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

A study of core domains, and the core domain-domain interaction of cytochrome c fragment complex

To gain insight into the folding mechanism of the cytochrome c complex, we prepared a complete set of homologous and hybrid two-fragment ferric complexes of four different types and related complexes from horse, tuna, yeast iso-l, and Candida cytochromes c. The complexes were characterized for structural properties. Apparent equilibrium constants of the complexes were determined to calculate delta G0 for binding. The results have allowed us to assign four core domains of the complex. A core domain is a structural region containing a hydrophobic core and the surrounding shell which folds and unfolds as a unit. Core domain 1 folds by itself and consists essentially of the right channel structure, found by R. E. Dickerson and colleagues, and a part of the heme. Core domains 2, 3, and 4, respectively, are assigned based on the cores located on the left (the Fe-S bond) and right sides and at the bottom of heme. Evidence of the core domain-domain interaction to stabilize the Fe-S bond, combined with the kinetic studies by G. R. Parr and H. Taniuchi, has led to a model of two alternative folding orders of the core domains for the horse type I complex: domain 1----3----2----4 or 1----2----3----4. Furthermore, delta G0 variation between the complexes has shown non-additive behavior, indicating the existence of a residue-residue interaction between the heme- and apofragments in the complex. Evidence suggests that this interaction in most cases occurs within or through the core groups of the ordered interface between the heme- and the apo-fragments formed by folding of core domains 1, 2, and 3. Evidence also suggests that such core group interaction manifests itself in the interaction to stabilize the Fe-S bond and may be manifested in the core domain-domain interaction.

Spectrophotometric detection of the interaction between cytochrome c and heparin

Heparin inhibits transport of electrons from reduced cytochrome c to cytochrome c oxidase. The effect is due to the interaction of heparin with cytochrome c. It has been observed that binding of heparin to the reduced or oxidized cytochrome c changes the spectrum of cytochrome c at the Soret region. Affinity chromatography of heparin in cytochrome c immobilized to thiol-Sepharose shows that commercial heparin is eluted in the low-affinity and high-affinity fractions. Both participate in the interaction with cytochrome c. Polylysine induces decay of the cytochrome c-heparin complex.

Horse heart ferricytochrome c: conformation and heme configuration of high ionic strength acidic forms

The absorption, circular dichroism, and resonance Raman spectra of horse heart ferricytochrome c in the presence of 0.2 M KCl, 0.1 M NaClO4, and 0.2 M KNO3, in the pH region 7 to 0.5, have been investigated to determine the nature and the course of the processes involved. As in the absence of salts (Myer, Y., and Saturno, A. F. (1990) J. Protein Chem, 9, 379-387), the change from neutral to low acidic pH's in the presence of salts is a three-step process: state IIIs----state IIIS,a----state IIS----state IS, with pKa's of 3.5 +/- 0.2, 2.2 +/- 0.2, and 1.1 +/- 0.2, and with two, one, and one number of protons, respectively. The addition of salts at neutral pH's has little or no effect on the protein conformation and the heme-iron configuration (i.e., they remain the same, low-spin hexacoordinated heme iron with a Met-80-Fe-His-18 axial coordination), but such addition does cause a slight tightening of the heme crevice and the enlargement of the porphyrin core. State IIIS,a is a folded state with about the same degree of folding and with a similar spin state and coordination configuration of iron, but the heme crevice is loosened and the porphyrin core is smaller. Both states IIS and IS are also essentially folded forms, but with a smaller degree of protein secondary structure. State IIS has a high-spin hexacoordinated heme iron with a water molecular and a protonated and/or hydrogen-bonded imidazole of his-18 as the two axial ligates; and state IS has a high-spin pentacoordinated heme iron, which is about 0.49 A out of the porphyrin plane, with a protonated and/or hydrogen-bonded imidazole nitrogen as the only axial ligate. The addition of anions causes the stabilization of the protein secondary structures and the state IIIa----state II transition. The mode of effectiveness of anions appears to be nonspecific (i.e., because of electrostatic shielding and/or disruption of salt bridges).

Complexation which facilitates rejoining of horse cytochrome c apofragment [Homoser-lactone65](1-65) or [Homoser-lactone65] (23-65) to apofragment (66-104)

