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

Characterization of zinc-substituted cytochrome c by circular dichroism and resonance Raman spectroscopic methods

Iron(III) in cytochrome c is replaced with zinc(II) by a modification of a method published by others, and the procedure is described in full detail. Three forms of cytochrome c-those containing iron(III), iron(II), and zinc(II)-are examined by circular dichroism spectroscopy and resonance Raman spectroscopy. Spectra of both kinds show that introduction of zinc(II) ions does not appreciably alter the overall structure and conformation of cytochrome c. Resonance Raman spectra indicate the size of the porphyrin "core" that is inconsistent with six-coordination and consistent with five-coordination. Unlike the iron(III) and iron(II) ions, which are bound to two axial ligands (His 18 and Met 80), the zinc(II) ion in cytochrome c seems to be bound to only one, most probably His 18. Evidence pertaining to the question of axial coordination is discussed.

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.

Circular dichroism studies of low-spin ferric cytochrome P-450CAM ligand complexes

Circular dichroism (CD) spectroscopy has been used to probe the active site of bacterial ferric cytochrome P-450CAM. The endogenous sixth ligand to the heme iron has been displaced by an extensive series of exogenous oxygen, nitrogen, sulfur and other neutral and anionic donor ligands in an attempt to examine systematically the steric and electronic factors that influence the coupling of the heme chromophore to its protein environment. General trends for each ligand class are reported and discussed. Both the wavelengths and the intensities of the CD bands vary with ligand type and structure. All but one of the complexes exhibit negative CD maxima in their delta and Soret bands. Comparison to ferric myoglobin-thiolate complexes indicates that the negative sign observed for the cytochrome P-450 spectra is not a property of the thiolate fifth ligand, but rather arises from a different interaction of the cytochrome P-450 heme with its protein environment. Complexes with neutral oxygen donors display CD spectra that most closely resemble the spectrum of the native low-spin enzyme. Hyperporphyrin (split Soret) cytochrome P-450 complexes with thiolates, phosphines and cyanide trans to cysteinate have complex CD spectra, reflecting the intrinsic non-degeneracy of the Soret pi pi transitions. The extensive work presented herein provides an empirical foundation for use in analyzing the interaction of heme chromophores with their protein surroundings, not only for the cytochrome P-450 monooxygenases but also for heme proteins in general.

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.

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.

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.