The structural and functional role of lysine residues in the binding domain of cytochrome c in the electron transfer to cytochrome c oxidase

Electron-transfer mechanism of the triplet state quenching of aluminium tetrasulfonated phthalocyanine by cytochrome c

The mechanism of electron-transfer from aluminium tetrasulfonated phthalocyanine triplet state to cytochrome c was investigated in this work. This reaction successfully quenches the dye triplet state due to the formation of complexes between the solute and the protein at the active site. The electron-transfer rate constant is around 3x10(7) s(-1), and is in accordance with previous results for the singlet excited state quenching [C.A.T. Laia, S.M.B. Costa, D. Phillips, A. Beeby. Electron-transfer kinetics in sulfonated aluminum phthalocyanines/cytochrome c complexes, J. Phys. Chem. B 108 (2004) 7506-7514.] in the framework of the Marcus theory, with a reorganization energy equal to 0.94 eV. The complex formation is diffusion controlled, but heterogeneities of the protein surface charge distribution lead to quenching rate constants smaller than predicted on a hard-spheres model with electrostatic interactions. Also the binding equilibrium constant is strongly affected by this phenomenon. Ionic strength plays an important role on the complex formation, but its effect on the unimolecular electron-transfer rate constant is negligible within experimental error.

Tuning the Rate and pH Accessibility of a Conformational Electron Transfer Gate

Methods to fine-tune the rate of a fast conformational electron transfer (ET) gate involving a His-heme alkaline conformer of iso-1-cytochrome c (iso-1-Cytc) and to adjust the pH accessibility of a slow ET gate involving a Lys-heme alkaline conformer are described. Fine-tuning the fast ET gate employs a strategy of making surface mutations in a substructure unfolded in the alkaline conformer. To make the slow ET gate accessible at neutral pH, the strategy involves mutations at buried sequence positions which are expected to more strongly perturb the stability of native versus alkaline iso-1-Cytc. To fine-tune the rate of the fast His 73-heme ET gate, we mutate the surface-exposed Lys 79 to Ala (A79H73 variant). This mutation also simplifies ET gating by removing Lys 79, which can serve as a ligand in the alkaline conformer of iso-1-Cytc. To adjust the pH accessibility of the slow Lys 73-heme ET gate, we convert the buried side chain Asn 52 to Gly and also mutate Lys 79 to Ala to simplify ET gating (A79G52 variant). ET kinetics is studied as a function of pH using hexaammineruthenium(II) chloride (a6Ru2+) to reduce the variants. Both variants show fast direct ET reactions dependent on [a6Ru2+] and slower gated ET reactions that are independent of [a6Ru2+]. The observed gated ET rates correlate well with rates for the alkaline-to-native state conformational change measured independently. Together with the previously reported H73 variant (Baddam, S.; Bowler, B. E. J. Am. Chem. Soc. 2005, 127, 9702-9703), the A79H73 variant allows His 73-heme-mediated ET gating to be fine-tuned from 75 to 200 ms. The slower Lys 73-heme (15-20 s time scale) ET gate for the A79G52 variant is now accessible over the pH range 6-8.

Mutation of asparagine 52 to glycine promotes the alkaline form of iso-1-cytochrome c and causes loss of cooperativity in acid unfolding

The kinetics and thermodynamics of the alkaline and acid conformational transitions of a Lys 79 --> Ala/Asn 52 --> Gly (A79G52) variant of iso-1-cytochrome c are studied. The Lys 79 --> Ala mutation is designed to limit heme ligation in the alkaline conformer to Lys 73. The Asn 52 --> Gly mutation is intended to shift the population of the alkaline conformer to physiological pH based on the hierarchical nature of the cooperative substructures of this protein. The midpoint pH for formation of the alkaline conformer is approximately 7.45. The kinetics for the alkaline conformational transition of the A79G52 variant are consistent with the ionization constant, pK(H), for the trigger group controlling formation of the alkaline conformer being approximately 9.5. This pK(H) is low for alkaline conformers involving lysine-heme ligation but is consistent with the pK(a) of the highest of three ionizable groups which modulate formation of the histidine-heme alkaline conformer of a His 73 variant of iso-1-cytochrome c [Martinez, R. E., and Bowler, B. E. (2004) J. Am. Chem. Soc. 126, 6751-6758]. The acid transition of the A79G52 variant is split into two phases. Both the Lys 79 --> Ala and Asn 52 --> Gly mutations are expected to affect the buried hydrogen bond network of cytochrome c, suggesting that this network is an important modulator of the acid unfolding of cytochrome c.