We have shown that two CNBr fragments of horse apocytochrome c, [Homoser-lactone65](1-65) and (66-104), bind to the ferric heme fragment (1-25)H to form a non-productive three-fragment complex, and that when the heme of this complex has been kept reduced for 48 h at 25 degrees, the peptide bond between residues 65 and 66 is restored with a yield of 24% or more. We have also shown that another CNBr fragment [Homoser-lactone65](23-65), but not [Homoser-lactone65](39-65), similarly rejoins to fragment (66-104) in the presence of the ferrous heme fragment with 25% or more yield. For complex of ferro-heme fragment [Hse-lacton65](1-65)H and apofragment (66-104) of horse cytochrome c, which restores the peptide bond between residues 65 and 66 (located on the left side of the heme) (cf. Harbury, H.A. (1978) in Semisynthetic Peptides and Proteins (Offord, R.E. & DiBello, C., eds.), pp. 73-89, Academic Press, New York). Corradin & Harbury have suggested that axial ligation of methionine 80 to the heme (on the left side) is important. Consistent with their idea, fragment [Hse80](66-104) was found not to link to [Hse-lactone65](1-65) in the presence of ferro(1-25)H. Furthermore, the present studies indicate that the interaction involving residues 26 to 38 (on the right side) is also important for such a conformation which assists in the rejoining of the two apofragments. Combining these two ideas, we suggest that restoration of the peptide bond between residues 65 and 66 reflects the structural integrity of these complexes in the reduced form. Thus, the present reaction system can be used not only for chemical synthesis of [Homoser65] apocytochrome c but also to extend amino acid substitution studies of cytochrome c to residues 1 to 64.

A spectroscopic analysis of the Pro35----Ala mutant of Rhodobacter capsulatus cytochrome c2. The strictly conserved Pro35 is not structurally essential

Visible, near-ultraviolet circular dichroic, near-infrared and nuclear magnetic resonance spectroscopies show that the secondary and tertiary structures of the mutant Pro35----Ala Rhodobacter capsulatus ferrocytochrome c2 are similar to the wild-type protein. The near-infrared spectrum shows that the methionine-S--Fe-heme bond is intact; however, a small red shift in the heme M transition of the near-ultraviolet circular dichroic spectrum of the mutant indicates that the heme environment may differ slightly between the two proteins. This difference may be a consequence of changes in the ligand and hydrogen bonds of His17 [Gooley, P. R. & MacKenzie, N. E. (1990) FEBS Lett. 260, 225-228]. 1H and 15N chemical shift differences suggest that the microenvironment of pyrrole rings III and IV of the heme prosthetic group differs between the two proteins. As the rings of the Phe51 and Tyr53 flip faster in the mutant protein than the wild type, these chemical shift differences may reflect changes in the time-average ring-current effects and not structural alterations.

The effects of surface charges on the redox potential of cytochrome c2 from the purple phototrophic bacterium Rhodobacter capsulatus

Four site-directed mutants of Rhodobacter capsulatus cytochrome c2, which substitute lysines at three positions with aspartate or glutamate, have been prepared. Mutations included the single charge substitutions K12D, K14E, and K32E and a double charge substitution K14E/K32E. Characterization of the ionic strength dependence of the wild-type and mutant redox potentials in the "nonbinding" buffer Tris-cacodylate suggests that (i) at zero ionic strength introduction of negatively charged groups stabilizes the oxidized state by 11-14 mV per charge and (ii) at high ionic strengths where the charged groups are masked, the effects of single charge substitutions are overcome; however, the redox potential of the double charge substitution is still affected. These results indicate that at physiological ionic strengths charge distribution only affects redox potential when the heme environment has been perturbed by a structural perturbation and that the determinants of redox potential in c-type cytochromes is primarily due to the local heme environment.

Resonance Raman investigation of a soluble cytochrome c552 from alkaliphilic Bacillus firmus RAB

The environment of the heme site of a low-potential soluble cytochrome (c552) from alkaliphilic Bacillus firmus RAB has been characterized with resonance Raman scattering and compared to that of horse heart cytochrome c. The Raman data indicate that vibrational bands sensitive to the axial ligation of the heme, as well as modes sensitive to the heme peripheral environment in cytochrome c552, are distinct from those of horse heart cytochrome c. The spectra of cytochrome c552 display resonance Raman modes indicative of a methionine as the sixth ligand in the oxidized form, while the reduced form appears to contain a nitrogenous-based sixth ligand. In addition, Q-band excitation reveals differences among vibrational modes in cytochrome c552 that are sensitive to the amino acid environment surrounding the heme.

Changing the invariant proline-30 of rat and Drosophila melanogaster cytochromes c to alanine or valine destabilizes the heme crevice more than the overall conformation

Drosophila melanogaster and rat cytochromes c in which proline-30 was converted to alanine or valine were expressed in a strain of baker's yeast, Saccharomyces cerevisiae, where they sustained aerobic growth. The mutations had no significant effect on the spectra or redox potentials but altered drastically the stability of the bond between the methionine-80 sulfur and the heme iron, as judged by four criteria: (i) the alkaline pKa values of the 695-nm band of the ferric form of the mutant proteins decreased by almost 1 pH unit as compared to the wild types; (ii) the acid pKa values increased by 0.5 to 1.2 pH units; (iii) the 695-nm band half-disappeared at temperatures 10-20 degrees C lower in the mutant proteins than in the wild types; and (iv) the 695-nm band of the mutant proteins was susceptible to concentrations of urea that had little influence on their overall structure. The valine-substituted rat cytochrome c had properties intermediate between those of the wild type and the alanine mutant. The destabilized coordinative bond is located in space a long distance from the mutation site. It is suggested that the mutations weaken the hydrogen bond between the carbonyl of residue 30 and the imino group of the imidazole of histidine-18, modifying the bonding of the heme iron by that imidazole, which, in turn, through a trans effect, weakens the bond between the heme iron and the other axial ligand, the sulfur of methionine-80. Alternatively, the effect of the mutations may be propagated allosterically along the peptide chain.

