NMR basis for interprotein electron transfer gating between cytochrome c and cytochrome c oxidase

The final interprotein electron transfer (ET) in the mammalian respiratory chain, from cytochrome c (Cyt c) to cytochrome c oxidase (CcO) is investigated by (1)H-(15)N heteronuclear single quantum coherence spectral analysis. The chemical shift perturbation in isotope-labeled Cyt c induced by addition of unlabeled CcO indicates that the hydrophobic heme periphery and adjacent hydrophobic amino acid residues of Cyt c dominantly contribute to the complex formation, whereas charged residues near the hydrophobic core refine the orientation of Cyt c to provide well controlled ET. Upon oxidation of Cyt c, the specific line broadening of N-H signals disappeared and high field (1)H chemical shifts of the N-terminal helix were observed, suggesting that the interactions of the N-terminal helix with CcO are reduced by steric constraint in oxidized Cyt c, while the chemical shift perturbations in the C-terminal helix indicate notable interactions of oxidized Cyt c with CcO. These results suggest that the overall affinity of oxidized Cyt c for CcO is significantly, but not very much weaker than that of reduced Cyt c. Thus, electron transfer is gated by dissociation of oxidized Cyt c from CcO, the rate of which is controlled by the affinity of oxidized Cyt c to CcO for providing an appropriate electron transfer rate for the most effective energy coupling. The conformational changes in Lys13 upon CcO binding to oxidized Cyt c, shown by (1)H- and (1)H, (15)N-chemical shifts, are also expected to gate intraprotein ET by a polarity control of heme c environment.     

Conversion of a c type cytochrome to a b type that spontaneously forms in vitro from apo protein and heme: implications for c type cytochrome biogenesis and folding

Cytochrome c(552) from Hydrogenobacter thermophilus, a thermophilic bacterium, has been converted into a b type cytochrome, after mutagenesis of both heme-binding cysteines to alanine and expression in the cytoplasm of Escherichia coli. The b type variant is less stable, with the guanidine hydrochloride unfolding midpoint occurring at a concentration 2 M lower than for the wild-type protein. The reduction potential is 75 mV lower than that of the recombinant wild-type protein. The heme can be removed from the b type variant, thus generating an apo protein that has, according to circular dichroism spectroscopy, an alpha-helical content different from that of the holo b type protein. The latter is readily reformed in vitro by addition of heme to the apo protein. This reforming suggests that previously observed assembly of cytochrome c(552), which has the typical class I cytochrome c fold, in the E. coli cytoplasm is a consequence of spontaneous thioether bond formation after binding of heme to a prefolded polypeptide. These observations have implications for the general problem of c type cytochrome biogenesis.     

Heme axial methionine fluxionality in Hydrogenobacter thermophilus cytochrome c552

The heme group in paramagnetic (S = 1/2) ferricytochromes c typically displays a markedly asymmetric distribution of unpaired electron spin density among the heme pyrrole beta substituents. This asymmetry is determined by the orientations of the heme axial ligands, histidine and methionine. One exception to this is ferricytochrome c(552) from Hydrogenobacter thermophilus, which has similar amounts of unpaired electron spin density at the beta substituents on all four heme pyrroles. Here, determination of the orientation of the magnetic axes and analysis of NMR line shapes for H. thermophilus ferricytochrome c(552) is performed. These data reveal that the unusual electronic structure for this protein is a result of fluxionality of the heme axial methionine. It is proposed that the ligand undergoes inversion at the pyramidal sulfur, and the rapid interconversion between two diastereomeric forms results in the unusual heme electronic structure. Thus a fluxional process for a metal-bound amino acid side chain has now been identified.     

