Oxidized Horse Heart Cytochrome Research Articles

Near-exact enthalpy-entropy compensation governs the thermal unfolding of protonation states of oxidized cytochrome c.

This paper reports the first quantitative analysis of the thermal transitions of all protonation states of oxidized horse heart cytochrome c at low anion concentration. Changes of secondary and tertiary structure were probed by ultraviolet (UV) as well as visible circular dichroism and absorption spectroscopy, respectively. The temperature dependence of spectra were recorded at pH values assignable to a set of different protonation states which encompass the canonical Theorell-Åkesson states and the recently discovered III* state. Our experimental data suggest a two-step process of thermal unfolding for all protonation states. The respective thermodynamic parameters were obtained from a global analysis of the temperature dependence of corresponding visible circular dichroism (CD) and absorption spectra. The results of this analysis revealed a statistically significant enthalpy-entropy compensation with different apparent compensation temperatures for the two consecutive thermal transitions (319 and 357K). This reflects the narrow distribution of the respective folding temperatures. UVCD spectra suggest that even the thermal transitions of protonation states occupied at acidic and alkaline pH cause only a very modest unfolding of the protein's helical structure. Our data indicate the protonation-induced unfolding at room temperatures predominantly affects the Ω-loops of the protein. The two thermal transitions involve changes of two foldons, i.e. the unfolding of two short β-strand segments (associated with the yellow foldon) followed by the unfolding of the 60' helix (green foldon) that connects the two Ω-loops of the protein. Apparently, intra-backbone hydrogen bonding is strong enough to mostly protect the terminal N- and C-helices from unfolding even at rather extreme conditions.

Internal Electric Field in Cytochrome C Explored by Visible Electronic Circular Dichroism Spectroscopy.

Electronic circular dichroism (ECD) is a valuable tool to explore the secondary and tertiary structure of proteins. With respect to heme proteins, the corresponding visible ECD spectra, which probe the chirality of the heme environment, have been used to explore functionally relevant structural changes in the heme vicinity. While the physical basis of the obtained ECD signal has been analyzed by Woody and co-workers in terms of multiple electronic coupling mechanism between the electronic transitions of the heme chromophore and of the protein (Hsu, M.C.; Woody, R.W. J. Am. Chem. Soc. 1971, 93, 3515), a theory for a detailed quantitative analysis of ECD profiles has only recently been developed (Schweitzer-Stenner, R.; Gorden, J. P.; Hagarman, A. J. Chem. Phys. 2007, 127, 135103). In the present study this theory is applied to analyze the visible ECD-spectra of both oxidation states of three cytochromes c from horse, cow and yeast. The results reveal that both B- and Q-bands are subject to band splitting, which is caused by a combination of electronic and vibronic perturbations. The B-band splittings are substantially larger than the corresponding Q-band splittings in both oxidation states. For the B-bands, the electronic contribution to the band splitting can be assigned to the internal electric field in the heme pocket, whereas the corresponding Q-band splitting is likely to reflect its gradient (Manas, E. S.; Vanderkooi, J. M.; Sharp, K. A. J. Phys. Chem. B 1999, 103, 6344). We found that the electronic and vibronic splitting is substantially larger in the oxidized than in the reduced state. Moreover, these states exhibit different signs of electronic splitting. These findings suggest that the oxidation process increases the internal electric field and changes its orientation with respect to the molecular coordinate system associated with the N-Fe-N lines of the heme group. For the reduced state, we used our data to calculate electric field strengths between 27 and 31 MV/cm for the investigated cytochrome c species. The field of the oxidized state is more difficult to estimate, owing to the lack of information about its orientation in the heme plane. Based on band splitting and the wavenumber of the band position we estimated a field-strength of ca. 40 MV/cm for oxidized horse heart cytochrome c. The thus derived difference between the field strengths of the oxidized and reduced state would contribute at least -55 kJ/mol to the enthalpic stabilization of the oxidized state. Our data indicate that the corresponding stabilization energy of yeast cytochrome c is smaller.