Horse heart ferricytochrome c: conformation and heme configuration of low ionic strength acidic forms

Resonance Raman, absorption and circular dichroism spectroscopic studies of the stable forms of horse heart ferricytochrome c in the pH range 6-0.8 and at the lowest possible ionic strengths, in water, and at 30 degrees C are reported. The neutral pH form, state III, changes to the acidic pH form, state I, through a three-step process: state III in equilibrium with IIIa in equilibrium with state II in equilibrium with state I, with pKa's of 3.6 +/- 0.3, 2.7 +/- 0.2, and 1.2 +/- 0.2, depending on the monitoring probe, respectively. State IIIa ferricytochrome c is like state III (i.e., with the Met-80-sulfur-iron linkage and a closed heme crevice) but with a higher degree of folding and a slightly larger porphyrin core. State II ferricytochrome c is an unfolded form with an open heme crevice and no Met-80-sulfur-iron linkage. The heme iron is high-spin, and hexacoordinated with weak ligand-field groups, water, and nitrogen of the protonated/hydrogen-bonded imidazole of the His-18 residue at the axial positions. The state I form also lacks the Met-80-sulfur-iron linkage and has an open heme crevice like the state II form; however, it is less unfolded and has a high-spin pentacoordinated heme iron, with the nitrogen of the imidazole of His-18 as the axial ligate, which is out of the porphyrin plane by about 0.45 A.

Avian kidney mitochondrial hemeprotein P-4501 alpha: isolation, characterization and NADPH-ferredoxin reductase-dependent activity

We describe the isolation of cytochrome P-4501 alpha from chick-kidney mitochondria. Although, gel permeation HPLC yielded 41% of the total amount of P-450 present in cholate-solubilized hemeproteins, it produced a highly purified mixture from which the P-4501 alpha could be purified to homogeneity in a final detergent-free state by a single-step application of hydrophobic interaction HPLC using hydroxypropyl silica. The purified P-4501 alpha traveled as a single band in SDS gel electrophoresis with an apparent Mr = 57,000. The absolute spectrum of the P-4501 alpha (Fe3+) form gave a lambda max at 403 nm. This characteristic lends support to the anomalous high-spin heme electron paramagnetic resonance spectrum and the heme structure of P-4501 alpha which we have previously reported (Ghazarian et al. (1980) J. Biol. Chem. 255, 8275-8281; Pedersen et al. (1976) J. Biol. Chem. 251, 3933-3941). In reconstitution experiments with ferredoxin-dependent NADPH-cytochrome c (P-450) reductase complexes, P-4501 alpha catalyzed the hydroxylation of 25-hydroxy-9,10-secocholesta-5,7,10(19)-trien-3 beta-ol at the C-1 position exclusively with a turnover number of 0.03 min-1. This number is identical to that obtained from measurements of the catalytic activity in intact mitochondria, indicating that only one major species of cytochrome P-450 occurs in chick-kidney mitochondria. The complete responsiveness of cytochrome P-450 concentrations in intact mitochondria to the vitamin D status of chicks provided additional evidence that the major cytochrome P-450 species present in renal mitochondria is uniquely associated with vitamin D metabolism.

Structural significance of an internal water molecule studied by site-directed mutagenesis of tyrosine-67 in rat cytochrome c

The tyrosine-67 to phenylalanine mutated rat cytochrome c is similar to the unmutated protein in its spectral, reduction potential, and enzymic electron-transfer properties. However, the loss of the 695-nm band, characteristic of the ferric form of the normal low-spin physiologically active configuration, occurs 1.2 pH units higher on the alkaline side and 0.7 pH unit lower on the acid side. Similarly, the heme iron-methionine-80 sulfur bond is more stable to temperature, with the midpoint of the transition being 30 degrees C higher, corresponding to an increase in delta H of 5 kcal/mol (1 cal = 4.184 J), partially mitigated by an increase of 11 entropy units in delta S. Urea has only slightly different effects on the two proteins. These phenomena are best explained by considering that the loss of one of the three hydrogen-bonding side chains, tyrosine-67, asparagine-52, and threonine-78, which hold an internal water molecule on the "left, lower front" side of the protein [Takano, T. & Dickerson, R. E. (1981) J. Mol. Biol. 153, 95-115], is sufficient to prevent its inclusion in the mutant protein, leading to a more stable structure, and, as indicated by preliminary proton NMR two-dimensional phase-sensitive nuclear Overhauser effect spectroscopy analyses, a reorganization of this area. This hypothesis predicts that elimination of the hydrogen-bonding ability of residue 52 or 78 would also result in cytochromes c having similar properties. It is not obvious why the space-filling structure involving the internalized water molecule that leads to a destabilization energy of about 3 kcal/mol should be subject to extreme evolutionary conservation, when a more stable and apparently fully functional structure is readily available.