Reversibility of Structural Transition of Cytochrome c on Interacting with and Releasing from Alternating Copolymers of Maleic Acid and Alkene

The interaction of cytochrome c (cyt c) with poly(isobutylene-alt-maleic acid) (PIMA) and poly(1-tetradecene-alt-maleic acid) (PTMA) was studied using circular dichroism, absorption spectroscopy, and atomic force microscopy to investigate the electrostatic and hydrophobic influence of the copolymers on the structure of cyt c. At pH 7.4, the interaction of PIMA with cyt c can only partly disturb the integrity of the heme pocket, while PTMA has very intensive influence on the structure of cyt c. After adding 0.15 M NaCl, PIMA-cyt c complexes dissociate, and the released cyt c recovers its native structure, whereas NaCl has no significant influence on PTMA-cyt c complexes. GuHCl (0.5 M) destroys PTMA-cyt c complexes, forming GuHCl-PTMA precipitates; the cyt c released from the complexes regenerates its native structure. In comparison with electrostatic interaction, hydrophobic interaction leads to more stable polymer-cyt c complexes and more intensive influence on cyt c structure, but cyt c can recover its native state after release.

Redox Processes of Cytochrome c Immobilized on Solid Supported Polyelectrolyte Multilayers

The heme protein cytochrome c (Cyt-c), immobilized on polyelectrolyte multilayers on a silver electrode, was studied by stationary and time-resolved surface-enhanced resonance Raman (SERR) spectroscopy to probe the redox site structure and the mechanism and dynamics of the potential-dependent interfacial processes. The layers were built up by sequential adsorption of polycations (poly[ethylene imine] (PEI); polyallylamine hydrochloride (PAH)) and polyanions (poly[styrene sulfonate] (PSS)). All multilayers terminated by PSS electrostatically bind Cyt-c. On PEI/PSS coatings, Cyt-c is peripherally bound and fully redox-active. Due to the interfacial potential drop, the apparent redox potential is lowered by 40 mV compared to that in solution. The rate constant for the heterogeneous electron transfer (ET) of ca. 0.1 s(-1) is consistent with electron tunneling through largely ordered PEI/PSS layers. ET is coupled to a reversible conformational transition of Cyt-c that involves a change of the coordination pattern of the heme. Additional (PAH/PSS) double layers cause a broadening of the redox transition and a drastic negative shift of the redox potential, which is attributed to the formation of PSS/Cyt-c complexes. It is concluded that Cyt-c can effectively compete with PAH for binding of PSS, resulting in a rearrangement of the layered structure and a penetration of the PSS-bound Cyt-c into the PAH/PSS double layers. This conclusion is consistent with SERR intensity and quartz microbalance measurements. ET was found to be overpotential-independent and faster than that for PEI/PSS coatings, which is interpreted in terms of specific PSS/Cyt-c complexes serving as gates for the heterogeneous ET.

Conformationally gated electron transfer in iso-1-cytochrome c: engineering the rate of a conformational switch

An engineered form of iso-1-cytochrome c with lysine 73 mutated to histidine is shown to increase by nearly 500-fold the rate of a conformational gate that modulates the rate of electron transfer into this protein. This result demonstrates the potential of protein engineering to provide electron transfer gates with tailored properties. The pH dependence of the rate of the conformational electron transfer gate correlates well with the pH dependence of the conformational change from a His 73-ligated heme to a Met 80-ligated heme, determined independently by pH jump methods, allowing unambiguous assignment of the conformational electron transfer gating step. The rate of the electron transfer gate is also modulated by a cis to trans proline isomerization, indicating that both amino acid sequence and the nature of the heme ligand provide avenues for rational design of electron transfer gates which open at different rates.

EPR and optical spectroscopic studies of Met80X mutants of yeast ferricytochrome c. Models for intermediates in the alkaline transition

The ferric forms of Met80X mutants of yeast iso-1-cytochrome c (X = Ala, Ser, Asp, and Glu) display EPR and optical spectra that are strongly pH dependent. At low pH values (pH approximately 5) the sixth coordination sites are filled by H(2)O that, on elevating the pH, is replaced by OH(-) in the cases of Met80Ala and -Ser (pK approximately 5.6 and 5.9, respectively) and by a lysine amino group in the cases of Met80Asp and -Glu (pK approximately 9.3 and 11.6, respectively). The ligand sets and the pK values of the transitions are rationalized in terms of the structure of the heme pocket, and a possible mechanism of the "trigger" in the alkaline transition of the native protein is suggested.

