Conformation of ferricytochrome c. IV. Relationship between optical absorption and protein conformation

Resonance Raman spectra of Pseudomonas cytochrome c peroxidase

Resonance Raman spectra of ferric, ferrous and ferrous-carbonyl forms of Pseudomonas cytochrome c peroxidase are presented. The porphyrin ring vibration frequencies are compared with those of other heme proteins which are in well defined spin and oxidation states. Both the native oxidized and the reduced forms of the enzyme show two sets of Raman lines, one having a low-spin and the other a high-spin character. Resolved bands can be assigned to heme c and heme c', the low-spin and the high-spin moiety of the enzyme, respectively. The low-spin heme moiety of the ferric enzyme is concluded to have an imidazole-nitrogen : heme-iron : methionine-sulphur hemochrome structure, whereas in the ferrous enzyme the methionine-sulphur ligation is exchanged with the nitrogen of histidine or lysine (N epsilon). The Raman spectra indicate that the high-spin ferric heme consists of a mixture of a five-coordinated form and a six-coordinated form with a carboxylate group as a ligand. In the reduced enzyme the high-spin heme is five-coordinated. The Raman spectrum of the carbonyl derivative of Pseudomonas cytochrome c peroxidase indicates that the compound has an electron structure similar to that of carboxyhemoglobin and carboxymyoglobin. The data confirm earlier results that the two heme moieties of the enzyme are bound to the apoprotein by covalent thioether bonds as in c-type cytochromes.

Perchlorate binding to cytochrome c: a magnetic and optical study

1. The effects of perchlorate on cytochrome c have been investigated by 1H and 35Cl NMR, electron paramagnetic resonance and optical spectroscopy. 2. The pK values for the formation and disappearance of the major alkaline conformation were found to be displaced from 9.3 to 8.3 and from 10.4 to 10.9, respectively. The displacement was dependent on the ClO4(-) concentration below 0.1 M. 3. Competition experiments between perchlorate and chloride show that ClO4(-) binds both to the neutral and alkaline forms but with a higher affinity for the latter. The appearance of a new binding site in the alkaline form accounts for the markedly enhanced relaxation rate of 35ClO4(-) in this pH range. Complex formation between cyanide and the alkaline species results in the loss of this binding site, which probably is located close to or within the heme crevice. 4. The neutral form of ferricytochrome c also binds perchlorate strongly as evidence by the unique appearance of a high-spin signal dependent on pH and perchlorate concentration. This signal disappears with the same pK value as the neutral form. The effects of perchlorate on cytochrome c are due to specific binding of this ion.

Heme-linked properties of Pseudomonas cytochrome c peroxidase. Evidence for non-equivalence of the hemes

Pseudomonas cytochrome c peroxidase contains two hemes, one of which is shown to be in low-spin and one in high-spin state. The ferric enzyme reveals absorption maxima at 640 and 705 nm. The alkaline transition of these bands indicates the sixth iron-binding ligand of the low-spin and high-spin heme to be, respectively, a methionyl residue and a water molecule. The high-spin heme reacts with hydrogen peroxide to form a ferryl structure, which is the reactive intermediate in the peroxidatic reaction. The ferrous enzyme binds carbon monoxide in a 1:1 molar ratio, whereas the ferric form is unreactive towards small anionic ligands like F- and CN-. On this basis the peroxidase may also be classified as a cytochrome cc'.

Denaturation of thermophilic ferricytochrome c-552 by acid, guanidine hydrochloride, and heat

The denaturation of Thermus thermophilus cytochrome c-552 by acid, guanidine hydrochloride, and heat was studied by measuring the changes in absorption and circular dichroism. Cytochrome c-552 was remarkably resistant to acid; the pK of the transition from the low- to the high-spin form was roughly 0.3. The effect of guanidine hydrochloride on the heme iron-methionine bond of Thermus and horse cytochromes c was also investigated; a comparison of the free-energy changes for the displacement of the bond indicated that the coordination in cytochrome c-552 is highly stable. The spectra of guanidine hydrochloride unfolded cytochrome c-552 were dependent on the pH; the titration curve showed the presence of a cooperative single transition of pK = 4.7, with a one-proton dissociation, suggesting the ionization of a histidine residue. In the presence of guanidine hydrochloride, the influence of the heat on the ligand bond in cytochrome c-552 was studied. The van't Hoff plots of the reaction were biphasic. The enthalpy changes in the higher temperature range were independent on the guanidine hydrochloride concentration, while those in the lower range were not.

