) changes in the EPR spectrum that are like those induced by formate, i.e., disappearance of signals at g = 7.3 and g = 3.6 and appearance of signals at g approximately 13, g = 3.18, and g = 2.59.(ABSTRACT TRUNCATED AT 250 WORDS)

Measurement of the spin concentration of metalloprotein samples from saturation-magnetization data with particular reference to cytochrome c oxidase

A protocol for obtaining high-quality saturation-magnetization data from metalloprotein samples, employing a superconducting quantum interference device (SQUID) magnetometer, has previously been reported [E. P. Day, T. A. Kent, P. A. Lindahl, E. Münck, W. H. Orme-Johnson, H. Roder and A. Roy (1987) Biophys. J. 52, 837-853 and E. P. Day (1993) Methods Enzymol. 227, 437-463]. Following studies of several dozen different metalloprotein derivatives, the methodology has been further refined, particularly in the area of sample preparation. The details of the sample-handling procedures now in use are described, and moreover, the critical issue of verifying that contamination by paramagnetic impurities remains insignificant is considered. Importantly, it is shown that an independent determination of the quantity of paramagnetic sample present in the magnetometer is undesirable. Much more reliable parameters concerning the ground-state magnetic properties of the system under study are obtained if enough saturation-magnetization data are collected to enable the spin concentration to be determined during the subsequent fitting procedure. As proof of the validity of this method, the results of magnetization studies on ferricytochrome c, ferrocytochrome c and the benzohydroxamic acid adduct of horseradish peroxidase are presented. The ability of saturation-magnetization measurements to routinely determine spin concentration to within +/- 4% of accepted values is firmly established. In addition, a saturation-magnetization study has been performed on resting and fully reduced derivatives of cytochrome c oxidase. These results provide an illustration of the usefulness of the technique in probing some systems which have proved difficult to study by other methods. The increased difficulties inherent in obtaining meaningful data from these cytochrome c oxidase and other integer spin systems are delineated.

Structure of the binuclear heme iron-copper site in the quinol-oxidizing cytochrome aa3 from Bacillus subtilis

Cytochrome aa3-600 is a terminal quinol oxidase of Bacillus subtilis, belonging to the large family of structurally and functionally related respiratory enzymes to which the mitochondrial cytochrome c oxidase also belongs. However, the CuA center typical of the cytochrome c oxidases is lacking from cytochrome aa3-600. The presence of only one copper, viz. CuB of the binuclear heme iron-copper site, makes cytochrome aa3-600 especially suitable for XAS analysis of this structure. Cu and Fe XAS data for fully oxidized cytochrome aa3-600 indicate a structure for the binuclear site similar to that previously reported for mitochondrial cytochrome c oxidase (see Powers et al. (1981) Biophys. J. 34, 465-468). Heme Fea3 has a proximal histidine nitrogen ligand 2.10 +/- 0.02 A from the iron, and a distal S or Cl ligand at 2.36 +/- 0.03 A. The latter is also a ligand of CuB (2.21 +/- 0.02 A), and apparently forms a bridge between the two metals which are 3.70 +/- 0.06 A apart. CuB has two more close-lying ligands at 1.95 +/- 0.02 A, which are likely histidine nitrogens. The similarity between EXAFS of CuB and type 1 'blue' copper is contrasted to EPR and optical spectroscopic properties of CuB, and the nature of the bridging ligand is discussed.