ATP specifically drives refolding of non-native conformations of cytochrome c

An increasing body of evidence ascribes to misfolded forms of cytochrome c (cyt c) a role in pathophysiological events such as apoptosis and disease. Here, we examine the conformational changes induced by lipid binding to horse heart cyt c at pH 7 and study the ability of ATP (and other nucleotides) to refold several forms of unfolded cyt c such as oleic acid-bound cyt c, nicked cyt c, and acid denatured cyt c. The CD and fluorescence spectra demonstrate that cyt c unfolded by oleic acid has an intact secondary structure, and a disrupted tertiary structure and heme environment. Furthermore, evidence from the Soret CD, electronic absorption, and resonance Raman spectra indicates the presence of an equilibrium of at least two low-spin species having distinct heme-iron(III) coordination. As a whole, the data indicate that binding of cyt c to oleic acid leads to a partially unfolded conformation of the protein, resembling that typical of the molten globule state. Interestingly, the native conformation is almost fully recovered in the presence of ATP or dATP, while other nucleotides, such as GTP, are ineffective. Molecular modeling of ATP binding to cyt c and mutagenesis experiments show the interactions of phosphate groups with Lys88 and Arg91, with adenosine ring interaction with Glu62 explaining the unfavorable binding of GTP. The finding that ATP and dATP are unique among the nucleotides in being able to turn non-native states of cyt c back to native conformation is discussed in the light of cyt c involvement in cell apoptosis.

Effect of mono-CDNP substitution of lysine residues on the redox reaction of cytochrome c electrostatically adsorbed on a mercaptoheptanoic acid modified Au(111) surface

The effect of charge-inverting modification of single surface lysine residue on the electron transfer (ET) reaction of horse heart cytochrome c (cyt c) is examined for 12 different types of mono-4-chloro-2,5-dinitrobenzoic acid substituted cyt c (mCDNPc) adsorbed on a Au(111) electrode modified with a self-assembled monolayer (SAM) of 7-mercapto-heptanoic acid (MHA). A negative shift in the redox potential by 10-35 mV as compared to that of native cyt c and a monolayer coverage in the range of 13-17 pmol cm(-2) are observed for electroactive mCDNPc's. The magnitude of the decrease in the ET rate constant (k(et)) of mCDNPc's compared with that of native cyt c depends on the position of the CDNP substitution. For mCDNPc's in which the modified lysine residue is outside of the interaction domain of cyt c with the SAM, the ratio of the k(et) of mCDNPc to that of native cyt c is correlated to the change in the dipole moment vector of cyt c due to the CDNP modification. This correlation suggests that the dipole moment of cyt c determines its orientation of adsorption on the SAM of MHA and significantly affects the rate of the ET. The CDNP modification of lysine residues at the interaction domain significantly decreases the rate, demonstrating the importance of the local charge environment in determining the rate of ET.

Investigating the Cause of the Alkaline Transition of Phytocyanins

The phytocyanins are a family of plant cupredoxins that have been subdivided into the stellacyanins, plantacyanins, and uclacyanins. All of these proteins possess the typical type 1 His(2)Cys equatorial ligand set at their mononuclear copper sites, but the stellacyanins have an axial Gln ligand in place of the weakly coordinated Met of the plantacyanins, uclacyanins, and most other cupredoxins. The stellacyanins exhibit altered visible, EPR, and paramagnetic (1)H NMR spectra at elevated pH values and also modified reduction potentials. This alkaline transition occurs with a pK(a) of approximately 10 [Dennison, C., Lawler, A. T. (2001) Biochemistry 40, 3158-3166]. In this study we demonstrate that the alkaline transition has a similar influence on the visible, EPR, and paramagnetic NMR spectra of cucumber basic protein (CBP), which is a plantacyanin. The mutation of the axial Gln95 ligand into a Met in umecyanin (UMC), the stellacyanin from horseradish roots, and the axial Met89 into a Gln in CBP have very limited, yet similar, influence on the pK(a) for the alkaline transition as judged from alterations in visible spectra. The complete removal of the axial ligand in the Met89Val variant of CBP results in a slightly larger decrease in the pK(a) for this effect, but similar spectral alterations are still observed at elevated pH. Thus, the axial Gln ligand is not the cause of the alkaline transition in Cu(II) stellacyanins, and alterations in the active site structures of the phytocyanins have a limited effect on this feature. The conserved Lys residue found adjacent to the axial ligand in the sequences of all phytocyanins, and implicated as the trigger for the alkaline transition, has been mutated to an Arg in UMC. The influence of increasing pH on the spectroscopic properties of Lys96Arg UMC is almost identical to those of the wild type protein, and thus, this residue is not responsible for the alkaline transition. However, a positively charged residue in this position seems to be important for the correct folding of UMC. Other possible triggers for the effects seen in the phytocyanins at elevated pH are discussed along with the relevance of the alkaline transition.