Role of arginine-38 in regulation of the cytochrome c oxidation-reduction equilibrium

Arg-38 is an internal residue of mitochondrial cytochrome c that is close to heme propionate-7. Previous work comparing the behavior of cytochromes c from several species [Moore, G. R., Harris, D. E., Leitch, F. A., & Pettigrew, G. W. (1984) Biochim. Biophys. Acta 764, 331-342] has suggested that Arg-38 lowers the pKa of this propionate group and thereby accounts for the relative pH independence of the cytochrome c reduction potential from pH 5 to pH 8. The influence of Arg-38 on the oxidation-reduction equilibrium of yeast iso-1-cytochrome c has now been investigated by electrochemical, NMR, and theoretical analysis of six specifically mutated forms of this protein in which Arg has been replaced by Lys, His, Gln, Asn, Leu, or Ala. As the electron-withdrawing character of the residue at position 38 decreases, the reduction potential of the protein also decreases, with the largest decrease (ca. 50 mV) observed for the Ala variant. However, the variation in the reduction potentials of the mutants as a function of pH was similar to that observed for the wild-type protein. The effects of some of these mutations on the pKa values of His-33 and His-39 have been determined by NMR spectroscopy and found to be minimal. Calculations of the electrostatic free energy for the Leu-38 variant predict a decrease in the reduction potential of this mutant that is remarkably close to that observed experimentally. This work establishes that while Arg-38 contributes to the relatively high reduction potential of cytochrome c, this residue does not appear to be the sole functionality responsible for lowering the heme propionate-7 pKa.

Free and membrane-bound forms of bacterial cytochrome c4

Cytochrome c4 was isolated from cells of Pseudomonas aeruginosa, Pseudomonas stutzeri and Azotobacter vinelandii. The dihaem nature, Mr of approx. 20,000 and ferrohaem spectra in the region of the alpha- and beta-peaks define this family of cytochromes c. The behaviour of the holocytochromes in SDS was atypical, but removal of the haem groups resulted in a normal migration. In all three organisms most of the cytochrome c4 was tightly bound to the membrane, but some free cytochrome was detected. The membrane-attached cytochrome could be extracted with butanol, and this solubilized form was then indistinguishable in properties from the free form. Denitrifying rather than aerobic growth conditions hardly affected the total cytochrome c4 in the two pseudomonads, but there was slightly more free form and less membrane-attached form in denitrifying growth. The nature of the attachment of cytochrome c4 to the membrane is discussed and a model is proposed for the process of solubilization.

Purification and characterization of two soluble cytochromes from the alkalophile Bacillus firmus RAB

A soluble cytochrome c and soluble cytochrome b were purified from the alkalophilic Bacillus firmus RAB. The cytochrome c, with an alpha band at 552 nm, had an apparent molecular weight of 16,500 and was acidic, with a pI of 3.4. At both pH 7.0 and 8.3, the midpoint potential of c-552 was +66 mV. Above pH 8.3, the cytochrome exhibited a pH-dependent decrease in midpoint potential. This property, among others, distinguished the cytochrome c-552 from other membrane-associated c-type cytochromes. The soluble cytochrome b, with an alpha band maximum at 558 nm, had a molecular weight of approx. 15,500 and was also an acidic protein, with a pI of 3.07. It exhibited a pH-independent midpoint potential of +28 mV.

The microaerophilic respiration of Campylobacter mucosalis

A model is proposed for the respiratory adaptation to falling oxygen concentration during growth of the microaerophilic bacterium Campylobacter mucosalis. During the early stages of growth, the oxidation of formate is a two-stage branched process involving the production of H2O2 followed by its peroxidatic removal. In later stages of growth, at lower oxygen concentrations, the predominant electron flow is linear to a membrane-bound cytochrome-c oxidase which reduces O2 directly to H2O. Several components of this model have been investigated. H2O2 was produced during formate oxidation and accumulated when electron transfer to the cytochrome-c peroxidase was inhibited. A cytochrome c-553, of the Class 1 types, was purified and shown to be the specific electron donor to both the peroxidase and the membrane-bound oxidase. The levels of this cytochrome c and of the peroxidase were higher in cells harvested early in growth. In later stages of growth, the activity of the membrane-bound oxidase increased. Proton pumping across the membrane was detected with either H2O2 or oxygen as terminal electron acceptor. The novel energy-conserving role of H2O2 in this catalase-negative bacterium is discussed in relation to its microaerophilic nature.

