Cytochrome c

The denatured states of cytochrome c

The unfolding of horse ferricytochrome c in the presence of several inorganic salts has been studied under a variety of denaturing conditions and followed by means of absorbance changes in the Soret region (390-450 nm) and visible region (450-750 nm), as well as by viscosity measurements. Change in the Soret region, usually sensitive to the heme environment, were characterized by gradual increases in absorbance at 409 nm for low concentrations of NaClO4 and LiClP4. As denaturant concentrations were increased, the low-spin state of the ferric heme is altered, as seen by a maximum shift to shorter wavelengths (402-407 nm) accompanied by a further increase in absorbance in the Soret region. Unlike the effect of several organic denaturants and the above salts, denaturation in the presence of LiCl and CaCl2 resulted in an overall decrease in the Soret region with a blue-shift to 401 and 400 nm, respectively. Visible spectra of ferricytochrome c exhibited new bands at 633 nm (9.0 M LiCl) and 636 nm (4.5 M CaCl2) indicative of a change in the spin state of the iron upon displacement of methionine 80. LiCl and LiBr produced intermediate states of protein unfolding with midpoints (D 1/2) at 4.0 and 8.6, and 2.6 and 6.4, respectively. A determination of delta GHU2O and m, the free energy of unfolding in the absence of denaturant and the dependence of free energy of denaturation on denaturant concentration, was used to analyze the relative effectiveness of these denaturants.

Antibacterial peptide from normal rabbit serum. 3. Inhibition of microbial electron transport

The influence of the primary rabbit serum bactericide, PC-III, on the respiratory activity of Bacillus subtilis has been examined. Glucose- or lactate-dependent respiration by whole cells was rapidly and completely inhibited by concentrations of the bactericide producing significant cell death. Similar results were observed with membrane vesicles oxidizing NADH. In both cases, bactericide-induced inhibition of respiration was calcium dependent and blocked electron transport between cytochromes b and a. PC-III competed with oxidized Saccharomyces cytochrome c when the latter was used as an electron acceptor in cytochrome c reductase reactions catalyzed by B. subtilis membrane vesicles. Competitive inhibition by PC-III was also observed when reduced Saccharomyces cytochrome c was used as electron donor in the cytochrome c oxidase reaction. At an ionic strength of 0.13, PC-III exhibits a Ki of 25.9 and 102 nM for the reductase and oxidase complexes, respectively. Increasing the ionic strength to that producing optimal antibacterial action against whole cells (0.24) increased the Ki of PC-III for the reductase (75.4 nM), while the oxidase decreased (92.3 nM).

Evolution of cytochrome C investigated by the maximum parsimony method

Rates of evolution for cytochrome c over the past one billion years were calculated from a maximum parsimony dendrogram which approximates the phylogeny of 87 lineages. Two periods of evolutionary acceleration and deceleration apparently occurred for the cytochrome c molecule. The tempo of evolutionary change indicated by this analysis was compared to the patterns of acceleration and deceleration in the ancestry of several other proteins. The synchrony of these tempos of molecular change supports the notion that rapid genetic evolution accompanied periods of major adaptive radiations. Rates of change at different time in several structural-functional areas of cytochrome c were also investigated in order to test the Darwinian hypothesis that during periods of rapid evolution, functional sites accumulate proportionately more substitutions than areas with no known functions. Rates of change in four proposed functional groupings of sites were therefore compared to rates in areas of unknown function for several different time periods. This analysis revealed a significant increase in the rate of evolution for sites associated with the regions of cytochrome c oxidase and reductase interaction during the period between the emergence of the eutherian ancestor to the emergence of the anthropoid ancestor.

Characterization of the partially reduced cyanide-inhibited derivative of cytochrome c oxidase by optical, electron-paramagnetic-resonance and magnetic-circular-dichroism spectroscopy

Optical. e.p.r. and near-infrared low-temperature m.c.d. (magnetic-circular-dichroism) spectroscopy were used to characterize the partially reduced cyanide-inhibited derivative of cytochrome c oxidase produced by anaerobic reductive titration with dithionite. The reductions of cytochrome a3+ and Cu2+a were followed by observation of the e.p.r. signals at g = 3.03, 2.21 and 1.5 and at g = 2.18, 2.03 and 1.99. As reduction proceeds new e.p.r. signals (g = 3.58 and 1.56) appear that quantify to give one haem per enzyme unit when a small excess of dithionite has been titrated in. The e.p.r. signal of the Cu2+a titrates in parallel with the disappearance of the band and 820nm in the optical absorption spectrum. The near-infrared m.c.d. spectrum shows the presence of the low-spin ferric haem, a3+, in the oxidized state of the enzyme, as a well-resolved positive peak at 1650nm. As reduction proceeds this band is replaced by one at 1550nm due to haem a3+(3)--CN in the partially reduced state. Hence as haem a3+(3)--CN becomes e.p.r.-detectable it also shows a near-infrared m.c.d. spectrum characteristic of a low-spin ferric haem. It is concluded that the partially reduced state of cyanide-inhibited cytochrome c oxidase contains a2+ . Cu+a . a3+(3)--CN . Cu+a3.

