Axial ligand replacement in horse heart cytochrome c by semisynthesis

Semisynthesis has been employed to replace the axial methionine in horse heart cytochrome c with histidine. The reduction potential of the His-80 protein (cyt c-His-80) is 41 mV vs NHE (0.1 M phosphate; pH 7.0; 25 degrees C). The absorption spectra of oxidized and reduced cyt c-His-80 are very similar to those of the native protein in the porphyrin region, but the 695 nm band is absent in the oxidized His-80 protein.     

Semisynthesis of the native sequence of horse heart cytochrome c-(66-104)-nonatriacontapeptide

The syntheses of some derivatives of horse cytochrome c-(66-79)-tetradecapeptide are presented. The syntheses are so designed that analogues of this phylogenetically well preserved sequence can be obtained also. The compounds were intended as synthons for the semisynthesis of 65-homoserine-cytochrome c, which we described earlier. A requisite for this project was the C-terminal tetracosapeptide fragment of the protein, accessible through degradation of cytochrome c with cyanogen bromide. The five epsilon amino groups in this compound are reversibly protected with the 2-(methylsulfonyl)ethyloxycarbonyl function, which is resistant to acid and causes little impairment of solubility. The condensation of the fragments leading to the native sequence of horse cytochrome c-(66-104)-nonatriacontapeptide is presented also. The syntheses were performed using the solution strategy. Some unexpected ring closing reactions involving tyrosine and tert.-butyl prolylasparaginylcarbazate, are described.     

Conformational studies of equilibrium structures in fragments of horse heart cytochrome c.

Ultraviolet absorption and circular dichroism studies have been carried out on horse heart apo-cytochrome c and heme-free peptide fragments obtained by cyanogen bromide cleavage of the native protein. It was noted that the various peptides assume predominantly an unordered conformation in water solution. Increasing ionic strength and addition of 2-chloroethanol increase the right-handed helical content. Guanidinium hydrochloride favors the coil state. It was also demonstrated that two non-interacting helical regions of different stability are present in the apo-protein in 2-chloroethanol.     

The semisynthesis of analogues of cytochrome c. Modifications of arginine residues 38 and 91.

The arginine residues at positions 38 and 91 of horse cytochrome c are absolutely conserved throughout eukaryotic evolution. For studies of the functional roles of these residues, we have prepared, by semisynthetic techniques, analogues of cytochrome c in which one or the other of the arginine residues has been modified. The products of modification by adduct formation with pentane-2,4-dione were purified and extensively characterized. In biological tests, the arginine-91-modified cytochrome c showed little difference in behaviour from native horse cytochrome c. Modification of arginine-38, however, led to extensive changes in biological and chemical properties. We also prepared and tested adducts with cyclohexane-1,2-dione and camphorquinone-10-sulphonic acid. The same effects on biological properties were noted irrespective of the nature of the modifying group. We suggest reasons for the differences in sensitivity of the two sites.     

Studies on cytochrome C. XII. Synthesis of the protected undecapeptide (sequence 66-76) and pentadecapeptide (sequence 66-80) of horse heart cytochrome c.

This paper is part of a series on synthesis of suitably protected peptides covering the 66-104 sequence of horse heart cytochrome c. It describes the preparation, by conventional procedures, of a partially protected N alpha-benzyloxycarbonyl-undecapeptide hydrazide corresponding to the sequence from 66 to 76 (Fragment F), which represents a building block for the synthesis of the entire 66-104 sequence. Moreover, the preparation is described of a partially protected pentadecapeptide corresponding to the sequence region 66 to 80, which represents the key peptide for the semisynthesis of the same COOH-terminal sequence utilizing the natural 81-104 N epsilon-trifluoroacetylated CNBr fragment.     