Activationless electron transfer through the hydrophobic core of cytochrome c oxidase

Electron transfer (ET) within proteins occurs by means of chains of redox intermediates that favor directional and efficient electron delivery to an acceptor. Individual ET steps are energetically characterized by the electronic coupling V, driving force DeltaG, and reorganization energy lambda. lambda reflects the nuclear rearrangement of the redox partners and their environment associated with the reactions; lambda approximately 700-1,100 meV (1 eV = 1.602 x 10(-19) J) has been considered as a typical value for intraprotein ET. In nonphotosynthetic systems, functional ET is difficult to assess directly. However, using femtosecond flash photolysis of the CO-poised membrane protein cytochrome c oxidase, the intrinsic rate constant of the low-DeltaG electron injection from heme a into the heme a(3)-Cu(B) active site was recently established at (1.4 ns)(-1). Here, we determine the temperature dependence of both the rate constant and DeltaG of this reaction and establish that this reaction is activationless. Using a quantum mechanical form of nonadiabatic ET theory and common assumptions for the coupled vibrational modes, we deduce that lambda is <200 meV. It is demonstrated that the previously accepted value of 760 meV actually originates from the temperature dependence of Cu(B)-CO bond breaking. We discuss that low-DeltaG, low-lambda reactions are common for efficiently channeling electrons through chains that are buried inside membrane proteins.     

Multiple pathways on a protein-folding energy landscape: kinetic evidence

The funnel landscape model predicts that protein folding proceeds through multiple kinetic pathways. Experimental evidence is presented for more than one such pathway in the folding dynamics of a globular protein, cytochrome c. After photodissociation of CO from the partially denatured ferrous protein, fast time-resolved CD spectroscopy shows a submillisecond folding process that is complete in approximately 10(-6) s, concomitant with heme binding of a methionine residue. Kinetic modeling of time-resolved magnetic circular dichroism data further provides strong evidence that a 50-microseconds heme-histidine binding process proceeds in parallel with the faster pathway, implying that Met and His binding occur in different conformational ensembles of the protein, i.e., along respective ultrafast (microseconds) and fast (milliseconds) folding pathways. This kinetic heterogeneity appears to be intrinsic to the diffusional nature of early folding dynamics on the energy landscape, as opposed to the late-time heterogeneity associated with nonnative heme ligation and proline isomers in cytochrome c.     

Molecular dynamics simulations of cooling in laser-excited heme proteins.

In transient optical experiments the absorbed photon raises the vibrational temperature of the chromophore. In heme proteins at room temperature conversion of a 530-nm photon into vibrational energy is estimated to raise the temperature of the heme by 500-700 K. Cooling of the heme is expected to occur mainly by interacting with the surrounding protein. We report molecular dynamics simulations for myoglobin and cytochrome c in vacuo that predict that this cooling occurs on the ps time scale. The decay of the vibrational temperature is nonexponential with about 50% loss occurring in 1-4 ps and with the remainder in 20-40 ps. These results predict the presence of nonequilibrium vibrational populations that would introduce ambiguity into the interpretation of transient ps absorption and Raman spectra and influence the kinetics of sub-ns geminate recombination.     

A two-dimensional view of the folding energy landscape of cytochrome c

Time-correlated single photon counting (TCSPC) was combined with fluorescence correlation spectroscopy (FCS) to study the transition between acid-denatured states and the native structure of cytochrome c (Cyt c) from Saccharomyces cerevisiae. The use of these techniques in concert proved to be more powerful than either alone, yielding a two-dimensional picture of the folding energy landscape of Cyt c. TCSPC measured the distribution of distances between the heme of the protein and a covalently attached dye molecule at residue C102 (one folding reaction coordinate), whereas FCS measured the hydrodynamic radius (a second folding reaction coordinate) of the protein over a range of pH values. These two independent measurements provide complimentary information regarding protein conformation. We see evidence for a well defined folding intermediate in the acid renaturation folding pathway of this protein reflected in the distribution of lifetimes needed to fit the TCSPC data. Moreover, FCS studies revealed this intermediate state to be in dynamic equilibrium with unfolded structures, with conformational fluctuations into and out of this intermediate state occurring on an approximately 30-micros time scale.     

Properties of a copper-containing cytochrome c1aa3 complex: a terminal oxidase of the extreme thermophile Thermus thermophilus HB8.

