Resonance Raman study of cytochrome b562-o complex, a terminal oxidase of Escherichia coli in its ferric, ferrous, and CO-ligated states

Molecular Details on Multiple Cofactor Containing Redox Metalloproteins Revealed by Infrared and Resonance Raman Spectroscopies

Vibrational spectroscopy and in particular, resonance Raman (RR) spectroscopy, can provide molecular details on metalloproteins containing multiple cofactors, which are often challenging for other spectroscopies. Due to distinct spectroscopic fingerprints, RR spectroscopy has a unique capacity to monitor simultaneously and independently different metal cofactors that can have particular roles in metalloproteins. These include e.g., (i) different types of hemes, for instance hemes c, a and a3 in caa3-type oxygen reductases, (ii) distinct spin populations, such as electron transfer (ET) low-spin (LS) and catalytic high-spin (HS) hemes in nitrite reductases, (iii) different types of Fe-S clusters, such as 3Fe-4S and 4Fe-4S centers in di-cluster ferredoxins, and (iv) bi-metallic center and ET Fe-S clusters in hydrogenases. IR spectroscopy can provide unmatched molecular details on specific enzymes like hydrogenases that possess catalytic centers coordinated by CO and CN- ligands, which exhibit spectrally well separated IR bands. This article reviews the work on metalloproteins for which vibrational spectroscopy has ensured advances in understanding structural and mechanistic properties, including multiple heme-containing proteins, such as nitrite reductases that house a notable total of 28 hemes in a functional unit, respiratory chain complexes, and hydrogenases that carry out the most fundamental functions in cells.

Disulfide bonds regulate binding of exogenous ligand to human cytoglobin

Cytoglobin (Cgb) was discovered a decade ago and is a fourth member of the group of hexacoordinated globin-folded proteins. Although some crystal structures have been reported and several functions have been proposed for Cgb, its physiological role remains uncertain. In this study, we measured cyanide binding to the ferric state of the wild-type (WT) Cgb, and found that the binding consisted of multiple steps. These results indicated that Cgb may be comprised of several forms, and the presence of monomers, dimers, and tetramers was subsequently confirmed by SDS-PAGE. Remarkably, each species contained two distinguishable forms, and, in the monomer, analyses of alternative cysteine states suggested the presence of an intramolecular disulfide bond (monomer SS form) and a structure with unpaired thiol groups (monomer SH form). These confirmed that forms were separated by gel-exclusion chromatography, and that the cyanide binding of the separated fractions was again measured; they showed different affinities for cyanide, with the monomer fraction showing the highest affinity. In addition, the ferrous state in each fraction showed distinct carbon monoxide (CO)-binding properties, and the affinities for cyanide and CO suggested a linear correlation. Furthermore, we also prepared several variants involving the two cysteine residues. The C38S and C83S variants showed a binding affinity for cyanide similar to the value for the monomer SH form, and hence the fraction with the highest affinity for exogenous ligands was designated as a monomer SS form. We concluded that polymerization could be a mechanism that triggers the exertion of various physiological functions of this protein and that an appropriate disulfide bond between the two cysteine residues was critical for regulating the binding affinity of Cgb, which can act as a ROS scavenger, for exogenous ligands.

Communication between R481 and Cu(B) in cytochrome bo(3) ubiquinol oxidase from Escherichia coli

The R481 residue of cytochrome bo(3) ubiquinol oxidase from E. coli is highly conserved in the heme-copper oxidase superfamily. It has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. Along these lines, proton pumping efficiency has been demonstrated to be abolished in many R481 mutants. However, R481Q in bo(3) from E. coli has been shown to be fully functional, implying that the positive charge of the arginine is not required for proton translocation [ Puustinen , A. and Wikstrom , M. ( 1999 ) Proc. Natl. Acad. Sci. U.S.A. 96 , 35 - 37 ]. In an effort to delineate the structural role of R481 in the bo(3) oxidase, we used resonance Raman spectroscopy to compare the nonfunctional R481L mutant and the functional R481Q mutant, to the wild type protein. Resonance Raman data of the oxidized and reduced forms of the R481L mutant indicate that the mutation introduces changes to the heme o(3) coordination state, reflecting a change in position and/or coordination of the Cu(B) located on the distal side of heme o(3), although it is approximately 10 A away from R481. In the reduced-CO adduct of R481L, the frequencies of the Fe-CO and C-O stretching modes indicate that, unlike the wild type protein, the Cu(B) is no longer close to the heme-bound CO. In contrast, resonance Raman data obtained from the various oxidation and ligation states of the R481Q mutant are similar to those of the wild type protein, except that the mutation causes an enhancement of the relative intensity of the beta conformer of the CO-adduct, indicating a shift in the equilibrium between the alpha and beta conformers. The current findings, together with crystallographic structural data of heme-copper oxidases, indicate that R481 plays a keystone role in stabilizing the functional structure of the Cu(B) site through a hydrogen bonding network involving ordered water molecules. The implications of these data on the proton translocation mechanism are considered.