Redox conformation changes in refined tuna cytochrome c

Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side.

Magnetization curves of haemoproteins measured by low-temperature magnetic-circular-dichroism spectroscopy

The magnetic-circular-dichroism (m.c.d.) spectra of methymyoglobin cyanide and oxidized horse heart cytochrome c were measured in the region of the Soret band over a range of temperatures from 1.5 to 50 K and in fields from 0 to 5T. A similar study has been made with reduced bovine heart cytochrome c oxidase, which contains one high-spin ferrous haem, namely a3. M.c.d. magnetization curves characteristic of an isolated Kramer's ground state with spin S = 1/2. These curves contrast with the magnetization curve of the high-spin ferrous haem with spin S = 2. The electronic ground state of the latter compound contains zero-field components that are thermally accessible over the temperature range of the experiment. Hence the magnetization curves are a complex nested set. The magnetization curves of the S = 1/2 proteins were analysed and it is shown that it is possible to make estimates of the ground-state g-factors even in the presence of rhombic anisotropy, provided that some knowledge of the polarizations of the electronic transitions is available. The striking difference between the m.c.d. magnetization curves of a simple S = 1/2 paramagnet and magnetically complex ground state should prove extremely useful when m.c.d. spectroscopy is sued to probe the magentic properties of metal centres in proteins, and should have wide application beyond the field of haemoproteins.

Protein conformation wheels: cytochromes and lysozymes

Conformation wheels, directly relating to amino acid sequence to the local torsion angles in a protein molecule, are presented for cytochromes c, c2, c550, and c551 and for lysozymes from hen egg-white and T4 bacteriophage. The circular plots for the cytochrome molecules aid in visualizing the common three-dimensional folding ("cytochrome fold") observed in this family of proteins. Conformation wheels for lysozymes from two different species reveal the characteristic differences in their folding patterns. These novel plots are also useful in storing and comparing the several sets of crystallographic data reported for lysozyme.

Nuclear-magnetic-resonance studies of ferrocytochrome c. pH and temperature dependence

The pH dependence and the temperature dependence of the nuclear magnetic resonance spectrum of horse ferrocytochrome c are described. This protein is very stable; it maintains an ordered structure over the pH range 4 to 12 at 25 degrees C and over the temperature range 4 degrees C to 97 degrees C at pH 7.0. The dynamic characteristics of the conformation of ferrocytochrome c were investigated. Particular emphasis was laid on the aromatic resonances and resonances of methyl groups shifted far upfield. Tyr-48 and Phe-46 were found to be relatively immobile whilst a region of the protein close to Ile-57 was found to be relatively flexible.

The stability of ferricytochrome c. Temperature dependence of its NMR spectrum

The temperature dependence of the nuclear magnetic resonance spectrum of horse ferricytochrome c is described. The protein maintains an ordered structure over the temperature range 20 degrees C to 77 degrees C. The temperature dependence of the spectrum of ferricytochrome c arises from a number of causes including the paramagnetism of the ferric ion and protein structural changes. Preliminary analysis of the data show that the region of the protein about Ile-57 is flexible. Comparison of the data with the analogous data for horse ferrocytochrome c reveals that there is a small difference in structure between cytochrome c in its two oxidation states in the region about Ile-57.

The solution structures of tuna and horse cytochromes c

The nuclear magnetic resonance spectra of tuna ferricytochrome c and tuna ferrocytochrome c are described. Resonance assignments are made using NMR double-resonance techniques. A comparison of the NMR data for tuna cytochrome c with the previously reported data for horse cytochrome c shows that the proteins have virtually identical main-chain folds. Three regions of local conformational differences have been distinguished.

Individual assignments of the heme resonances in the 360 MHz 1H NMR spectra of cytochrome c-557 from Crithidia oncopelti

With the use of nuclear Overhauser effects, spin decoupling and saturation transfer experiments individual assignments for numerous resonances of the heme group in the 360 MHz 1H NMR spectra of reduced and oxidized cytochrome c-557 from Crithidia oncopelti were obtained. These data provide direct evidence that the heme substituent in position 2 is a vinyl group. They further show that in spite of the different covalent structures of the heme groups the heme crevice and the electronic heme structure in the oxidized state are nearly identical in cytochrome c-557 and in mammalian cytochromes c.

Cyanide reactivity of cytochrome c derivatives

The kinetic rates and equilibrium association constants for cyanide binding have been measured for a series of cytochrome c derivatives as a probe of heme accessibility. The series included horse and yeast cytochromes iodinated at Tyr 67 and 74, horse cytochrome formylated at Trp 59 in both a low and high redox potential form, the Met 80 sulfoxide derivative of horse cytochrome and the N-acylisourea heme propionate derivative of tuna cytochrome. Native cytochromes c are well known to bind cyanide slowly in a reaction simply first order both in cytochrome and cyanide up to at least 100 mM in cyanide. The derivative demonstrate markedly different kinetics which indicate the following conclusions. (1) In spite of chemical modification at different loci, all the derivatives have highly similar reactivity, suggesting common ligation structures and mechanisms for reaction. (2) Compared to native cytochromes, reaction rates are 10-20 fold greater. This is in accord with a more accessible heme crevice, but not a completely opened crevice. For the completely opened case, rate increases are expected to be between three and five orders of magnitude. (3) Reaction rates are either independent of cyanide concentration (zero order) or show only slight variation. A mechanism which accounts for the data over four orders of magnitude in concentration postulates a protein conformation step, opening of the heme crevice, as the rate determining step. This conformation change has a limiting rate of 6 . 10(-2) s-1.