From the plasma membrane of Thermus thermophilus HB8 we have partially purified a detergent-solubilized complex of cytochromes a and c1 that actively catalyzes the transfer of electrons from ascorbate via a redox dye to oxygen. The complex is composed of two types of polypeptides, with molecular weights of approximately 55,000 and 33,000. Quantitative analysis revealed the presence of heme a, heme c, and copper in a ratio of 2:1:2, with the heme a being present at 10 +/- 1.3 nmol/mg of protein. The heme c was shown to be associated with the molecular weight 33,000 peptide and is suggested to be of the c1 type. The optical and electron paramagnetic resonance properties of this complex were found to be similar to those of eukaryotic cytochrome oxidase, suggesting the following arrangement of chromophores: a magnetically isolated cytochrome c1 and an oxygen-reducing functional unit consisting of two heme a groups and two copper ions associated with one or more larger peptides.     

Regulation of bacterial sugar-H+ symport by phosphoenolpyruvate-dependent enzyme I/HPr-mediated phosphorylation.

The lactose-H+ symport protein (LacS) of Streptococcus thermophilus has a C-terminal hydrophilic domain that is homologous to IIA protein(s) domains of the phosphoenolpyruvate:sugar phosphotransferase system (PTS). C-terminal truncation mutants were constructed and expressed in Escherichia coli and their properties were analyzed. Remarkably, the entire IIA domain (160 amino acids) could be deleted without significant effect on lactose-H+ symport and galactoside equilibrium exchange. Analysis of the LacS mutants in S. thermophilus cells suggested that transport is affected by PTS-mediated phosphorylation of the IIA domain. For further studies, membrane vesicles of S. thermophilus were fused with cytochrome c oxidase-containing liposomes, and, when appropriate, phosphoenolpyruvate (PEP) plus purified enzyme I and heat-stable protein HPr were incorporated into the hybrid membranes. Generation of a protonmotive force (delta p) in the hybrid membranes resulted in accumulation of lactose, whereas uptake of the PTS sugar sucrose was not observed. With PEP and the energy-coupling proteins enzyme I and HPr of the PTS on the inside, high rates of sucrose uptake were observed, whereas delta p-driven lactose uptake by wild-type LacS was inhibited. This inhibition was not observed with LacS(delta 160) and LacS(H552R), indicating that PEP-dependent enzyme I/HPr-mediated phosphorylation of the IIA domain (possibly the conserved His-552 residue) modulates lactose-H+ symport activity.     

Early events in the folding of four-helix-bundle heme proteins

Topologically homologous four-helix-bundle heme proteins exhibit striking diversity in their refolding kinetics. Cytochrome b562 has been reported to fold on a sub-millisecond time scale, whereas cytochrome c' refolding requires 10 s or more to complete. Heme dissociation in cytochrome b562 interferes with studies of folding kinetics, so a variant of cytochrome b562 (cytochrome c-b562) with a covalent c-type linkage to the heme has been expressed in Escherichia coli. Early events in the electron transfer-triggered folding of Fe(II)-cytochrome c-b562, along with those of Fe(II)-cytochrome c556, have been examined by using time-resolved absorption spectroscopy. Coordination of S(Met) to Fe(II) occurs within 10 mus after reduction of the denatured Fe(III)-cytochromes, and shortly thereafter (100 micros) the heme spectra are indistinguishable from those of the folded proteins. Under denaturing conditions, carbon monoxide binds to the Fe(II)-hemes in approximately 15 ms. By contrast, CO binding cannot compete with refolding in the Fe(II)-cytochromes, thereby confirming that the polypeptide encapsulates the heme in <10 ms. We suggest that Fe-S(Met) ligation facilitates refolding in these four-helix-bundle heme proteins by reducing the conformational freedom of the polypeptide chain.     

Protein influence on the heme in cytochrome c: evidence from Raman difference spectroscopy.