Protein engineering of cytochrome c by semisynthesis: substitutions at glutamic acid 66

We have used protein semisynthesis to prepare four analogues of horse cytochrome c, in which the glutamic acid residue at position 66 has been removed and replaced by norvaline, glutamine, lysine and, as a methodological control, glutamic acid. This residue is quite strongly conserved in mitochondrial cytochrome c, and forms part of a cluster of acidic residues that occurs in all cytochromes c but whose function is obscure. Comparative studies of the physical and biochemical properties of the analogues have now disclosed two specific roles for Glu66 in the protein. It contributes significantly to the stabilization of the active conformation of the protein, probably by salt bridge formation, and it appears to participate in the redox-state-dependent ATP-binding site of cytochrome c. Our results also support two general views of the role of surface charged residues in cytochrome c, namely that their disposition influences both redox potential, through the electrostatic field felt at the redox centre, and the kinetics of electron transfer, through the dipole moment they generate.     

Cocrystals of yeast cytochrome c peroxidase and horse heart cytochrome c

Yeast cytochrome c peroxidase and horse heart cytochrome c have been cocrystallized in a form suitable for x-ray diffraction studies and the structure determined at 3.3 A. The asymmetric unit contains a dimer of the peroxidase which was oriented and positioned in the unit cell using molecular replacement techniques. Similar attempts to locate the cytochrome c molecules were unsuccessful. The peroxidase dimer model was subjected to eight rounds of restrained parameters least squares refinement after which the crystallographic R factor was 0.27 at 3.3 A. Examination of a 2Fo-Fc electron density map showed large "empty" regions between peroxidase dimers with no indication of cytochrome c molecules. Electrophoretic analysis of the crystals demonstrated the presence of the peroxidase and cytochrome c in an approximate equal molar ratio. Therefore, while cytochrome c molecules are present in the unit cell they are orientationally disordered and occupy the space between peroxidase dimers.     

Synthesis of fragments by classical solution methods for use in cytochrome c semisynthesis

We report details of the chemical synthesis of two fragments reproducing the C-terminal sequences 71-108 and 70-108 of Saccharomices cerevisiae cytochrome c. Preparation of the fragments employed classical solution methods and a fragment-condensation strategy; they have been used, together with a third fragment (sequence 67-108) [L. Moroder, B. Filippi, G. Borin & F. Marchiori (1975) Biopolymers 14 , 2061–2074], in the semisynthesis of chimeric cytochromes [C. J. A. Wallace, G. Corradin, F. Marchiori & G. Borin (1986) Biopolymers 25 , 2121–2132].     

Comparative solvent perturbation of horse heart cytochrome c and Rhodospirillum rubrum cytochrome c2.

The extent of exposure of heme to solvent in horse heart cytochrome c and Rhodospirillum rubrum c2 was investigated to determine whether a correlation exists between the properties of these oxidation-reduction proteins and their heme environments. Solvent perturbation absorption difference spectra were measured using ethylene glycol, glycerol, and sucrose at concentrations between 0 and 30%. Cytochrome c appears to exhibit a somewhat greater extent of heme exposure than cytochrome c2 for both the oxidized and reduced states. These results suggest that the lower oxidation-reduction potential of cytochrome c may in part be due to a greater extent of exposure of the heme. The oxidized state of both proteins appears to exhibit a greater exposure than that of the reduced state which is consistent with a more favorable environment for the charge on the ferric heme coordination center.     

High-resolution three-dimensional structure of horse heart cytochrome c

The 1.94 A resolution three-dimensional structure of oxidized horse heart cytochrome c has been elucidated and refined to a final R-factor of 0.17. This has allowed for a detailed assessment of the structural features of this protein, including the presence of secondary structure, hydrogen-bonding patterns and heme geometry. A comprehensive analysis of the structural differences between horse heart cytochrome c and those other eukaryotic cytochromes c for which high-resolution structures are available (yeast iso-1, tuna, rice) has also been completed. Significant conformational differences between these proteins occur in three regions and primarily involve residues 22 to 27, 41 to 43 and 56 to 57. The first of these variable regions is part of a surface beta-loop, whilst the latter two are located together adjacent to the heme group. This study also demonstrates that, in horse cytochrome c, the side-chain of Phe82 is positioned in a co-planar fashion next to the heme in a conformation comparable to that found in other cytochromes c. The positioning of this residue does not therefore appear to be oxidation-state-dependent. In total, five water molecules occupy conserved positions in the structures of horse heart, yeast iso-1, tuna and rice cytochromes c. Three of these are on the surface of the protein, serving to stabilize local polypeptide chain conformations. The remaining two are internally located. One of these mediates a charged interaction between the invariant residue Arg38 and a nearby heme propionate. The other is more centrally buried near the heme iron atom and is hydrogen bonded to the conserved residues Asn52, Tyr67 and Thr78. It is shown that this latter water molecule shifts in a consistent manner upon change in oxidation state if cytochrome c structures from various sources are compared. The conservation of this structural feature and its close proximity to the heme iron atom strongly implicate this internal water molecule as having a functional role in the mechanism of action of cytochrome c.     