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 characterization of a binuclear center of a Cu-containing NO reductase homologue from Roseobacter denitrificans: EPR and resonance Raman studies

Aerobic phototrophic bacterium Roseobacter denitrificans has a nitric oxide reductase (NOR) homologue with cytochrome c oxidase (CcO) activity. It is composed of two subunits that are homologous with NorC and NorB, and contains heme c, heme b, and copper in a 1:2:1 stoichiometry. This enzyme has virtually no NOR activity. Electron paramagnetic resonance (EPR) spectra of the air-oxidized enzyme showed signals of two low-spin hemes at 15 K. The high-spin heme species having relatively low signal intensity indicated that major part of heme b3 is EPR-silent due to an antiferromagnetic coupling to an adjacent CuB forming a Fe-Cu binuclear center. Resonance Raman (RR) spectrum of the oxidized enzyme suggested that heme b3 is six-coordinate high-spin species and the other hemes are six-coordinate low-spin species. The RR spectrum of the reduced enzyme showed that all the ferrous hemes are six-coordinate low-spin species. Nu(Fe-CO) and nu(C-O) stretching modes were observed at 523 and 1969 cm(-1), respectively, for CO-bound enzyme. In spite of the similarity to NOR in the primary structure, the frequency of nu(Fe-CO) mode is close to those of aa3- and bo3-type oxidases rather than that of NOR.

Characterization of insulin-like growth factor binding protein-3 (IGFBP-3) binding to human breast cancer cells: kinetics of IGFBP-3 binding and identification of receptor binding domain on the IGFBP-3 molecule

Insulin-like growth factor binding protein-3 (IGFBP-3) binds to specific membrane proteins located on human breast cancer cells, which may be responsible for mediating the IGF-independent growth inhibitory effects of IGFBP-3. In this study, we evaluated IGFBP-3 binding sites on breast cancer cell membranes by competitive binding studies with IGFBP-1 through -6 and various forms of IGFBP-3, including synthetic IGFBP-3 fragments. Scatchard analysis revealed the existence of high-affinity sites for IGFBP-3 in estrogen receptor-negative Hs578T human breast cancer cells (dissociation constant (Kd) = 8.19 +/- 0.97 x 10(-9) M and 4.92 +/- 1.51 x 10(5) binding sites/cell) and 30-fold fewer receptors in estrogen receptor-positive MCF-7 cells (Kd = 8.49 +/- 0.78 x 10(-9) M and 1.72 +/- 0.31 x 10(4) binding sites/cell), using a one-site model. These data demonstrate binding characteristics of typical receptor-ligand interactions, strongly suggesting an IGFBP-3:IGFBP-3 receptor interaction. Among IGFBPs, only IGFBP-5 showed weak competition, indicating that IGFBP-3 binding to breast cancer cell surfaces is specific and cannot be attributed to nonspecific interaction with glycosaminoglycans. This was confirmed by showing that synthetic IGFBP-3 peptides containing IGFBP-3 glycosaminoglycan-binding domains competed only weakly for IGFBP-3 binding to the cell surface. Rat IGFBP-3 was 20-fold less potent in its ability to compete with human IGFBP-3(Echerichia coli), as well as 10- to 20-fold less potent for cell growth inhibition than human IGFBP-3, suggesting the existence of species specificity in the interaction between IGFBP-3 and the IGFBP-3 receptor. When various IGFBP-3 fragments were evaluated for affinity for the IGFBP-3 receptor, only those fragments that contain the midregion of the IGFBP-3 molecule were able to inhibit 125I-IGFBP-3(Escherichia coli) binding, indicating that the midregion of the IGFBP-3 molecule is responsible for binding to its receptor. These observations demonstrate that specific, high-affinity IGFBP-3 receptors are located on breast cancer cell membranes. These receptors have properties that support the notion that they may mediate the IGF-independent inhibitory actions of IGFBP-3 in breast cancer cells.

Differential characterization of neutrophil cytochrome p30 and cytochrome b-558 by low-temperature absorption and resonance Raman spectroscopies

Cytochrome p30, a novel hemoprotein isolated from rabbit peritoneal neutrophils [Escriou, V., Laporte, F., Garin, J., Brandolin, G. & Vignais, P. V. (1994) J. Biol. Chem. 269, 14007-14014] has been characterized by low-temperature (77 K) absorption and resonance Raman spectroscopies. The spectral data have been compared with those obtained with neutrophil cytochrome b-558. At room temperature, the absorption difference spectra (reduced minus oxidized) of cytochrome p30 and cytochrome b-558 could not been distinguished from each other. However, at 77 K, significant differences were observed. In particular, the alpha band of cytochrome p30 was split whereas that of cytochrome b-558 was symmetrical, but particularly broad. The resonance Raman spectra of cytochrome p30 provided evidence for the presence of two hemes both in the ferric and ferrous states. One of them was a six-coordinated low-spin heme either oxidized or reduced whereas the other one was a high-spin heme, five-coordinated in the reduced state and six-coordinated in the oxidized state. It is probable that two histidine residues constitute the axial ligands of the six-coordinated low-spin heme of cytochrome p30. The resonance Raman spectra of cytochrome b-558 allowed the detection of a six-coordinated low-spin heme, similar to that found in cytochrome p30. The component typical of the high-spin heme of cytochrome p30 was however absent in the spectra of oxidized and reduced cytochrome b-558.