Effect of Axial Coordination on the Kinetics of Assembly and Folding of the Two Halves of Horse Heart Cytochrome c

The kinetics of the assembly of two complementary fragments of oxidized horse heart cytochrome c (cyt c), namely the heme-containing fragment-(1-56) and the fragment-(57-104), have been characterized at different pH values. At neutral pH the fragment-(1-56) is hexacoordinated and has two histidines axially ligated to the heme-Fe(III) (Santucci, R., Fiorucci, L., Sinibaldi, F., Polizio, F., Desideri, A., and Ascoli, F. (2000) Arch. Biochem. Biophys. 379, 331-336), thus mimicking what occurs in the folding intermediate of cyt c. The kinetics of the formation of the complex between the two fragments are characterized at pH 7.0 by a slow rate constant that is independent of the concentration of the reactants; conversely, at a low pH the kinetics are much faster and depend on the concentration of the fragments. This behavior suggests that the rate-limiting step observed in the recombination process of the fragments at neutral pH (that leads to the final coordination of Met-80) has to be ascribed to the detachment of the "misligated" histidine. Thus, the faster recombination rate at a low pH can be related to the fact that histidine is protonated and not able to coordinate to the metal. Furthermore, the independence of the rate constant on the concentration of the reactants observed at pH 7.0 can be accounted for by the occurrence of a conformational transition, which takes place immediately after the two fragments collapse together, likely simulating what induces the detachment of the misligated histidine during cytochrome folding.

Effects of extrinsic imidazole ligation on the molecular and electronic structure of cytochrome c

Although imidazole ligand binding to cytochrome c is not directly related to its physiological function, it has the potential to provide valuable information on the molecular and electronic structure of the protein. The solution structure of the imidazole adduct of oxidized horse heart cytochrome c (Im-cyt c) has been determined through 2D NMR spectroscopy. The Im-cyt c, 8 mM in 1.2 M imidazole solution at pH 5.7 and 313 K, provided altogether 2,542 NOEs (1,901 meaningful NOEs) and 194 pseudocontact shifts. The 35 conformers of the family show the RMSD values to the average structure of 0.063+/-0.007 nm for the backbone and 0.107+/-0.007 nm for all heavy atoms, respectively. The characterization of Im-cyt c is discussed in detail both in terms of structure and electronic properties. The replacement of the axial ligand Met80 with the exogenous imidazole ligand induces significant conformation changes in both backbone and side chains of the residues located in the distal axial ligand regions. The imidazole ligand binds essentially parallel to the imidazole of the proximal histidine, the two planes forming an angle of 8+/-7 degrees. The electron delocalization on the heme moiety and the magnetic susceptibility tensor are consistent with these structural features.

Protein hydration and location of water molecules in oxidized horse heart cytochrome c by (1)H NMR.

The hydration properties of the oxidized form of horse heart cytochrome c have been studied by (1)H NMR spectroscopy. Two-dimensional, homonuclear ePHOGSY-NOESY experiments are used to map water-protein interactions. The detected NOEs reveal interactions between nonexchangeable protein protons and both water protons and labile protein protons which exchange with water protons. Among the many water molecules apparent in the X-ray structure, three have been identified with a residence time longer than 300 ps. One of them is located inside the distal heme cavity, in the deepest part of a hydration pathway extending toward the surface. The identification of hydrophilic regions and detection of three long-lived water molecules settles some ambiguities and provides a better representation of the water-protein interactions in oxidized cytochrome c.

Solution structure of oxidized horse heart cytochrome c.

The solution structure of oxidized horse heart cytochrome c was obtained at pH 7.0 in 100 mM phosphate buffer from 2278 NOEs and 241 pseudocontact shift constraints. The final structure was refined through restrained energy minimization. A 35-member family, with RMSD values with respect to the average structure of 0.70 +/- 0.11 A and 1.21 +/- 0.14 A for the backbone and all heavy atoms, respectively, and with an average penalty function of 130 +/- 4.0 kJ/mol and 84 +/- 3.7 kJ/mol for NOE and pseudocontact shift constraints, respectively (corresponding to a target function of 0.9 A2 and 0.2 A2), was obtained. The solution structure is somewhat different from that recently reported (Qi et al., 1996) and appears to be similar to the X-ray structure of the same oxidation state (Bushnell et al., 1990). A noticeable difference is a rotation of 17 +/- 8 degrees of the imidazole plane between solid and solution structure. Detailed and accurate structural determinations are important within the frame of the current debate of the structural rearrangements occurring upon oxidation or reduction. From the obtained magnetic susceptibility tensor a separation of the hyperfine shifts into their contact and pseudocontact contributions is derived and compared to that of the analogous isoenzyme from S. cerevisiae and to previous results.

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

The 1.94A˚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 β-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.