Redox and redox-coupled processes of heme proteins and enzymes at electrochemical interfaces

Modern bioelectrochemical methods rely upon the immobilisation of redox proteins and enzymes on electrodes coated with biocompatible materials to prevent denaturation. However, even when protein denaturation is effectively avoided, heterogeneous protein electron transfer is often coupled to non-Faradaic processes like reorientation, conformational transitions or acid-base equilibria. Disentangling these processes requires methods capable of probing simultaneously the structure and reaction dynamics of the adsorbed species. Here we provide an overview of the recent developments in Raman and infrared surface-enhanced spectroelectrochemical techniques applied to the study of soluble and membrane bound redox heme proteins and enzymes. Possible biological implications of the findings are critically discussed.

Involvement of protein radical, protein aggregation, and effects on NO metabolism in the hypochlorite-mediated oxidation of mitochondrial cytochrome c

Cytochrome c (cyt c)-derived protein radicals, radical adduct aggregates, and protein tyrosine nitration have been implicated in the pro-apoptotic event connecting inflammation to the development of diseases. During inflammation, one of the reactive oxygen species metabolized via neutrophil activation is hypochlorite (HOCl); destruction of the mitochondrial electron transport chain by hypochlorite is considered to be a damaging factor. Previous study has shown that HOCl induces the site-specific oxidation of cyt c at met-80. In this work, we have assessed the hypothesis that exposure of cyt c to physiologically relevant concentrations of HOCl leads to protein-derived radical and consequent protein aggregation, which subsequently affects cyt c's regulation of nitric oxide metabolism. Reaction intermediates, chemical pathways available for protein aggregation, and protein nitration were examined. A weak ESR signal for immobilized nitroxide derived from the protein was detected when a high concentration of cyt c was reacted with hypochlorite in the presence of the nitroso spin trap 2-methyl-2-nitrosopropane. When a low concentration of cyt c was exposed to the physiologically relevant levels of HOCl in the presence of 5,5-dimethyl-pyrroline N-oxide (DMPO), we detected DMPO nitrone adducts derived from both protein and protein aggregate radicals as assessed by Western blot using an antibody raised against the DMPO nitrone adduct. The cyt c-derived protein radicals formed by HOCl were located on lysine and tyrosine residues, with lysine predominating. Cyt c-derived protein aggregates induced by HOCl involved primarily lysine residues and hydrophobic interaction. In addition, HOCl-oxidized cyt c (HOCl-cyt c) exhibited a higher affinity for NO and enhancement of nonenzymatic NO synthesis from nitrite reduction. Furthermore, HOCl-mediated cyt c oxidation also resulted in a significant elevation of cyt c nitration derived from either NO trapping of the cyt c-derived tyrosyl radical or cyt c-catalyzed one-electron oxidation of nitrite.

Proton-mediated dynamics of the alkaline conformational transition of yeast iso-1-cytochrome c

The kinetics of the alkaline conformational transition of a Lys 73-->His variant of iso-1-cytochrome c have been investigated using pH jump stopped-flow methods to probe the nature of the ionizable "trigger" group for this conformational change. This mutation moves the pK(a) of the ligand replacing Met 80 from about 10.5 to approximately 6.6 and has unmasked two other ionizable groups, besides the ligand replacing Met 80, that modulate the kinetics of this process. The results are discussed in terms of the impact of ionization equilibria on protein folding mechanisms.

Electron-transfer processes of cytochrome C at interfaces. New insights by surface-enhanced resonance Raman spectroscopy

The heme protein cytochrome c acts as an electron carrier at the mitochondrial-membrane interface and thus exerts its function under the influence of strong electric fields. To assess possible consequences of electric fields on the redox processes of cytochrome c, the protein can be immobilized to self-assembled monolayers on electrodes and studied by surface-enhanced resonance Raman spectroscopy. Such model systems may mimic some essential features of biological interfaces including local electric field strengths. It is shown that physiologically relevant electric field strengths can effectively modulate the electron-transfer dynamics and induce conformational transitions.