Guanidine hydrochloride induced equilibrium unfolding of mutant forms of iso-1-cytochrome c with replacement of proline-71

Proline-71, an evolutionally conserved residue that separates two short alpha-helical regions, is replaced by valine, threonine, or isoleucine in at least partially functional forms of iso-1-cytochrome c from Saccharomyces cerevisiae [Ernst, J. F., Hampsey, D. M., Stewart, J. W., Rackovsky, S., Goldstein, D., & Sherman, F. (1985) J. Biol. Chem. 260, 13225-13236]. Treatment of these proteins with a specific sulfhydryl blocking reagent (methyl methanethiosulfonate) to block Cys-102 has allowed investigation of the properties of monomeric forms of the proteins, denoted iso-1-MS. Comparison of the UV-visible absorbance properties (pH 6, 20 degrees C) shows minor differences between the normal Pro-71 iso-1-MS and two of the three mutant proteins. The Val-71 iso-1-MS protein has absorbance properties indistinguishable from those of the normal Pro-71 iso-1-MS protein, but the Ile-71 iso-1-MS and Thr-71 iso-1-MS proteins show reduced intensity of the 695-nm absorbance band and a small shift in the Soret maximum, from 408 nm for the Pro-71 iso-1-MS and Val-71 iso-1-MS proteins to 406 nm for the Thr-71 iso-1-MS and Ile-71 iso-1-MS proteins. Second derivative spectroscopy is used to assess differences in the polarity of the environment of tyrosine residues. The average degree of exposure of tyrosines to solvent is similar in all four proteins: 0.39 for the normal Pro-71 iso-1-MS and Val-71 iso-1-MS proteins; 0.40 for the Ile-71 iso-1-MS protein.(ABSTRACT TRUNCATED AT 250 WORDS)

Methionine-80-sulfoxide cytochrome c: preparation, purification and electron-transfer capabilities

In order to explore the electron-transferring properties of methionine-80-sulfoxide cytochrome c, the pure, chromatographically homogeneous methionine-80-sulfoxide cytochrome c was previously published procedure (Ivanetich, K.M., Bradshaw, J.J. and Kaminsky, L.S. (1976) Biochemistry 15, 1144-1153) was found to produce a mixture of products. In the pure derivative, visible spectroscopy indicates that the 695 nm band indicative of the Met-80-Fe coordination is missing, amino acid analysis indicates that only one methionine is modified to the sulfoxide, and the E0' is found to be 240 mV vs. N.H.E. For succinate cytochrome c reductase activity, the Km for modified cytochrome was about one-ninth that of the native protein, while the maximum turnover number of the reductase with the modified protein was only about 54% of that with native protein. In contrast, the activity with cytochrome oxidase measured polarographically using ascorbate and TMPD under two different buffer/pH conditions, gave Km values that were very similar for both the native and modified cytochromes c, but the maximum turnover numbers of the oxidase with the modified protein were less than 40% of native in either buffer. It is concluded that the Met-80-sulfoxide cytochrome c in the reduced form is able to maintain substantially its heme crevice structure and thus maintain Km values similar to those of native protein. However, the low maximum turnover numbers for oxidase activity with the modified protein in the reduced state indicate that electron transfer itself has been significantly decreased, probably because the parity of acid/base and electrostatic interactions of Met-80 sulfur with the Fe in the two redox states has been disrupted.

The oxidation-state-dependent ATP-binding site of cytochrome c. A possible physiological significance

Cytochrome c binds certain physiological anions that are known to modulate the biological properties of the protein, although it is not known whether this effect is fortuitous or has physiological significance. We have examined the ability of the protein and its semisynthetic analogues to associate with certain of these anions, e.g. ATP, ADP, Pi and citrate. Our results show that specific residues or clusters of residues on the surface of horse heart cytochrome c are involved in the recognition sites for these anions. We also observed that binding at one site is linked to the oxidation state of the protein.

Native or nativelike species are transient intermediates in folding of alkaline iso-2 cytochrome c

Titration to high pH converts yeast iso-2 cytochrome c to an inactive but more stable alkaline form lacking a 695-nm absorbance band [Osterhout, J. J., Jr., Muthukrishnan, K., & Nall, B. T. (1985) Biochemistry 24, 6680-6684]. The kinetics of absorbance-detected refolding of the alkaline form have been measured by dilution of guanidine hydrochloride in a stopped-flow instrument. Fast-folding species (tau 2) are detected, as in refolding to the native state at neutral pH. An additional kinetic phase (tau a) is observed with an amplitude opposite in sign to the fast phase. The amplitude of this phase increases and the rate increases with increasing pH. Comparison to pH-jump measurements of the fully folded protein shows that phase tau a has the same sign, rate, and pH dependence as the alkaline isomerization reaction, suggesting that this new phase involves isomerization of native or nativelike species following fast folding. Absorbance difference spectra are taken at 5-s intervals during refolding at high pH. The spectra verify that nativelike species--with a 695-nm absorbance band--are formed transiently, before conversion of the protein to the alkaline form. Refolding in the presence of ascorbate shows that the transient, nativelike species are reducible, unlike alkaline iso-2. Thus, (1) refolding to the alkaline form of iso-2 cytochrome c proceeds through transient native or nativelike species, and (2) a folding pathway leading to native or nativelike forms is maintained at high pH, where native species are no longer the thermodynamically favored product.(ABSTRACT TRUNCATED AT 250 WORDS)