pH dependence of the oxidation-reduction potential of cytochrome c2

The pH dependence of the spectra and of the oxidation-reduction potential of three cytochromes c2, from Rhodopseudomonas capsulata, Rhodopseudomonas sphaeroides and Rhodomicrobium vannielii, were studied. A single alkaline pK was observed for the spectral changes in all three ferricytochromes. In Rps. capsulata cytochrome c2 this spectroscopic pK corresponds to the pK observed in the dependence of oxidation-reduction potential on pH. For the other two cytochromes the oxidation-reduction potential showed a complex dependency on pH which can be fitted to theoretical curves involving three ionizations. The third ionization corresponds to the ionization observed in the spectroscopic studies but the first two occur without changes in the visible spectra. The possible structural bases for these ionizations are discussed.

Methionine sulfoxide cytochrome c

Cytochrome c has been chemically modified by methylene blue mediated photooxidation. It is established that the methionine residues of the protein have been specifically converted to methionine sulfoxide residues. No oxidation of any other amino acid residues or the cysteine thioether bridges of the molecule occurs during the photooxidation reaction. The absorbance spectrum of methionine sulfoxide ferricytochrome c at neutrality is similar to that of the unmodified protein except for an increase in the extinction coefficient of the Soret absorbance band and for the complete loss of the ligand sensitive 695 nm absorbance band in the spectrum of the derivative. The protein remains in the low spin configuration which implies the retention of two strong field ligands. Spin state sensitive spectral titrations and model studies of heme peptides indicate that the sixth ligand is definitely not provided by a lysine residue but may be methionine-80 sulfoxide coordinated via its sulfur atom. Circular dichroism spectra indicate that the heme crevice of methionine sulfoxide ferri- and ferrocytochrome c is weakened relative to native cytochrome c. The redox potential of methionine sulfoxide cytochrome c is 184 mV which is markedly diminished from the 260 mV redox potential of native cytochrome c. The modified protein is equivalent to native cytochrome c as a substrate for cytochrome oxidase and is not autoxidizable at neutral pH but is virtually inactive with succinate-cytochrome c reductase. These results indicate that the major role of the methionine-80 in cytochrome c is to preserve a closed hydrophobic heme crevice which is essential for the maintainance of the necessary redox potential.

Stabilization of the globular structure of ferricytochrome c by chloride in acidic solvents

Increasing concentrations of chloride were found to increase the resolution between two visible absorbance spectral transitions associated with acidification of ferricytochrome c. Analysis of a variety of spectral and viscosity measurements indicates that protonation of a single group having an apparent pK of 2.1 +/- 0.2 and an intrinsic pK of about 5.3 displaces the methionine ligand without significantly perturbing the native globular conformation. Analysis of methylated ferricytochrome c suggests that protonation of a carboxylate ion, most likely a heme propionate residue, is responsible for displacement of the methionine ligand. Addition of a proton to a second group having an apparent pK of 1.2 +/- 0.1 displaces the histidine ligand and unfolds the protein from a globular conformation into a random coil. It is most likely that the second protonation occurs on the imidazole ring of the histidine ligand itself. Chloride is proposed to perturb these transitions by ligation in the fifth coordination position of the heme ion. Such ligation stabilizes a globular conformation of ferricytochrome c at pH 0.0 and 25 degrees.

Conformational and functional studies of chemically modified cytochrome c: nitrated and iodinated cytochromes c