Raman difference spectra have been obtained for the cytochromes c of a number of species by simultaneous data acquisition from two samples. Frequency differences as small as 0.1 cm-1 can be measured reproducibly by the technique we have developed. In comparisons between cytochromes c isolated from two different species, the frequency differences in the heme vibrational modes range from 0 to 6 cm-1. The vibrational frequencies of the heme are sensitive to the electronic charge density on the porphyrin macrocycle. The frequency differences are interpreted in terms of the influence of the heme-packed aromatic and highly electronegative amino acid side chains on the pi* charge density and distribution on the heme. Such a control of the electronic properties of the heme by the protein may be important for the function of cytochrome c.     

Properties of a copper-containing cytochrome ba3: a second terminal oxidase from the extreme thermophile Thermus thermophilus.

We describe an alternate terminal oxidase found in the plasma membrane of Thermus thermophilus and designate it cytochrome ba3. The enzyme consists of a single approximately equal to 35-kDa polypeptide that binds one heme B molecule, one heme A molecule, and two Cu ions. Optical spectra suggest the presence of cytochrome b, cytochrome a3, and CuA in this protein. Quantitative EPR and M?ssbauer studies of the oxidized protein indicate the presence of one low-spin ferric heme, which is assigned to cytochrome b. M?ssbauer studies of the reduced protein show the presence of one low-spin ferrous heme, assigned to cytochrome b, and a predominant high-spin ferrous heme that reacts quantitatively with CO to yield an additional low-spin ferrous heme. The latter Fe atom is associated with the heme A and is designated cytochrome a3. The EPR spectrum of the oxidized protein also reveals the presence of a CuA-type center that accounts for half the total Cu. The remainder of the Cu would appear to be present as CuB that is magnetically coupled to the heme A. Amino acid analyses of cytochrome ba3 show the presence of eight to nine histidine residues and one cysteine residue.     

Separate Intramolecular Pathways for Reduction and Oxidation of Cytochrome c in Electron Transport Chain Reactions

The monoiodotyrosine 74, formyltryptophan 59, mononitrotyrosine 67, and carboxymethylmethionine 80 derivatives of horse cytochrome c are defective in their ability to accept electrons from the succinate-cytochrome c reductase system, while their reactions with purified cytochrome c oxidase are essentially those of the native protein. The 4-nitrobenzo-2-oxa-1,3-diazole derivative of lysine 13 of horse cytochrome c and the bis-phenylglyoxal derivative of arginine 13 of Candida krusei cytochrome c have the opposite properties, in that they are readily reduced by the succinate-cytochrome c reductase (EC 1.3.99.1) system but are defective in their capability of transferring electrons to cytochrome c oxidase (EC 1.9.3.1). We conclude that electrons from mitochondrial cytochrome c reductase are transmitted to ferricytochrome c by a different pathway than electrons from ferrocytochrome c to cytochrome c oxidase. The present results are compatible with the concept that the mechanism of reduction involves an aromatic ring channel comprising residues 74, 59, 67, and 80, leading from the "left back" part of the protein to the heme iron. On the other hand, since residue 13 is immediately above the edge of the heme that is at the "front surface" of the molecule, we suggest that the electron leaves ferrocytochrome c to cytochrome c oxidase by way of the edge of pyrrole ring II or the adjacent surface-located sulfur of cysteinyl residue 17, which is thioether bonded to the heme. On this basis, the sites of electron entry and exit in cytochrome c would appear to be some 110 degrees of arc away from each other along the surface of the protein, explaining several previously observed phenomena.     