Protection and deprotection of horse cytochrome c

The last step in the semisynthesis of horse cytochrome c analogues (formation of the bond 65-66) requires the conformation of the complex between two complementary fragments, (1-65) lactone and (66-104). The fragments can be obtained from a limited degradation with cyanogen bromide. The amino component in this reaction can also be obtained from organo chemical synthesis in which the C-terminal fragment (81-104) is required in a selectively protected form. The latter is available from a cyanogen bromide degradation of ubiquitously protected cytochrome c. The details of the protection/deprotection reaction and the properties of nonadecamethylsulfonylethyloxycarbonyl cytochrome c are described.

Solubilisation of ferricytochrome c in methanol using a crown ether: absorption, circular dichroism and EPR spectral properties

Ferricytochrome c is normally insoluble in methanol, but its solution is facilitated by complexation with 18-crown-6. Absorption, circular dichroism and EPR spectroscopy indicate that the solubilised protein in MeOH exists in at least three conformational states, all different from the native state in neutral aqueous solution. In two states the haem iron (III) is low spin and in one state it is high spin, but it seems likely that all three forms are globular. The proportion in the high spin form increases at increasing crown ether concentration and on ageing the protein solution. The protein appears to return to its native conformation when it is restored to an aqueous environment.

Modulation of the alkaline transition in cytochrome c and cytochrome c-T by full or specific partial acetimidylation

Acetimidylated horse cytochrome c and related derivatives exhibit more or less marked changes, both upscale and downscale, in apparent pK of the alkaline transition. This transition occurs when the normal methionine-80 residue is replaced at the sixth haem co-ordination position by another strong-field ligand. Analysis of the relationship between structural change and pK shift in these derivatives supports the view that the replacement ligand is a lysine residue, probably 72 or 79, and contradicts an alternative hypothesis. The results add further detail to a comprehensive view of the mechanism of this isomerization.

Partial purification and characterization of two soluble c-type cytochromes from Chromatium vinosum

Two c-type cytochromes from Chromatium vinosum have been partially purified and characterized. Cytochrome c550, which appears to function as an electron carrier in the cyclic electron transport chain of this photosynthetic purple sulfur bacterium, has a molecular weight of approximately 15,000 and an oxidation-reduction midpoint potential (Em) of +240 mV at pH 7.4. It has (in the reduced form) an alpha band at 550 nm and a beta band at 520 nm. Cytochrome c551 is characterized by absorbance maxima at 354 and 409 nm in the oxidized form and 418, 523, and 551 nm in the reduced form. The reduced cytochrome reacts with CO. Cytochrome c551 is a monomeric protein with a molecular weight of 18,800 +/- 700 and Em = -299 +/- 5 mV (pH independent between pH 6.3 and 8.0). It appears to lack a methionine axial ligand as indicated by the absence of an absorbance band at 695 nm in the oxidized form.

Folding of yeast iso-1-AM cytochrome c

We describe a specific modification of iso-1 cytochrome c which results in blocking a single free sulfhydryl group. The derivative differs from the unmodified protein by the introduction of a small, uncharged group, thus maintaining the same charge balance as the native protein. The modified protein, obtained by treatment of iso-1 cytochrome c with iodoacetamide, has an activity indistinguishable from that of the unmodified protein in the lactate dehydrogenase-cytochrome c reductase system from yeast and has the same stability toward denaturation by guanidine hydrochloride. The kinetics of fluorescence changes associated with the guanidine hydrochloride induced folding-unfolding transition for modified iso-1 cytochrome c (iso-1-AM) have been investigated throughout the transition zone by using stopped-flow mixing. The results are compared to those for the yeast isozyme, iso-2 cytochrome c. The main features of the fluorescence-detected folding kinetics are similar, as might be expected for homologous proteins; however, the limiting value of the fraction of fast refolding protein (alpha 2) below the transition zone is smaller for iso-1-AM (approximately 0.7) than for iso-2 (approximately 0.9).

