Interaction of cytochrome c with cytochrome c oxidase studied by monoclonal antibodies and a protein modifying reagent

Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting

Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs.

Mass spectrometry-based carboxyl footprinting of proteins: method evaluation

Protein structure determines function in biology, and a variety of approaches have been employed to obtain structural information about proteins. Mass spectrometry-based protein footprinting is one fast-growing approach. One labeling-based footprinting approach is the use of a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and glycine ethyl ester (GEE) to modify solvent-accessible carboxyl groups on glutamate (E) and aspartate (D). This paper describes method development of carboxyl-group modification in protein footprinting. The modification protocol was evaluated by using the protein calmodulin as a model. Because carboxyl-group modification is a slow reaction relative to protein folding and unfolding, there is an issue that modifications at certain sites may induce protein unfolding and lead to additional modification at sites that are not solvent-accessible in the wild-type protein. We investigated this possibility by using hydrogen deuterium amide exchange (H/DX). The study demonstrated that application of carboxyl group modification in probing conformational changes in calmodulin induced by Ca(2+) binding provides useful information that is not compromised by modification-induced protein unfolding.

Chemical primer extension at submillimolar concentration of deoxynucleotides

Template-directed primer extension usually requires a polymerase, nucleoside triphosphates, and magnesium ions as cofactors. Enzyme-free, chemical primer extensions are known for preactivated nucleotides at millimolar concentrations. Based on a screen of carbodiimides, heterocyclic catalysts, and reactions conditions, we now show that near-quantitative primer conversion can be achieved at submillimolar concentration of any of the four deoxynucleotides (dAMP, dCMP, dGMP and dTMP). The new protocol relies on in situ activation with EDC and 1-methylimidazole and a magnesium-free buffer that was tested successfully for different sequence motifs. The method greatly simplifies chemical primer extension assays, further reduces the cost of such assays, and demonstrates the potential of the in situ activation approach.

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).

A general method for the chemical synthesis of gamma-32P-labeled or unlabeled nucleoside 5(')-triphosphates and thiamine triphosphate

Several methods for the chemical synthesis of gamma-32P-labeled and unlabeled nucleoside 5(')-triphosphates and thiamine triphosphate (ThTP) have been described. They often proved unsatisfactory because of low yield, requirement for anhydrous solvents, procedures involving several steps or insufficient specific radioactivity of the labeled triphosphate. In the method described here, all these drawbacks are avoided. The synthesis of [gamma-32P]ThTP was carried out in one step, using 1,3-dicyclohexyl carbodiimide as condensing agent for thiamine diphosphate and phosphoric acid in a dimethyl sulfoxide/pyridine solvent mixture. Anhydrous solvents were not required and the yield reached 90%. After purification, [gamma-32P]ThTP had a specific radioactivity of 11Ci/mmol and was suitable for protein phosphorylation. The method can also be used for the synthesis of [gamma-32P]ATP of the desired specific radioactivity. It can easily be applied to the synthesis of unlabeled ThTP or ribo- and deoxyribonucleoside 5(')-triphosphates. In the latter case, inexpensive 5(')-monophosphate precursors can be used as reactants in a 20-fold excess of phosphoric acid. Deoxyribonucleoside 5(')-triphosphates were obtained in 6h with a yield of at least 70%. After purification, the nucleotides were found to be suitable substrates for Taq polymerase during polymerase chain reaction cycling. Our method can easily be scaled up for industrial synthesis of a variety of labeled and unlabeled triphosphoric derivatives from their mono- or diphosphate precursors.

Mutations in the docking site for cytochrome c on the Paracoccus heme aa3 oxidase. Electron entry and kinetic phases of the reaction

Introducing site-directed mutations in surface-exposed residues of subunit II of the heme aa3 cytochrome c oxidase of Paracoccus denitrificans, we analyze the kinetic parameters of electron transfer from reduced horse heart cytochrome c. Specifically we address the following issues: (a) which residues on oxidase contribute to the docking site for cytochrome c, (b) is an aromatic side chain required for electron entry from cytochrome c, and (c) what is the molecular basis for the previously observed biphasic reaction kinetics. From our data we conclude that tryptophan 121 on subunit II is the sole entry point for electrons on their way to the CuA center and that its precise spatial arrangement, but not its aromatic nature, is a prerequisite for efficient electron transfer. With different reaction partners and experimental conditions, biphasicity can always be induced and is critically dependent on the ionic strength during the reaction. For an alternative explanation to account for this phenomenon, we find no evidence for a second cytochrome c binding site on oxidase.