Modulation of mammalian cell growth and death by prokaryotic and eukaryotic cytochrome c

Cytochrome c(551), an 8,685-Da haem-containing protein, is known to be involved in electron transfer during dissimilative denitrification by Pseudomonas aeruginosa. Both cytochrome c(551) and copper-containing redox protein azurin have been used in vitro as partners in electron transfer. Azurin has been reported to induce apoptosis in macrophages and cancer cells. We now report that, unlike azurin, cytochrome c(551), termed Cyt c(551), has very little ability to induce apoptosis in J774 cell line-derived macrophages but demonstrates significant inhibition of cell cycle progression in such cells. A mutant form of Cyt c(551), V23DI59E, has significantly reduced ability to inhibit cell cycle progression but demonstrates a higher level of apoptosis-inducing activity in macrophages, compared with WT Cyt c(551). Interestingly, the WT Cyt c(551), but not the mutant form, significantly enhances the level of tumor suppressor protein p16(Ink4a), a known inhibitor of cell cycle progression whereas the mutant form seems to form a complex with tumor suppressor protein p53, thereby enhancing its intracellular level to some extent. Eukaryotic cytochromes such as horse and bovine cytochrome c have also been shown to induce apoptosis but not inhibition of cell cycle progression in J774 cells, thus signifying a role of this redox protein in entry to, and in the induction of, cell death in mammalian cells.     

Spectroscopic analysis of the cytochrome c oxidase-cytochrome c complex: circular dichroism and magnetic circular dichroism measurements reveal change of cytochrome c heme geometry imposed by complex formation.

Binding of cytochrome c to cytochrome c oxidase induces a conformational change in both proteins as well as a change of the electronic structure of the heme of cytochrome c, indicating an altered heme c-protein interaction. This follows from the observation that the induced circular dichroism (CD) and magnetic circular dichroism (MCD) spectra of the oxidase-cytochrome c complex in the Soret region differ from the summed spectra of oxidase plus cytochrome c. Spectral changes occur in the complex composed of either the two ferric or the two ferrous hemoproteins. The difference CD and MCD signals saturate at a ratio of 1 heme c per heme aa3. The difference spectra are specific to the cognate complex. The results are interpreted to reflect a direct relationship between the recognition/binding step and the electron-transfer reaction. The conformational rearrangement induced in cytochrome c by cytochrome c oxidase consists of a structural rearrangement of the heme environment and possibly a change of the geometry of the heme iron-methionine-80 sulfur axial bond. This rearrangement may decrease the reorganizational free energy of electron transfer by adjusting the heme c geometry to a state between that of ferri- and ferrocytochrome c.     

The metal reductase activity of some multiheme cytochromes c: NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c(7)

The redox reaction between CrO(4)(2-) and the fully reduced three-heme cytochrome c(7) from Desulfuromonas acetoxidans to give chromium(III) and the fully oxidized protein has been followed by NMR spectroscopy. The hyperfine coupling between the oxidized protein protons and chromium(III), which remains bound to the protein, gives rise to line-broadening effects on the NMR resonances that can be transformed into proton-metal distance restraints. Structure calculations based on these unconventional constraints allowed us to demonstrate that chromium(III) binds at a unique site and to locate it on the protein surface. The metal ion is located 7.9 +/- 0.4 A from the iron of heme IV, 16.3 +/- 0.7 A from the iron of heme III, and 22.5 +/- 0.5 A from the iron of heme I. Shift changes caused by the presence of unreactive MoO(4)(2-), a CrO(4)(2-) analogue, indicate the involvement of the same protein area in the anion binding. The titration of the oxidation of cytochrome c(7) shows a detailed mechanism of action. The presence of a specific binding site supports the hypothesis of the biological role of this cytochrome as a metal reductase.     

A funneled energy landscape for cytochrome c directly predicts the sequential folding route inferred from hydrogen exchange experiments

Proteins fold through a variety of mechanisms. For a given protein, folding routes largely depend on the protein's stability and its native-state geometry, because the landscape is funneled. These ideas are corroborated for cytochrome c by using a coarse-grained topology-based model with a perfect funnel landscape that includes explicit modeling of the heme. The results show the importance of the heme as a nucleation site and explain the observed hydrogen exchange patterns of cytochrome c within the context of energy landscape theory.     

Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations

The vibrational energy relaxation of carbon monoxide in the heme pocket of sperm whale myoglobin was studied by using molecular dynamics simulation and normal mode analysis methods. Molecular dynamics trajectories of solvated myoglobin were run at 300 K for both the delta- and epsilon-tautomers of the distal His-64. Vibrational population relaxation times of 335 +/- 115 ps for the delta-tautomer and 640 +/- 185 ps for the epsilon-tautomer were estimated by using the Landau-Teller model. Normal mode analysis was used to identify those protein residues that act as the primary "doorway" modes in the vibrational relaxation of the oscillator. Although the CO relaxation rates in both the epsilon- and delta-tautomers are similar in magnitude, the simulations predict that the vibrational relaxation of the CO is faster in the delta-tautomer with the distal His playing an important role in the energy relaxation mechanism. Time-resolved mid-IR absorbance measurements were performed on photolyzed carbonmonoxy hemoglobin (Hb(13)CO). From these measurements, a T(1) time of 600 +/- 150 ps was determined. The simulation and experimental estimates are compared and discussed.     

Cobalt Induction of Hepatic Heme Oxygenase; with Evidence That Cytochrome P-450 Is Not Essential for This Enzyme Activity

Treatment of rats in vivo with cobalt chloride stimulated heme oxidation by hepatic microsomes to levels up to 800% above controls. This treatment also caused increases in liver weight and in total microsomal protein; in contrast, marked decreases were produced in microsomal oxidation of ethylmorphine (80%), and in cytochrome P-450 (60-70%) and heme (30-50%) contents. Cobalt chloride treatment did not affect heme oxidation by the spleen heme oxygenase system.The rate of heme oxidation by hepatic microsomal enzymes and the microsomal content of cytochrome P-450 were found to be unrelated. This conclusion was reached from studies in which microsomal heme oxygenase activity from cobalt-treated animals could be increased by 900% above control levels in the same microsomal preparation in which cytochrome P-450 content was decreased to spectrally unmeasurable amounts after incubation with 4 M urea. The same treatment eliminated ehtylmorphine demethylation and decreased microsomal NADPH-cytochrome c reductase (EC 1.6.2.4) activity by 75%.It is concluded that (i) the hepatic microsomal enzyme system that oxidizes heme compounds is not the same as that which metabolizes drugs, (ii) cytochrome P-450 is not essential for the oxidation of heme by liver cells, (iii) there is no direct relationship between the rate of heme oxidation and the level of NADPH-cytochrome c reductase activity, and (iv) the oxidation of heme is protein-dependent and the active proteins are inducible, but are different from those involved in drug metabolism.     

Transition state and encounter complex for fast association of cytochrome c2 with bacterial reaction center

Electrostatic interactions strongly enhance the electron transfer reaction between cytochrome (Cyt) c(2) and reaction center (RC) from photosynthetic bacteria, yielding a second-order rate constant, k(2) approximately 10(9) s(-1).M(-1), close to the diffusion limit. The proposed mechanism involves an encounter complex (EC) stabilized by electrostatic interactions, followed by a transition state (TS), leading to the bound complex active in electron transfer. The effect of electrostatic interactions was previously studied by Tetreault et al. [Tetreault, M., Cusanovich, M., Meyer, T., Axelrod, H. & Okamura, M. Y. (2002) Biochemistry 41, 5807-5815] by measuring k(2) for RC and Cyt molecules with modified charged residues at the binding interface. The present work is a computational analysis of this kinetic study to determine the ensemble of configurations of the TS and EC. Changes in the TS energies due to different mutations were compared with differences in the calculated electrostatic energies for a wide range of Cyt/RC configurations. The TS ensemble, obtained from structures having the highest correlation coefficients in the comparison with experimental data, has the Cyt displaced by approximately 10 A from its position in x-ray crystal structure, close to the average position of the EC ensemble, with strong electrostatic interactions between Cyt on the M subunit side of the RC surface. The heme of the Cyt is oriented toward Tyr L162 on the RC, the tunneling contact in the bound final state on the RC. The similarity between the structures of the EC, TS, and bound state can account for the rapid rate of association responsible for fast diffusion-controlled electron transfer.