Structural intermediates in folding of yeast iso-2 cytochrome c

The kinetic properties of the folding reactions of iso-2 cytochrome c from Saccharomyces cerevisiae have been investigated by stopped-flow and temperature-jump methods. Three different structural probes are compared: (1) absorbance changes in the visible reflecting changes in heme environment, (2) ultraviolet absorbance changes due to the exposure of aromatic groups to solvent, and (3) tryptophan fluorescence attributable principally to the average distance between the tryptophan residue (donor) and the heme (quencher). In addition, two probes either indicative of or correlated with function, ascorbic acid reducibility and the 695-nm absorbance band, have been used to monitor specifically the rate of formation of the native protein on refolding. The fastest phase observed (tau 3) has a measurable relative amplitude only when monitored by visible absorbance changes, suggesting that this reaction involves changes in heme environment in the absence of significant changes in the heme to tryptophan distance or in the extent to which aromatic groups are exposed to solvent. Different slow phases are observed when complete refolding is monitored by visible or ultraviolet absorbance (tau 1a) as opposed to tryptophan fluorescence (tau 1b), the fluorescence changes being complete on a time scale 4-8-fold faster than for absorbance. A mid-range kinetic phase (tau 2) is detected by all three structural probes. When ascorbic acid reducibility or 695-nm absorbance changes are used to monitor the rate of formation of the native protein, two phases are detected: tau 2 and tau 1a. Taken together these results demonstrate that kinetic phase tau 1b results in the formation of a structural intermediate in folding with fluorescence close to that of the native protein but with distinct absorbance properties.

13C-NMR spectroscopy of acetyltyrosyl-guanidinated horse heart cytochrome c

The tyrosine residues of guanidinated horse heart cytochrome c have been specifically acetylated by reaction with N-[1-13C]acetylimidazole (90 atom%). Acetylation was monitored by 13C-NMR spectroscopy. The tyrosine residues were found to show widely varying reactivities ranging from one that is completely and exclusively acetylated at low reagent concentration (residue 67) to one that is acetylated only when the protein is unfolded (residue 97). Homogeneous derivatives were prepared containing one (either residue 67 or 97), three 48, 67 and 74), or four (residues 48, 67, 74 and 97) O-[1-13C]acetyl groups. 13C-NMR spectra of selected derivatives were obtained at pH 5.8, in the presence of cyanide ion, in the ferrous and ferric oxidation states, and after denaturation with 6M guanidine hydrochloride. The O-[1-13C]acetyltyrosyl resonances gave chemical shift values ranging from 171.8 to 176.0 ppm. These resonances were assigned to specific groups based on the known order of reactivity of the tyrosyl side chains toward N-acetylimidazole. The chemical shift of O-[1-13C]acetyltyrosyl 67 was found to be particularly sensitive to changes in protein structure. The proximity of this group to the heme makes it subject to distance-dependent paramagnetic and ring current effects. Acetylation of tyrosyl 74 gives rise to a pH-dependent equilibrium between conformers in the ferric state and a conformation change in the ferrous state. Acetylation of this residue also leads to an absorbance decrease at 695 nm that can be related to the 13C-NMR-detected conformational equilibrium. Addition of cyanide ion abolished this equilibrium.

A functioning complex of two cytochrome c fragments with deletion of the (39-58) eicosapeptide

Two major fragments of horse heart cytochrome c involving the sequences (1-38) and (60-104) were found to produce a stable complex. The two fragments were devoid of any cytochrome c activity. The complex exhibited a hardly measurable electron transfer capacity with respect to cytochrome c oxidase and missed the 695 nm absorption band. The introduction of tryptophan in position 59 restored the intrinsic activity of the complex to the level of native cytochrome c. This was concluded from the convergence of the Eady-Hofstee plots which extrapolate to the same Vmax at high substrate concentrations. The absorption spectrum of the complex in the ferriform contained a clear absorption band at 695 nm (84% of that found with native cytochrome c). The investigation proves the indispensability of tryptophan in position 59 for the transfer of an electron to cytochrome c oxidase and supports the conclusions of Parr et al. about the existence of two consecutive processes in the folding of the two fragments (vide infra).

Time-resolved resonance Raman spectroscopy of cytochrome c reduced by pulse radiolysis

The first investigation of the dynamics of a redox transition of an electron-transfer enzyme by time-resolved resonance Raman spectroscopy in combination with pulse-radiolytic reduction is described by an application to cytochrome c. A long-lived transient state is observed upon reduction of the alkaline form of cytochrome c as a distinct frequency shift of one resonance Raman band. From the frequency in the stable oxidized state, 1567 cm(-1), this particular resonance Raman band shifts within less than 1 microsecond to 1533 cm(-1) in the transient reduced state, which has a lifetime longer than 20 ms but shorter than a few seconds. Finally, in the stable reduced state, this band is located at 1547 cm(-1). According to a previous normal coordinate analysis, this resonance Raman band can be assigned predominantly to a stretching mode of the outermost C-C bonds in the four pyrrole rings of porphyrin. This vibrational mode is influenced by the protein most directly through the covalent thioether linkages of two cysteines to porphyrin. We interpret the long lifetime of the transient state as due to the slow return of Met-80 as sixth ligand to the heme iron upon reduction of the alkaline form of cytochrome c.