A novel [formula omitted]-type terminal oxidase from [formula omitted] with cytochrome [formula omitted] oxidase activity

Cytochrome c oxidase was solubilized with a nonionic detergent n -decanoyl-N-methyl glucamide from the membranes of Sulfolobus acidocaldarius , a thermoacidophilic archaebacterium, and was purified. The enzyme oxidized horse heart cytochrome c with a Vmax of 63 μmol/min/mg at 50°C. The activity was sensitive to cyanide. The enzyme also catalyzed oxygen uptake dependent on N,N,N′,N′-tetramethyl p -phenylene diamine. An apparent molecular mass was estimated to be 150 kDa. The enzyme is composed of three subunits of 37, 23, and 14 kDa. Spectral characteristics were similar to typical bacterial aa 3 except for the presence of a novel 583 nm peak observed in reduced minus oxidized difference spectrum.

Influence of 8 alpha-imidazole substitution of the FMN cofactor on the rate of electron transfer from the neutral semiquinones of two flavodoxins to cytochrome c.

The effects of substituting an imidazole ring onto the 8 alpha-position of the FMN cofactor on the kinetics of electron transfer from the neutral semiquinone forms of Azotobacter and Clostridium flavodoxins to oxidized horse heart cytochrome c have been investigated by stopped-flow methods. Although 8 alpha-substitution does not alter the mechanistic pathway of the reaction, the rate constants are decreased by factors of 10-30, without significant changes in the equilibrium association constants of the intermediate electron-transfer complexes. Protonation of the imidazole ring further decreases the observed second-order rate constants for the electron-transfer reaction by factors of 20-50. The pKa values for the 8 alpha-imidazole ring in both flavodoxin semiquinones were determined to be approximately 7. In contrast, the reactions of the native flavodoxins with cytochrome c are pH independent. The results are consistent with a structural model of the intermediate complex [Simondsen, R. P., Weber, P. C., Salemme, F. R., & Tollin, G. (1982) Biochemistry 21, 6366-6375], which postulates a close fit between the exposed dimethylbenzene ring of the FMN and the heme edge within a nonpolar interface region. The results further indicate that electron transfer is uncoupled from proton transfer, that it is the rate-limiting step, and that it occurs prior to proton transfer at all pH values. Finally, the results do not provide support for a direct role of the imidazole ring in the facilitation of one-electron transfer in those enzymes containing 8 alpha-N-histidylflavin coenzymes.

Analysis of the ionization constants and heats of ionization of reduced and oxidized horse heart cytochrome c.

AbstractSimultaneous curve fitting for the ionization parameters of oxidized and reduced horse heart cytochrome c in 0.15M KCl and 20°C yields values for the ionization constants (as pK′) and the heats of ionization (ΔHi) which can reconstruct either the potentiometric or thermal titration curves. Reduced cytochrome c requires 8 sets of groups, whereas oxidized cytochrome c requires 10 sets of groups. The additional groups in the oxidized preparation appear to involve the ferriheme (pK′, 9.25; ΔHi, 13.7 kcal/mol) and a tyrosine (pK′ ≃ 10.24) that is not present in the reduced form. The potentiometric and thermal difference curves (reduced – oxidized) involve the appearance of 17 kcal/mol centered at pH 9.7 and 5.8 kcal/mol centered at pH 4.9. The carboxyl groups in both species appear to be normal for the hydrogen‐bonded form. Only one histidine has normal ionization properties (pK′, 6.7; ΔHi, 7.5 kcal/mol), as do 17 of the lysine residues (pK′, 10.8; ΔHi, 11.5 kcal/mol).

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.

An Evaluation of the Average Heats of Ionization of Reduced and Oxidized Horse Heart Cytochrome c

Abstract Evaluation of the average heats of ionization ΔHi.) for oxidized and reduced horse heart cytochrome c reveals that the heats of ionization for both redox species as a function of pH are identical within the precision of the method. Since this result is obtained in spite of the differences in the numbers of groups titrated in the two forms of the protein, the redox forms must have the same heats of ionization per group titrated. When the heats of ionization are plotted as a function of the groups titrated, the differences are more clearly seen. For proteins with one or two imidazoyl ionizations between many carboxyl and ∊-amino ionizations, there is no clearly indicated plateau and the heats of ionization of the imidazole groups of histidines cannot be obtained by this procedure. The analysis is, however, useful for eliminating heats of ionization which are abnormal since the shape of the calculated curves are at variance with the experimental data.