Cyanide-binding site of bd-type ubiquinol oxidase from Escherichia coli

We extended our investigation on the structure of the redox centers of bd-type ubiquinol oxidase from Escherichia coli using cyanide as a monitoring probe. We found that addition of cyanide to the air-oxidized O2-bound enzyme caused appearance of an infrared C-N stretching band at 2161 cm-1 and concomitant disappearance of the 647 nm absorption band of the cytochrome d (Fe2+)-O2 species. Addition of cyanide to the air-oxidized CO-bound enzyme also resulted in disappearance of the 635 nm absorption band and the 1983.4 cm-1 C-O infrared band of the cytochrome d (Fe2+)-CO species. The resulting species had a derivative-shaped electron paramagnetic resonance signal at g = 3.15. Upon partial reduction with sodium dithionite, this species was converted partly to a transient heme d (Fe3+)-C = N species having an electron paramagnetic resonance signal at gz = 2.96 and a C-N infrared band at 2138 cm-1. These observations suggest that the active site of the enzyme has a heme-heme binuclear metal center distinct from that of the heme-copper terminal oxidase and that the treatment of the air-oxidized enzyme with cyanide resulted in a cyanide-bridging species with "heme d(Fe3+)-C = N-heme b595(Fe3+)" structure.

Comparison of ubiquinol and cytochrome c terminal oxidases. An alternative view

There have been numerous instances in the recent literature where the properties of ubiquinol and cytochrome c terminal oxidases are compared. Here we specifically examine the cytochrome bo3-type ubiquinol oxidase from Escherichia coli and the cytochrome aa3-type cytochrome c oxidases. A second redox-active copper site (CuA) is present only in the cytochrome c oxidases and the physiological electron donors for the two enzymes are different (ubiquinol-8 vs. ferrocytochrome c). In our opinion, these differences are significant and most likely indicate that distinct turnover mechanisms are operative in the two enzymes.

Reactions of the membrane-bound cytochrome bo terminal oxidase of Escherichia coli with carbon monoxide and oxygen

The cytochrome 'bo' quinol oxidase of Escherichia coli contains 2 mol of haem, one or both of which are 'haem O'. One of the haems forms, with the single copper present, a binuclear site for ligand binding and oxygen reduction. Cytoplasmic membranes from a strain of E. coli lacking the alternative cytochrome bd quinol oxidase, and having amplified levels of cytochrome bo, were used to study oxygen and carbon monoxide reactivity with this oxidase. The high-spin ligand-binding haem was identified from its contribution to the Soret region and the shift in midpoint potential from +211 to +477 mV in the presence of CO. Oxidative titration of a CO-liganded sample was accompanied by a decrease in the contribution from a photodissociable CO-binding haem. The photodissociation spectrum was typical of a high-spin haem. Photolysis of CO-liganded, reduced membranes in the presence of O2 at sub-zero temperatures revealed O2 binding and cytochrome oxidation characterized by differential absorbance changes in the alpha-spectral region. Monitoring by epr spectroscopy of the same reaction sequence at -80 degrees C revealed a slight increase in g = 6 signal intensity immediately after photolysis attributable to cytochrome o oxidation prior to Cu oxidation. Subsequent decline in the g = 6 signal and appearance of a g = 3 signal indicated sequential electron flow from low-spin to high-spin haems and copper oxidation, suggesting that a second haem carries electrons from ubiquinol to the binuclear centre.

Spectral evidence for cytochrome o in the brown membrane of Halobacterium halobium

The brown membrane domain of Halobacterium halobium is a developmental precursor of the purple membrane and it contains a b-type cytochrome in addition to bacterio-opsin. In this report we provide spectroscopic evidence that the majority of the cytochrome content is a halobacterial cytochrome o. This cytochrome has absorption spectral properties in the oxidized, reduced, and CO liganded states which are characteristic of cytochrome o. The CD spectra show a complex bilobed pattern in the Soret spectral region which reflects the similarity of the heme environment to those of other b-type cytochromes involved in electron transport. We have also demonstrated a positive cooperativity of CO binding which, combined with CD spectral results, suggests two interacting heme moieties per cytochrome o. Size exclusion HPLC of solubilized brown membrane preparations shows a heme b containing protein with an Mr 42,000-46,000. The cytochrome may be easily separated from bacterio-opsin using a hydroxyapatite elution method on Triton X-100 solubilized preparations. The relative ease with which brown membrane disks may be oriented in high optical quality films should make the brown membrane a valuable model system for future spectroscopic investigations of cytochrome o.