Kinetic and equilibrium studies of alkaline isomerization of vertebrate cytochromes c

Equilibria and kinetics of alkaline isomerization of seven ferricytochromes c from vertebrates were studied by pH-titration and pH-jump methods in the pH region of 7-12. In the equilibrium behavior, no significant difference was detected among the cytochromes c, whereas marked differences in the kinetic behavior were observed. According to the kinetic behavior of the isomerization, the cytochromes c examined fall into three classes: Group I (horse, sheep, dog and pigeon cytochromes c), Group II (tuna and bonito cytochromes c) and Group III (rhesus monkey cytochrome c). The kinetic results are interpreted in terms of the sequential scheme: Neutral form in equilibrium with fast Transient form in equilibrium with slow Alkaline form where the neutral and alkaline forms are the species stable at neutral and alkaline pH, respectively, and the transient form is a kinetic intermediate. From comparison of the primary sequences of the seven cytochromes c and the classification of these cytochromes c, it is concluded that the amino acid substitution Phe/Tyr at the 46-th position has a major influence on the kinetic behavior. In Group II and III cytochromes c, the ionization of Tyr-46 is suggested to bring about loosening of the heme crevice and thus facilitate the ligand replacement involved in the isomerization.

Nature of the fast and slow refolding reactions of iron(III) cytochrome c

The fast and slow refolding reactions of iron(III) cytochrome c (Fe(III) cyt c), previously studied by Ikai et al. (Ikai, A., Fish, W. W., & Tanford, C. (1973) J. Mol. Biol. 73, 165--184), have been reinvestigated. The fast reaction has the major amplitude (78%) and is 100-fold faster than the slow reaction in these conditions (pH 7.2, 25 degrees C, 1.75 M guanidine hydrochloride). We show here that native cyt c is the product formed in the fast reaction as well as in the slow reaction. Two probes have been used to test for formation of native cyt c. absorbance in the 695-nm band and rate of reduction of by L-ascorbate. Different unfolded species (UF, US) give rise to the fast and slow refolding reactions, as shown both by refolding assays at different times after unfolding ("double-jump" experiments) and by the formation of native cyt c in each of the fast and slow refolding reactions. Thus the fast refolding reaction is UF leads to N and the slow refolding reaction is Us leads to N, where N is native cyt c, and there is a US in equilibrium UF equilibrium in unfolded cyt c. The results are consistent with the UF in equilibrium US reaction being proline isomerization, but this has not yet been tested in detail. Folding intermediates have been detected in both reactions. In the UF leads to N reaction, the Soret absorbance change precedes the recovery of the native 695-nm band spectrum, showing that Soret absorbance monitors the formation of a folding intermediate. In the US leads to N reaction an ascorbate-reducible intermediate has been found at an early stage in folding and the Soret absorbance change occurs together with the change at 695 nm as N is formed in the final stage of folding.

Kinetic studies on isomerization of ferricytochrome c in alkaline and acid pH ranges by the circular dichroism stopped-flow method

The isomerization of horse-heart ferricytochrome c caused by varying pH was kinetically studied by using circular dichroism (CD) and optical absorption stopped-flow techniques. In the pH range of 7--13, the existence of the three different forms of ferricytochrome c (pH less than 10, pH 10--12, and pH greater than 12) was indicated from the statistical difference CD spectra. On the basis of analyses of the stopped-flow traces in the near-ultraviolet and Soret wavelength regions, the isomerization of ferricytochrome c from neutral form to the above three alkaline forms was interpreted as follows (1) below pH 10, the replacement of the intrinsic ligand of methionine residue by lysine residue occurs; (2) between pH 10 and 12, the uncoupling of the polypeptide chain from close proximity of the heme group occurs first, followed by the interconversion of the intrinsic ligands; and (3) above pH 12, hydroxide form of ferricytochrome c is formed, though the replacement of the intrinsic ligand by extrinsic ligands may occur via different routes from those below pH 12. The CD changes at 288 nm and in the Soret region caused by the pH-jump (down) from pH 6.0 to 1.6 were compared with the appearance of the 620-nm absorption band ascribed to the formation of the high-spin form of ferricytochrome c. Both CD and absorption changes indicated that the isomerization at pH 1.6 consisted of two processes: one proceeded within the dead-time (about 2 ms) of the stopped-flow apparatus and the other proceeded at a determinable rate with the apparatus. On the basis of these results, the isomerization of ferricytochrome c at pH 1.6 was explained as follows: (1) the transition from the low-spin form to the high-spin forms occurs within about 2 ms, the dead-time of the stopped-flow apparatus; and (2) the polypeptide chain is unfolded after the formation of the high-spin form.