Solution structure of reduced horse heart cytochrome c

 In the frame of a broad study on the structural differences between the two redox forms of cytochromes to be related to the electron transfer process, the NMR solution structure of horse heart cytochrome c in the reduced form has been determined. The structural data obtained in the present work are compared to those already available in the literature on the same protein and the presence of conformational differences is discussed in the light of the experimental method employed for the structure determination. Redox-state dependent changes are analyzed and in particular they are related to the role of propionate-7 of the heme. Also some hydrogen bonds are changed upon reduction of the heme iron. A substantial similarity is observed for the backbone fold, independently of the oxidation state. At variance, some meaningful differences are observed in the orientation of a few side chains. These changes are related to those found in the case of the highly homologous cytochrome c from Saccharomyces cerevisiae. The exchangeability of the NH protons has been investigated and found to be smaller than in the case of the oxidized protein. We think that this is a characteristic of reduced cytochromes and that mobility is a medium for molecular recognition in vivo. Received: 8 June 1998 / Accepted: 13 October 1998     

Spectral studies of horse heart porphyrin cytochrome c

Removal of the heme iron from cytochrome c to generate porphyrin cytochrome c relieves the quenching of porphyrin fluorescence and enhances the fluorescence of the single tryptophan residue and the 4 tyrosine residues. The intensity of the porphyrin fluorescence is not perturbed by denaturation of the protein at neutral pH using either urea or guanidine hydrochloride. However, the amplitude of tryptophan fluorescence is increased by these denaturants from 5 to about 85% of a model tryptophan residue using solutions of 2 microM tryptophan. In contrast to cytochrome c, the tryptophan fluorescence amplitude of denatured porphyrin cytochrome c is independent of pH over the range pH 3.0 to 7.4. Acidification of solutions of either native or denatured porphyrin cytochrome c markedly alters both the visible absorbance and fluorescence of the protein consistent with protonation of two pyrrole nitrogens on the porphyrin. Preliminary analysis of the spectral changes occurring in the acid transition suggests the presence of an intermediate form having only one of these two pyrrole nitrogens protonated.     

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.     

Lactoperoxidase-catalyzed iodination of horse cytochrome c:monoiodotyrosyl 74 cytochrome c.

Iodination of horse cytochrome c with the lactoperoxidase-hydrogen peroxide-iodide system results initially in the formation of the monoiodotyrosyl 74 derivative. This singly modified protein was obtained in pure form by ion exchange chromatography and preparative column electrophoresis. It shows an intact 695 nm absorption band, the midpoint potential of the native protein, a nuclear magnetic resonance spectrum which indicates an undisturbed heme crevice structure, a normal reaction with antibodies directed against native horse cytochrome c, and circular dichroic spectra in which the only changes from those of the native protein can be ascribed to the spectral properties of iodotyrosine itself. This conformationally intact derivative reacts with the succinate-cytochrome c reductase and the cytochrome c oxidase systems of beef mitochondrial particle preparations indistinguishably from the unmodified protein, showing that the region including tyrosine 74 is not involved in these enzymic electron transfer functions of the protein. The circular dichroic spectra of this derivative indicate that the minima observed at 288 and 282 nm in the spectrum of native ferricytochrome c originate from tyrosyl residue 74.