Characterization of YpmQ, an accessory protein required for the expression of cytochrome c oxidase in Bacillus subtilis

A search of the Bacillus subtilis genome identifies a potential homolog, ypmQ, of the inner mitochondrial membrane protein Sco1 from yeast. Sco1 has been found to aid the delivery of copper to cytochrome c oxidase. B. subtilis expresses two members of the cytochrome oxidase family, a cytochrome c oxidase that has two copper centers, Cu(A) and Cu(B), and a menaquinol oxidase that has only Cu(B). Deletion of ypmQ in B. subtilis depresses expression of cytochrome c oxidase but not menaquinol oxidase. Levels of cytochrome c oxidase recover when copper is added to the growth medium of the DeltaypmQ strain or when ypmQ is expressed from a plasmid. Neither treatment affects the amount or activity of menaquinol oxidase. YpmQ in which two conserved cysteines are replaced by serines and a conserved histidine is replaced by alanine do not complement the deletion of ypmQ even though these mutant forms are found in the membrane extract at a level similar to the wild type protein. We propose that the two cysteines and the histidine are critical for the function of YpmQ and suggest they are involved in copper exchange between YpmQ and the Cu(A) site of cytochrome c oxidase.

Definition of the interaction domain for cytochrome c on cytochrome c oxidase. I. Biochemical, spectral, and kinetic characterization of surface mutants in subunit ii of Rhodobacter sphaeroides cytochrome aa(3)

To determine the interaction site for cytochrome c (Cc) on cytochrome c oxidase (CcO), a number of conserved carboxyl residues in subunit II of Rhodobacter sphaeroides CcO were mutated to neutral forms. A highly conserved tryptophan, Trp(143), was also mutated to phenylalanine and alanine. Spectroscopic and metal analyses of the surface carboxyl mutants revealed no overall structural changes. The double mutants D188Q/E189N and D151Q/E152N exhibit similar steady-state kinetic behavior as wild-type oxidase with horse Cc and R. sphaeroides Cc(2), showing that these residues are not involved in Cc binding. The single mutants E148Q, E157Q, D195N, and D214N have decreased activities and increased K(m) values, indicating they contribute to the Cc:CcO interface. However, their reactions with horse and R. sphaeroides Cc are different, as expected from the different distribution of surface lysines on these cytochromes c. Mutations at Trp(143) severely inhibit activity without changing the K(m) for Cc or disturbing the adjacent Cu(A) center. From these data, we identify a Cc binding area on CcO with Trp(143) and Asp(214) close to the site of electron transfer and Glu(148), Glu(157), and Asp(195) providing electrostatic guidance. The results are completely consistent with time-resolved kinetic measurements (Wang, K., Zhen, Y., Sadoski, R., Grinnell, S., Geren, L., Ferguson-Miller, S., Durham, B., and Millett, F. (1999) J. Biol. Chem. 274, 38042-38050) and computational docking analysis (Roberts, V. A., and Pique, M. E. (1999) J. Biol. Chem. 274, 38051-38060).

Genes involved in the formation and assembly of rhizobial cytochromes and their role in symbiotic nitrogen fixation