Semisynthetic analogs of cytochrome c reconstructed from natural and synthetic peptides

A biologically active semisynthetic hybrid of horse heart cytochrome c has been prepared by combining the heme peptide 1 through 65 (HP 1-65), prepared by CNBr cleavage of natural cytochrome c, with a semisynthetic peptide corresponding to positions 66 through 104. A fully protected synthetic peptide 66--79 was prepared by a modified solid phase peptide synthesis procedure and was converted to its N-hydroxysuccinimide ester. A peptide corresponding to residues 81--104 of cytochrome c was also isolated from the CNBr cleavage mixture and its epsilon-amino groups and tyrosyl hydroxyl group were protected selectively with the t-butyloxycarbonyl group. This partially protected peptide was reacted with t-butyloxycarbonyl methionine N-hydroxysuccinimide ester to give a derivative having methionine at position 80. This product was deprotected, purified and then t-butyloxycarbonyl groups were again introduced specifically on the epsilon-amino groups to give the peptide, Boc(Lys,Tyr)80--104. A semisynthetic peptide corresponding to residues 66 through 104 of cytochrome c was prepared by condensing the synthetic peptide 66--79 N-hydroxysuccinimide ester with t-butyloxycarbonyl (Lys,Tyr)80--104. The semisynthetic product was deprotected, purified and combined under anaerobic conditions with a heme peptide, HP 1-65, that was isolated from the products of CNBr cleavage of native cytochrome c. The reconstituted semisynthetic cytochrome c was purified by ion exchange chromatography and was shown to have the same oxygen uptake as native cytochrome c when assayed in the succinate oxidase system.

Cytochrome c from Schizosaccharomyces pombe. 1. Purification, spectral properties, and amino-acid composition

Cytochrome c from the fission yeast Schizosaccharomyces pombe has been purified. Its chromatographic and spectral properties are reported and compared to those of iso-1-cytochrome c from baker's yeast; the amino-acid composition is described. Schiz. pombe cytochrome c has a much lower affinity for Amberlite IRP64 than Sacch. cerevisiae iso-1-cytochrome c. Its alpha absorption band splits into three maxima (calpha1, calpha2, and calpha3) at -190 degrees C; this is unusual in yeasts, as shown by the low-temperature whole-cell absorption spectra which were examined in various yeast genera, species, and strains. A minor component can be separated by Amberlite chromatography. It exhibits the same low-temperature splitting of the alpha absorption band as the main fraction and it has a similar amino-acid composition with a notable exception: it is an unmethylated form of the cytochrome.

Cytochrome c from Schizosaccharomyces pombe. 2. Amino-acid sequence

The amino acid sequence of Schizosaccharomyces pombe cytochrome c has been established by automatic degradation of the protein and by manual degradation of fragments obtained by cyanogen bromide cleavage and chymotryptic digestion. The chymotryptic peptides were aligned by homology with other known cytochrome c sequences. The protein is 108 residues long, with a four-residue amino-terminal tail. It has only one methionine residue and differs from other fungal cytochromes c in lacking the one-residue deletion at the C-terminal end. After a cyanogen bromide step, an unexpected cleavage of the peptide chain before a cysteine residue was observed. This is ascribed to formation of a dehydroalanyl residue during an incomplete S-carboxymethylation of the apoprotein, and subsequent cleavage under acidic conditions. Experimental evidence is presented in favour of the proposed mechanisms.

Assignment of the heme c resonances in the 360 MHz H NMR spectra of cytochrome c

In the 360 MHz 1H NMR spectra of horse heart ferrocytochrome c recorded after suitable digital resolution enhancement, the resonances of all the heme c protons with the exception of those of the propionic acid side chains were observed as well resolved lines. From spin decoupling and nuclear Overhauser effects in homonuclear double resonance experiments, all these resonances were assigned to their respective positions in heme c. With saturation transfer experiments in solutions of partially reduced cytochrome c, individual assignments were further obtained for the six heme c methyl resonances in ferricytochrome c. The present experiments add individual assignments to the earlier identifications of the heme c ring methyl and meso-proton resonances, and show that the earlier identifications of the thioether bridge methyl resonances must be revised. These data provide a basis for more detailed descriptions of the electronic structure of heme c and its possible relations with the pathway of the electron transfer in and out of the cytochrome c molecule. Furthermore, the pseudocontact shifts of the thioether bridge methyl resonances could be related to the electronic g-tensor measured by EPR in ferricytochrome c single crystals at low temperature. From this it will now be possible without chemical modification of the protein, to compare in detail the solution conformations near the heme c in reduced and oxidized cytochrome c and thus hopefully to obtain additional insights into the mechanism of the biological redox reaction of this protein.