Direct monitoring of the electron pool effect of cytochrome c3 by highly sensitive EQCM measurements

Cytochrome c(3) from Desulfovibrio vulgaris has four hemes per molecule, and a redox change at the hemes alters the conformation of the protein, leading to a redox-dependent change in the interaction of cytochrome c(3) with redox partners (an electron acceptor or an electron donor). The redox-dependent change in this interaction was directly monitored by the high-performance electrochemical quartz crystal microbalance (EQCM) technique that has been improved to give high sensitivity in solution. In this method, cytochrome c(3) molecules in solution associate electrostatically with a viologen-immobilized quartz crystal electrode as a monolayer, and redox of the associating cytochrome c(3) is controlled by the immobilized viologen. This technique makes it possible to measure the access of cytochrome c(3) to the electrode or repulsion from the electrode, and hence interconversion between an electrostatic complex and an electron transfer complex on the cytochrome c(3) and the viologen as a mass change accompanying a potential sweep is monitored. In addition, simultaneous measurement of a mass change and a potential step reveals that the cytochrome c(3) stores electrons when the four hemes are reduced (an electron pool effect), that is, the oxidized cytochrome c(3) facilitates acceptance of electrons from the immobilized viologen molecule, but the reduced cytochrome c(3) donates the accepted electrons to the viologen with difficulty.

Direct Immobilization of Native Yeast Iso-1 Cytochrome c on Bare Gold: Fast Electron Relay to Redox Enzymes and Zeptomole Protein-Film Voltammetry

Cyclic voltammetry shows that yeast iso-1-cytochrome c (YCC), chemisorbed on a bare gold electrode via Cys102, exhibits fast, reversible interfacial electron transfer (k(0) = 1.8 x 10(3) s(-1)) and retains its native functionality. Vectorially immobilized YCC relays electrons to yeast cytochrome c peroxidase, and to both cytochrome cd(1) nitrite reductase (NIR) and nitric oxide reductase from Paracoccus denitrificans, thereby revealing the mechanistic properties of these enzymes. On a microelectrode, we measured nitrite turnover by approximately 80 zmol (49 000 molecules) of NIR, coadsorbed on 0.65 amol (390 000 molecules) of YCC.

Interaction of cytochrome c with cytochrome oxidase: two different docking scenarios

Cytochrome c is the specific and efficient electron transfer mediator between the two last redox complexes of the mitochondrial respiratory chain. Its interaction with both partner proteins, namely cytochrome c(1) (of complex III) and the hydrophilic Cu(A) domain (of subunit II of oxidase), is transient, and known to be guided mainly by electrostatic interactions, with a set of acidic residues on the presumed docking site on the Cu(A) domain surface and a complementary region of opposite charges exposed on cytochrome c. Information from recent structure determinations of oxidases from both mitochondria and bacteria, site-directed mutagenesis approaches, kinetic data obtained from the analysis of isolated soluble modules of interacting redox partners, and computational approaches have yielded new insights into the docking and electron transfer mechanisms. Here, we summarize and discuss recent results obtained from bacterial cytochrome c oxidases from both Paracoccus denitrificans, in which the primary electrostatic encounter most closely matches the mitochondrial situation, and the Thermus thermophilus ba(3) oxidase in which docking and electron transfer is predominantly based on hydrophobic interactions.

Cytochrome c and SDS: a molten globule protein with altered axial ligation

Saccharomices cerevisiae (yeast iso-1) cytochrome c has been investigated in the presence of 100 mM SDS in order to simulate the interaction of cytochrome c with membrane. Under these circumstances, a high spin species with detached methionine axial ligand is observed through NMR, in analogy to findings on the horse heart protein. However, at variance with the latter system, for the yeast protein also a low spin species is detected, which appears to be present with a concentration of about 40% with respect to that of the high spin species. The R(1), R(2), [1H]-15N NOE of backbone amides which are not affected by paramagnetism are homogeneous and allow a simultaneous analysis of the data for the two species. The result is that the rotational correlation time is larger than in water and larger than expected on the basis of viscosity of the SDS-containing solution. This finding suggests interactions of cytochrome c with SDS. Furthermore, it appears that there is subnanosecond backbone mobility, which also accounts for the decreased intensity of NOE cross-peaks and may be associated with equilibria between helical and random coil structure. The dynamic behavior appears to be a common feature of the high spin and low spin species and is consistent with the presence of a molten globule state. The molten globule nature of the protein could account for the presence of the different axial coordination of the heme iron. Such findings are meaningful with respect to the physiology of cytochrome c as electron transfer protein and as promoter of apoptosis.