The purification of iodinated (E. B. McGowan and E. Stellwagen (1970), Biochemistry 9, 3074) and of nitrated (M. Sokolovsky et al. (1970), Biochemistry 9, 5113) cytochromes c resulted in the recovery from the former preparation of diiododityrosyl-cytochrome c (DIDT-) with modification of Tyr-67 and Tyr-74, and, from the latter, a mononitromonotyrosyl-cytochrome c (MNMT-), with modification of Tyr-67, and mononitrodityrosyl-cytochrome c (MNDT-), with the added modification of Tyr-48. The three purified preparations were conformationally characterized using pH-spectroscopy, circular dichroism, thermal denaturation, reducibility with ascorbate, autoxidation with molecular oxygen, and binding with CO. These results are related to the two aspects of biological function, reducibility, measured by NADH-cytochrome c reductase, and oxidizability, with cytochrome c oxidase, as well as to structure-function relationships in the protein. MNMT-cytochrome c was found to be, structurally and conformationally, a single isomer, reducible with ascorbate, with a small, but definite affinity for both oxidation with molecular oxygen and binding of CO. Conformationally, in both valence states of the metal atom, it represents a molecular form with native-like conformation with small but definite perturbations in the immediate vicinity of the heme group, reflected by the destabilization of the Met-80-S-Fe linkage. MNMT-ferricytochrome c exhibits a pK of 6.2 for the transformation of the low-spin, native-like spectral form II containing the 695-nm band to form lacking lacking the 695-nm band. The isomerization at pK = 6.2, when analyzed in terms of the isomerization of the native protein with a pK of 9.2 and the nature of the group involved, indicates that Tyr-67 is not involved in the isomerization of the modified preparation, and possibly not in the native protein as well. In terms of biological function, the partial derangement of redecibility (24%) and the unaltered oxidizability point to the functional significance of Tyr-67, and provide another example of selectivity between the two aspects of physiological functional function, in agreement with the two-function, two-path operational model of the protein. The MNDT- and DIDT-ferricytochromes c exhibited physicochemical properties indicative of gross derangement of both the conformation of the protein as well as of the coordination configuration of the metal atom. The complete inability to accept an electron from NADH-cytochrome c reductase in both cases, and the retention of 50% of the oxidizability property of DIDT-cytochrome c, were interpreted to be the result of conformational derangement, rather than the added modification of Tyr-48 or of Tyr-74.

Cobalt-cytochrome c. II. Magnetic resonance spectra and conformational transitions

Between pH approximately 4 and 10 cobaltocytochrome c (Cocyt-c) gives an electron paramagnetic resonance (EPR) spectrum with g parallel = 2.035, g the perpendicular = 2.223, CoA PARALLEL = 61.4 G, CoA the perpendicular = 49.8 G, NA parallel = 15.3 G, and NA THE PERPENDICULAR = 12.5 G. Comparisons with the EPR spectra of deoxycobaltomyoglobin, deoxycobaltohemoglobin, and model compounds and together with other evidence showed cobaltocytochrome c to have Met-80 and His-18 as its axial ligands. The protons of these ligands are seen as resonances shifted by the ring-current field of the porphyrin in the 300-MHZ 1H nuclear magnetic resonance (NMR) spectra of cobalticytochrome c (Cocyt-c+). The methyl and gamma-methylene protons of Met-80 in this molecule occupy positions with respect to heme c which are somewhat different from those in ferrocytochrome c. The 1H NMR spectra also showed that the methyl groups of Leu-32, Ile-75, Thr-63, thioether bridges, and the porphyrin ring in the cobalt protein are in the same state as in native enzyme; the same is also true for Tyr-59, His-26, and His-33 and also possibly Tyr-67, Tyr-74, and Phe-82. Above pH 11, Cocyt-c is converted to a five-coordinated form having g parallel = 2.026, g the perpendicular = 2.325, CoA parallel = 80 G, CoA the perpendicular approximately 10 G, NA parallel = 17.5 G, and NA the perpendicular not resolved. Below pH 1.0 the EPR spectrum of Cocyt-c is also five-coordinated with g parallel = 2.014, g the perpendicular = 2.359, CoA parallel = 93.8 G, and CoA the perpendicular = 38.8 G. The axial ligands in the alkaline and the acidic forms of Cocyt-c are His-18 and Met-80, respectively. New prominent proton resonance peaks are observed in cobalt-cytochrome c which are either absent or weak in native cytochrome c. These are situated at 3.0, 1.7, and 1.44 ppm, attributable, respectively, to the epsilon-CH2, DELTA-CH2 + beta-CH2, and gamma-CH2 of lysyl residues in random-coil-peptides. From the areas of these peaks, it is estimated that one-two lysyl residues in Cocyt-c have been modified; four-five lysyl residues in Cocyt-c+ have been modified. These alterations of surface charged groups are probably responsible for the lowered reactivity of Cocyt-c with cytochrome oxidase and the lack of reactivity of Cocyt-c+ with several cytochrome reductase systems.

Conformational and functional studies of chemically modified cytochromes: N-bromosuccinimide- and formyl-cytochromes c