Rhizobia fix nitrogen in a symbiotic association with leguminous plants and this occurs in nodules. A low-oxygen environment is needed for nitrogen fixation, which paradoxically has a requirement for rapid respiration to produce ATP. These conflicting demands are met by control of oxygen flux and production of leghaemoglobin (an oxygen carrier) by the plant, coupled with the expression of a high-affinity oxidase by the nodule bacteria (bacteroids). Many of the bacterial genes encoding cytochrome synthesis and assembly have been identified in a variety of rhizobial strains. Nitrogen-fixing bacteroids use a cytochrome cbb3-type oxidase encoded by the fixNOQP operon; electron transfer to this high-affinity oxidase is via the cytochrome bc1 complex. During free-living growth, electron transport from the cytochrome bc1 complex to cytochrome aa3 occurs via a transmembrane cytochrome c (CycM). In some rhizobia (such as Bradyrhizobium japonicum) there is a second cytochrome oxidase that also requires electron transport via the cytochrome bc1 complex. In parallel with these cytochrome c oxidases there are quinol oxidases that are expressed during free-living growth. A cytochrome bb3 quinol oxidase is thought to be present in B. japonicum; in Rhizobium leguminosarum, Rhizobium etli and Azorhizobium caulinodans cytochrome d-type oxidases have been identified. Spectroscopic data suggest the presence of a cytochrome o-type oxidase in several rhizobia, although the absence of haem O in B. japonicum may indicate that the absorption attributed to cytochrome o could be due to a high-spin cytochrome b in a cytochrome bb3-type oxidase. In some rhizobia, mutation of genes involved in cytochrome c assembly does not strongly affect growth, presumably because the bacteria utilize the cytochrome c-independent quinol oxidases. In this review, we outline the work on various rhizobial mutants affected in different components of the electron transport pathways, and the effects of these mutations on symbiotic nitrogen fixation and free-living growth.

Projection structure of the cytochrome bo ubiquinol oxidase from Escherichia coli at 6 A resolution

The haem-copper cytochrome oxidases are terminal catalysts of the respiratory chains in aerobic organisms. These integral membrane protein complexes catalyse the reduction of molecular oxygen to water and utilize the free energy of this reaction to generate a transmembrane proton gradient. Quinol oxidase complexes such as the Escherichia coli cytochrome bo belong to this superfamily. To elucidate the similarities as well as differences between ubiquinol and cytochrome c oxidases, we have analysed two-dimensional crystals of cytochrome bo by cryo-electron microscopy. The crystals diffract beyond 5 A. A projection map was calculated to a resolution of 6 A. All four subunits can be identified and single alpha-helices are resolved within the density for the protein complex. The comparison with the three-dimensional structure of cytochrome c oxidase shows the clear structural similarity within the common functional core surrounding the metal-binding sites in subunit I. It also indicates subtle differences which are due to the distinct subunit composition. This study can be extended to a three-dimensional structure analysis of the quinol oxidase complex by electron image processing of tilted crystals.

Identification of essential amino acids within the proposed CuA binding site in subunit II of Cytochrome c oxidase

To explore the nature of proposed ligands to the CuA center in cytochrome c oxidase, site-directed mutagenesis has been initiated in subunit II of the enzyme. Mutations were introduced into the mitochondrial gene from the yeast Saccharomyces cerevisiae by high velocity microprojectile bombardment. A variety of single amino acid substitutions at each of the proposed cysteine and histidine ligands (His-161, Cys-196, Cys-200, and His-204 in the bovine numbering scheme), as well as at the conserved Met-207, all result in yeast which fails to grow on ethanol/glycerol medium. Similarly, all possible paired exchange Cys,His and Cys,Met mutants show the same phenotype. Furthermore, protein stability is severely reduced as evidenced by both the absence of an absorbance maximum at 600 nm in the spectra of mutant cells and the underaccumulation of subunit II, as observed by immunolabeling of mitochondrial extracts. In the same area of the protein, a variety of amino acid substitutions at one of the carboxylates previously implicated in binding cytochrome c, Glu-198, allow (reduced) growth on ethanol/glycerol medium, with normal intracellular levels of protein. These results suggest that a precise folding environment of the CuA site within subunit II is essential for assembly or stable accumulation of cytochrome c oxidase in yeast.

Site-directed mutagenesis of cytochrome c oxidase reveals two acidic residues involved in the binding of cytochrome c

Site-directed mutagenesis in subunit II of the cytochrome c oxidase (haem aa3) from Paracoccus denitrificans reveals that two carboxylic residues, Glu-246 and Asp-206 (corresponding to 198 and 158 in the bovine subunit II), are involved in the binding of cytochrome c. Spectrophotometric and polarographic measurements with the isolated enzymes of both mutant strains show a strongly reduced activity compared to wild-type oxidase, with the overall catalytic capacity (kcat/KM) of both mutants decreased about 8-fold. EPR spectra reveal no significant differences between the wild-type and the mutant enzymes, indicating that neither residue contributes significantly to the structure of the CuA centre. We conclude that Glu-246 and Asp-206 constitute an essential part of the binding site for cytochrome c.