Conformational equilibria and dynamics of cytochrome c induced by binding of sodium dodecyl sulfate monomers and micelles

Circular dichroism, nuclear magnetic resonance, electron paramagnetic resonance, UV-vis absorption, and resonance Raman (RR) spectroscopic techniques were employed to study protein and heme structural changes of cytochrome c (Cyt-c) induced by sodium dodecyl sulfate (SDS) monomers and micelles via hydrophobic and electrostatic interactions, respectively. Both modes of interactions cause the transition to the conformational state B2, which is implicated to be involved in the physiological processes of Cyt-c. At sub-micellar concentrations of SDS, specific binding of only ca. three SDS monomers, which is likely to occur at the hydrophobic peptide segment 81-85, is sufficient for a complete conversion to a B2 state in which Met80 is replaced by His33 (His26). These heme pocket structural changes are not linked to secondary structure changes of the protein brought about by nonspecific binding of SDS monomers in different regions of the protein. Upon binding of micelles, B2 high-spin species can also be stabilized by electrostatic interactions. In addition, the micelle interaction domain is located on the front surface of Cyt-c, which includes a ring-like arrangement of lysine residues appropriate for binding one micelle. According to freeze-quench RR and stopped-flow experiments, state B2 is formed on the long millisecond timescale and reveals a complex dependence on the SDS concentration that can be interpreted in terms of competitive binding of monomers and micelles.

Redox and conformational equilibria and dynamics of cytochrome c at high electric fields

Cytochrome c (Cyt-c) adsorbed in the electrical double layer of the Ag electrode/electrolyte interface has been studied by stationary and time-resolved surface-enhanced resonance Raman spectroscopy to analyse the effect of strong electric fields on structure and reaction equilibria and dynamics of the protein. In the potential range between +0.1 and -0.55 V (versus saturated calomel electrode), the adsorbed Cyt-c forms a potential-dependent reversible equilibrium between the native state B1 and a conformational state B2. The redox potentials of the bis-histidine-coordinated six-coordinated low-spin and five-coordinated high-spin substates of B2 were determined to be -0.425 and -0.385 V, respectively, whereas the additional six-coordinated aquo-histidine-coordinated high-spin substate was found to be redox-inactive. The redox potential for the conformational state B1 was found to be the same as in solution in agreement with the structural identity of the adsorbed B1 and the native Cyt-c. For all three redox-active species, the formal heterogeneous electron transfer rate constants are small and of the same order of magnitude (3-13 s-1), which implies that the rate-limiting step is largely independent of the redox-site structure. These findings, as well as the slow and potential-dependent transitions between the various conformational (sub-)states, can be rationalized in terms of an electric field-induced increase of the activation energy for proton-transfer steps linked to protein structural reorganisation. Further increasing the electric field strength by shifting the electrode potential above +0.1 V leads to irreversible structural changes that are attributed to an unfolding of the polypeptide chain.

NMR investigation of the alkaline-like conformational transition of horse heart cytochrome c in the presence of exogenous thiazole

The conformational transition of horse heart cyt c in the presence of exogenous thiazole is investigated by NMR spectroscopy. Surprisingly, besides the native form and the ligand-bound form, another species (species A) exists at neutral pH. Titration of thiazole at alkaline condition indicates that this form has Lys as the axial ligands and in fact is one of alkaline cyt c conformers. At a high concentration of thiazole, species A has a dominant population at a pH of approximately 7. It is the first time that a pure alkaline conformer of cyt c is obtained at neutral pH. The observed NOEs show that species A maintains the overall protein fold although large structural rearrangements are expected in the distal pocket. Furthermore, the different effect of imidazole, pyridine and thiazole on the alkaline transformation of cyt c is discussed.

Resonance Raman investigations of cytochrome c conformational change upon interaction with the membranes of intact and Ca2+-exposed mitochondria

The conformational states of cytochrome c inside intact and Ca(2+)-exposed mitochondria have been investigated using resonance Raman spectroscopy. Intact and swelling bovine heart and rat liver mitochondria were examined with an excitation wavelength (413.1 nm) in resonance with the Soret transition of ferrous cytochrome c. The different b- to c-type cytochrome concentration ratio in mitochondria from two different tissues was used to help assign the Raman spectral components. Resonance Raman spectra were also recorded for mitochondria fractions (supernatants and pellets) obtained from swollen (Ca(2+)-exposed) mitochondria after differential centrifugation. The results illustrate that cytochrome c has an altered vibrational spectrum in solution, in intact, and in swollen mitochondria. When cytochrome c is released from mitochondria, its Raman spectrum becomes identical to that of ferrous cytochrome c in solution. The spectra of mitochondrial pellets indicate that a small amount of structurally modified cytochrome c remains associated with the heavy membrane fraction. Indeed, spectroscopic shifts in the low-frequency fingerprint and the high-frequency marker-band regions suggest that membrane binding leads to a partial opening of the heme pocket and an alteration of the heme thioether bonds. The results support the conclusion that most cytochrome c molecules in mitochondria are membrane-bound and that the cytochrome c structure changes upon binding. Furthermore, changes in the resonance Raman active mode located at 675 cm(-)(1) in the spectra of intact, swollen, and fractionated mitochondria indicate that b-type cytochromes may also undergo structural alterations during mitochondrial swelling and disruption.