N-bromosuccinimide-cytochromes c (Myer, Y. P. (1972), Biochemistry 11, 4195) and formyl-cytochrome c (Aviram, I and Schejter, A. (1971), Biochim. Biophys. Acta 229, 113) have been chromatographically purified, and the resulting components have been characterized in terms of their structure, conformation, and function. The activity measurements are considered in terms of the oxidizability, as the transference of an electron to solubilized cytochrome c oxidase, and reducibility, as the tendency to accept an electron from NADH-cytochrome c reductase. Conformational characterization has been carried out by absorption measurements, pH-spectroscopic behavior, circular dichroism, thermal denaturation, ionization of phenolic hydroxyls, the tendency to form the CO complex, and autoxidation with molecular oxygen. NBS-cytochrome c yields two major components, the relative proportions of which, with increasing modification of the protein, exhibit a pattern typical of the formation of the two in a consecutive manner. The first product contains the modification of the Trp-59 and Met-65 side chains, and the second contains the added modification of Met-80. The former in both valence states of iron is more or less like the native protein, except for an apparently slightly loosened heme crevice; the latter, as in other modifications involving modification of centrally coordinated Met-80, was found to be in a conformational state characteristic of the native protein with a disrupted central coordination complex, a loosened heme crevice, and small, but finite derangement of the polypeptide conformation. Functionally, the first component reflected 55% of the reducibility property and an unimpaired oxidizability property, while the latter exhibited derangement of both aspects of cytochrome c activity. Formyl-cytochrome c yielded a single component with modification of Trp-59. Conformationally, in both valence states, it is a molecular form with a disrupted central coordination complex, a loosened heme crevice, and gross derangement of the overall protein conformation. It exhibits a minimal reducibility property, 12%, whereas it retains a native-like tendency to transfer an electron to cytochrome c oxidase. The data from the NBS-cytochrome c components are analyzed with reference to the two forms in the earlier studies of the unpurified preparations. The results are found to be in agreement with one another. The selectivity between the reducibility and the oxidizability exhibited by the first NBS component and formyl-cytochrome c, irrespective of significant differences in the conformational and coordinational configurations of the two, has been viewed in light of a two-path, two-function model for oxidoreduction, as well as with reference to conformational and structural requirements for the oxidizability and reducibility properties of the molecule.

Haem ligands of the ferricytochrome c of Ustilago sphaerogena

The mammalian-type cytochrome c of the basidiomycete Ustilago sphaerogena contains in a single polypeptide chain of 107 residues, two histidine residues located at positions 18 and 33, and one methionine residue situated at position 80 (Bitar et al., 1972). The reaction of Ustilago ferricytochrome c with bromoacetate at neutral pH resulted in the modification of histidine-33, but not of histidine-18 or of the invariant methionine residue. The activities of Ustilago cytochrome c with mitochondrial cytochrome c oxidase and with NADH-cytochrome c reductase were unaltered by the modification. The equilibrium constants for the formation of low-spin complexes of the ferrihaem octapeptide of horse cytochrome c (residues 14-21, including the haem bound covalently to cysteines 14 and 17) with imidazole, N(2)-acetylhistidine and monocarboxymethyl derivatives of N(2)-acetylhistidine were determined spectrophotometrically. Alkylation of the imidazole side-chain group of N(2)-acetylhistidine resulted in a marked decrease in its ability to form low-spin ferrihaem complexes. These results indicate that in Ustilago ferricytochrome c in solution histidine-33 is not involved in the central co-ordination complex. Since side-chain groups of residues other than histidine and methionine do not appear to be involved in the central complexes of other mammalian-type cytochromes c (Hettinger & Harbury, 1964, 1965; Myer & Harbury, 1965) it is likely that in Ustilago ferricytochrome c in solution at neutral pH, the side-chain groups of histidine-18 and methionine-80 are involved in the central co-ordination complex. The latter is stable over the pH range 2.6-8.4.

Reconstitution of horse heart cytochrome c: interaction of the components obtained upon cleavage of the peptide bond following methionine residue 65

Horse heart cytochrome c can be divided into a heme peptide of 65 residues (H65CNBr) and a nonheme peptide of 39 residues (N39CNBr) by treatment of the molecule with cyanogen bromide. Upon mixture of the two peptides in aqueous solution, a 1: 1 complex with properties closely resembling those of the parent heme protein can be formed. The reaction can conveniently be effected in sodium acetate buffer of pH 4.7, with the H65CNBr in the reduced form. The heme peptide is predominantly in the high-spin state under these conditions, and, upon the addition of N39CNBr, is converted to a complex with absorption and circular dichroism spectra which correspond closely to those of ferrocytochrome c. If N39CNBr is added to the oxidized form of H65CNBr, the spectral properties of the product differ appreciably from those of the parent protein. A complex with absorption and circular dichroism spectra comparable to those of ferricytochrome c can readily be obtained, however, through oxidation of the product of the reaction of N39CNBr with H65CNBr in the reduced state. The complex formed in this manner has an absorption band at 695 nm, exhibits no tryptophan or tyrosine fluorescence, and is active in the succinate oxidase system.