A second terminal oxidase in Sulfolobus acidocaldarius

We previously found that the soxABCD operon encodes a quinol oxidase complex in Sulfolobus acidocaldarius and this enzyme was purified and characterized. In this study, we have used a cloning procedure based on the conservation of oxidase sequences and the polymerase chain reaction to isolate a new gene (soxM) encoding a subunit of another terminal oxidase. This terminal oxidase is a fusion between two central components of cytochrome oxidases, subunits I and III. soxM forms a transcriptional unit which is expressed under heterotrophic growth conditions. The corresponding protein was detected by direct protein sequencing in a preparation enriched with a cytochrome absorbing light at 562 nm. This preparation contains a terminal oxidase which is able to oxidize the artificial substrate N,N,N',N'-tetramethyl-p-phenylenediamine. This preparation also contains SoxC, a protein homologous to the mitochondrial cytochrome b, and a Rieske iron-sulphur center. We suggest that SoxM is the core component of a second terminal oxidase complex and that this complex may share a subunit (SoxC) with the SoxABCD complex.

The purified SoxABCD quinol oxidase complex of Sulfolobus acidocaldarius contains a novel haem

A respiratory quinol oxidase complex that is encoded by the soxABCD operon has been purified from the thermoacidophilic archaeon Sulfolobus acidocaldarius. The enzyme was solubilized with dodecyl maltoside and purified in the presence of this detergent and ethylene glycol. The complex is hydrodynamically homogeneous and contains at least five different polypeptides. In addition to the major subunits SoxA, SoxB and SoxC, it has two small polypeptides. One of these is the translation product of a short open reading frame (now called the soxD gene) at the end of the operon. The optical and electron paramagnetic resonance spectra of the SoxABCD complex have been characterized. It probably contains four A-type haems which are bound to SoxB and SoxC. The structure of these haems is not identical to haem A. The novel haem As has a 2-hydroxyethyl geranylgeranyl in position 2 of the porphyrin ring whereas haem A has the related farnesyl-containing side-chain.

Cytochrome oxidase evolved by tinkering with denitrification enzymes

The cytochrome bc complex which is encoded by the fixNOPQ operon in Bradyrhizobium japonicum, is the most distant member of the haem-copper cytochrome oxidase family. We have found that its major subunit, FixN, is homologous to the NorB subunit of nitric oxide reductase in a purple bacterium. A second evolutionary link between cytochrome oxidases and denitrification enzymes is the presence of a similar binuclear copper site in cytochrome aa3 (the mitochondrial oxidase) and nitrous oxide reductase. This centre was probably acquired by a primitive FixN-type oxidase, leading to the evolution of the mitochondrial-type oxidase. These links suggest that the oxygen-reducing respiratory chain developed from the anaerobic, denitrifying respiratory system.

ENDOR and ESEEM studies of cytochrome c oxidase: evidence for exchangeable protons at the CuA site

Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies were used to study whether protons in the immediate protein environment around CuA in cytochrome c oxidase are susceptible to solvent exchange. The enzyme was incubated in buffered D2O under resting or turnover conditions for 90 min and then frozen to quench the hydrogen/deuterium-exchange process. ENDOR spectra of the deuterated sample were essentially identical to those of control samples. The ESEEM spectra, however, provided a clear indication of the introduction of deuterium into the CuA environment following incubation in buffered D2O. The extent of deuterium incorporation was not affected by enzyme turnover. An analysis of the ESEEM data indicated that water is in reasonably close proximity to the CuA site, but not in the immediate coordination sphere of the metal(s). We estimate a minimum distance of 5.4 A between the CuA center and the protein/water interface. This relatively short surface separation distance is consistent with the role of CuA as the immediate oxidant of cytochrome c in the cytochrome oxidase (Hill, B. C. (1991) J. Biol. Chem. 266, 2219-2226).

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.