Structural model for an alkaline form of ferricytochrome C

An (15)N-enriched sample of the yeast iso-1-ferricytochrome c triple variant (Lys72Ala/Lys79Ala/Cys102Thr) in an alkaline conformation was examined by NMR spectroscopy. The mutations were planned to produce a cytochrome c with a single conformer. Despite suboptimal conditions for the collection of spectra (i.e., pH approximately equal to 11), NMR remains a suitable investigation technique capable of taking advantage of paramagnetism. 76% of amino acids and 49% of protons were assigned successfully. The assignment was in part achieved through standard methods, in part through the identification of groups maintaining the same conformation as in the native protein at pH 7 and, for a few other residues, through a tentative analysis of internuclear distance predictions. Lys73 was assigned as the axial ligand together with His18. In this manner, 838 meaningful NOEs for 108 amino acids, 50 backbone angle constraints, and 203 pseudocontact shifts permitted the convergence of randomly generated structures to a family of conformers with a backbone RMSD of 1.5 +/- 0.2 A. Most of the native cytochrome c conformation is maintained at high pH. The NOE pattern that involves His18 clearly indicates that the proximal side of the protein, including the 20s and 40s loops, remains essentially intact. Structural differences are concentrated in the 70-80 loop, because of the replacement of Met80 by Lys73 as an axial ligand, and in the 50s helix facing that loop; as a consequence, there is increased exposure of the heme group to solvent. Based on several spectral features, we conclude that the folded polypeptide is highly fluxional.

Probing electrostatic interactions in cytochrome c using site-directed chemical modification

This communication reports the generation of an electrostatic probe using chemical modification of methionine side chains. The alkylation of methionine by iodoacetamide was achieved in a set of Saccharomyces cerevisiae iso-1-cytochrome c mutants, introducing the nontitratable, nondelocalized positive charge of a carboxyamidomethylmethionine sulfonium (CAMMS) ion at five surface and one buried site in the protein. Changes in redox potential and its variation with temperature were used to calculate microscopic effective dielectric constants operating between the probe and the heme iron. Dielectric constants (epsilon) derived from deltadeltaG values were not useful due to entropic effects, but epsilon(deltadeltaH) gave results that supported the theory. The effect on biological activity of surface derivatization was interpreted in terms of protein-protein interactions. The introduction of an electrostatic probe in cytochrome c often resulted in marked effects on activity with one of two physiological partners: cytochrome c reductase, especially if introduced at position 65, and cytochrome c oxidase, if at position 28.

Specificity of the interaction between the Paracoccus denitrificans oxidase and its substrate cytochrome c: comparing the mitochondrial to the homologous bacterial cytochrome c(552), and its truncated and site-directed mutants

Under in vitro conditions, bacterial cytochrome c oxidases may accept several nonhomologous c-type electron donors, including the evolutionarily related mitochondrial cytochrome c. Several lines of evidence suggest that in intact membranes the heme aa(3) oxidase from Paracoccus denitrificans receives its electrons from the membrane-bound cytochrome c(552). Both the structures of the oxidase and of a heterologously expressed, soluble fragment of the c(552) have been determined recently, but no direct structural information about a static cocomplex is available. Here, we analyze the kinetic properties of the isolated oxidase with the full-size c(552), with two truncated soluble forms, and with a set of site-specific mutants within the presumed docking site of the cytochrome, all heterologously expressed in Escherichia coli. Our data indicate that all three forms, the wild type and both truncations, are fully competent kinetically and exhibit biphasic kinetic behavior, however, under widely different ionic strength conditions. When mutations in lysine residues clustered around the interaction domain were introduced into the smallest fragment of c(552), both kinetic parameters, K(M) and k(cat), were drastically influenced. On the other hand, when the nonmutated truncated form was used to donate electrons to a set of oxidase mutants with replacements clustered along the docking site on subunit II, we observe distinct differences when comparing the kinetic properties of the widely used horse heart cytochrome c with those of the bacterial c(552). We conclude that the specific docking sites for the two types of cytochromes differ to some extent.

Cytochrome c/cytochrome c oxidase interaction. Direct structural evidence for conformational changes during enzyme turnover

We investigated the interaction between cytochrome c oxidase and its substrate cytochrome c by catalyzing the covalent linkage of the two proteins to yield 1 : 1 covalent enzyme-substrate complexes under conditions of low ionic strength. In addition to the 'traditional' oxidized complex formed between oxidized cytochrome c and the oxidized enzyme we prepared complexes under steady-state reducing conditions. Whereas for the 'oxidized' complex cytochrome c became bound exclusively to subunit II of the enzyme, for the 'steady-state' complex cytochrome c became bound to subunit II and two low molecular mass subunits, most likely VIb and IV. For both complexes we investigated: (a) the ability of the covalently bound cytochrome c to relay electrons into the enzyme, and (b) the ability of the covalently bound enzyme to catalyze the oxidation of unbound (exogenous) ferrocytochrome c. Steady-state spectral analysis (400-630 nm) combined with stopped-flow studies, confirmed that the bound cytochrome c mediated the efficient transfer of electrons from the reducing agent ascorbate to the enzyme. In the case of the latter, the half life for the ascorbate reduction of the bound cytochrome c and that for the subsequent transfer of electrons to haem a were both < 5 ms. In contrast the covalent complexes, when reduced, were found to be totally unreactive towards oxidized cytochrome c oxidase confirming that the previously observed reduction of haem a within the complexes occurred via intramolecular rather than intermolecular electron transfer. Additionally, stopped-flow analysis at 550 nm showed that haem a within both covalent complexes catalyzed the oxidation of exogenous ferrocytochrome c: The second order rate constant for the traditional complex was 0.55x10(6) m(-1) x s(-1) while that for the steady-state was 0.27x10(6) m(-1) x s(-1). These values were approximately 25-50% of those observed for 1 : 1 electrostatic complexes of similar concentrations. These results combined with those of the ascorbate and the electrophoresis studies suggest that electrons are able to enter cytochrome c oxidase via two independent pathways. We propose that during enzyme turnover the enzyme cycles between two conformers, one with a substrate binding site at subunit II and the other along the interface of subunits II, IV and VIb. Structural analysis suggests that Glu112, Glu113, Glu114 and Asp125 of subunit IV and Glu40, Glu54, Glu78, Asp35, Asp49, Asp73 and Asp74 of subunit VIb are residues that might possibly be involved.

Vibrational spectroscopy as a tool for probing protein function

Vibrational spectroscopy has become increasingly important as a tool for understanding the mechanisms of photosystem II, phytochrome and terminal oxidases. More general enzymatic or receptor systems have been studied, opening a new field of applications. Femtosecond infrared pump/probe studies of the important amide-I band seem to provide a basis for its molecular and structural interpretation.

Structural changes in cytochrome c oxidase induced by cytochrome c binding. A resonance raman study

Electrostatically stabilized complexes of fully oxidized cytochrome c oxidase from Paracoccus denitrificans and horse heart cytochrome c were studied by resonance Raman spectroscopy. The experiments were carried out with the wild-type oxidase and a variant in which a negatively charged amino acid in the binding domain (D257) is replaced by an asparagine. It is shown that cytochrome c induces structural changes at heme a and heme a(3) which are reminiscent to those found in mammalian cytochrome c oxidase-cytochrome c complex. The spectral changes are attributed to subtle changes in the heme-protein interactions implying that there is a structural communication from the binding domain even to the remote catalytic center. Only for the heme a modes minor spectral differences were found in the response of the wild-type and the D257N variant oxidase upon cytochrome c binding indicating that electrostatic interactions of aspartate 257 are not crucial for the perturbation of the catalytic site structure in the complex. On the other hand, in none of the complexes, structural changes were detected in the bound cytochrome c. These findings are in contrast to previous results obtained with beef heart cytochrome c oxidase which triggers the formation of a new conformational state of cytochrome c assumed to be involved in the biological electron transfer process.

The active site structure of ba3 oxidase from Thermus thermophilus studied by resonance raman spectroscopy

The ba3 cytochrome oxidase from Thermus thermophilus was studied by resonance Raman spectroscopy. The component spectra of both heme groups were determined by using different excitation wavelengths. In the ferric state the heme a3 group reveals resonance Raman marker bands characteristic for two high spin species with the heme iron in an in-plane and an out-of-plane configuration that reflects a coordination equilibrium. This equilibrium obviously results from protonation of one of the axial ligands that is ascribed to a hydroxide. Coordination by its protonated form, a water molecule, may be too weak to keep the heme iron in the porphyrin plane. The corresponding Fe-OH2 stretching mode was attributed to a weak H/D-sensitive band at 464 cm(-1). The coordination equilibrium not only depends on the pH but is also affected by the buffer, the salt concentration, and the binding of the natural redox partner cytochrome c552. These changes of the coordination equilibrium are attributed to the perturbation of the hydrogen bonding network at the catalytic center that is connected to the protein surface via a relay of hydrogen bonds. Environmental changes at the catalytic site are sensitively reflected by the formyl stretching of heme a3. The unique structural properties of the ba3 oxidase may be related to the unusual proton pump efficiency and heme a3 redox potential.