Application of exciton coupling theory to the structure of mitochondrial cytochrome b

Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design

Nature has evolved diverse electron transport proteins and multiprotein assemblies essential to the generation and transduction of biological energy. However, substantially modifying or adapting these proteins for user-defined applications or to gain fundamental mechanistic insight can be hindered by their inherent complexity. De novo protein design offers an attractive route to stripping away this confounding complexity, enabling us to probe the fundamental workings of these bioenergetic proteins and systems, while providing robust, modular platforms for constructing completely artificial electron-conducting circuitry. Here, we use a set of de novo designed mono-heme and di-heme soluble and membrane proteins to delineate the contributions of electrostatic micro-environments and dielectric properties of the surrounding protein medium on the inter-heme redox cooperativity that we have previously reported. Experimentally, we find that the two heme sites in both the water-soluble and membrane constructs have broadly equivalent redox potentials in isolation, in agreement with Poisson-Boltzmann Continuum Electrostatics calculations. BioDC, a Python program for the estimation of electron transfer energetics and kinetics within multiheme cytochromes, also predicts equivalent heme sites, and reports that burial within the low dielectric environment of the membrane strengthens heme-heme electrostatic coupling. We conclude that redox cooperativity in our diheme cytochromes is largely driven by heme electrostatic coupling and confirm that this effect is greatly strengthened by burial in the membrane. These results demonstrate that while our de novo proteins present minimalist, new-to-nature constructs, they enable the dissection and microscopic examination of processes fundamental to the function of vital, yet complex, bioenergetic assemblies.

An expandable, modular de novo protein platform for precision redox engineering

The electron-conducting circuitry of life represents an as-yet untapped resource of exquisite, nanoscale biomolecular engineering. Here, we report the characterization and structure of a de novo diheme "maquette" protein, 4D2, which we subsequently use to create an expanded, modular platform for heme protein design. A well-folded monoheme variant was created by computational redesign, which was then utilized for the experimental validation of continuum electrostatic redox potential calculations. This demonstrates how fundamental biophysical properties can be predicted and fine-tuned. 4D2 was then extended into a tetraheme helical bundle, representing a 7 nm molecular wire. Despite a molecular weight of only 24 kDa, electron cryomicroscopy illustrated a remarkable level of detail, indicating the positioning of the secondary structure and the heme cofactors. This robust, expressible, highly thermostable and readily designable modular platform presents a valuable resource for redox protein design and the future construction of artificial electron-conducting circuitry.

Catalytic Reactions and Energy Conservation in the Cytochrome bc1 and b6f Complexes of Energy-Transducing Membranes

This review focuses on key components of respiratory and photosynthetic energy-transduction systems: the cytochrome bc1 and b6f (Cytbc1/b6f) membranous multisubunit homodimeric complexes. These remarkable molecular machines catalyze electron transfer from membranous quinones to water-soluble electron carriers (such as cytochromes c or plastocyanin), coupling electron flow to proton translocation across the energy-transducing membrane and contributing to the generation of a transmembrane electrochemical potential gradient, which powers cellular metabolism in the majority of living organisms. Cytsbc1/b6f share many similarities but also have significant differences. While decades of research have provided extensive knowledge on these enzymes, several important aspects of their molecular mechanisms remain to be elucidated. We summarize a broad range of structural, mechanistic, and physiological aspects required for function of Cytbc1/b6f, combining textbook fundamentals with new intriguing concepts that have emerged from more recent studies. The discussion covers but is not limited to (i) mechanisms of energy-conserving bifurcation of electron pathway and energy-wasting superoxide generation at the quinol oxidation site, (ii) the mechanism by which semiquinone is stabilized at the quinone reduction site, (iii) interactions with substrates and specific inhibitors, (iv) intermonomer electron transfer and the role of a dimeric complex, and (v) higher levels of organization and regulation that involve Cytsbc1/b6f. In addressing these topics, we point out existing uncertainties and controversies, which, as suggested, will drive further research in this field.

Outer membrane compositions enhance the rate of extracellular electron transport via cell-surface MtrC protein in Shewanella oneidensis MR-1

While cell membrane composition is critical for the function of membrane proteins, membrane modification has not been used to control the rate of extracellular electron transfer (EET) via the outer membrane protein complexes. Here, the rate of electron flow via the cell-surface redox protein, MtrC, was highly enhanced upon change in the outer membrane composition in Shewanella oneidensis MR-1. The MR-1 strain was pre-cultured at 4 °C and 30 °C to initiate differentiation of membrane composition. The whole-cell difference electrochemical assay of wild-type and mutant strains lacking MtrC suggested that the rate of EET via MtrC increased approximately 18 times at 4 °C than 30 °C. Circular dichroism spectroscopy showed that the molar exciton coupling coefficient for inter-heme interaction in MtrC increased in MR-1 at 4 °C than 30 °C. Results suggest that membrane modification may be a novel strategy for improving the efficiency of EET-based technologies.

Geometrical Changes in the Hemes of Bacterial Surface c-Type Cytochromes Reveal Flexibility in Their Binding Affinity with Minerals

Microbial extracellular electron transport occurs via the physical and electrical association of outer-membrane c-type cytochromes (OM c-Cyts) with extracellular solid surfaces. However, studies investigating the characteristics of cytochrome binding with solid materials have been limited to the use of purified units of OM c-Cyts dissolved in solution, rather than OM c-Cyts in intact cells, because of the lack of a methodology that specifically allows for the monitoring of OM c-Cyts in whole-cells. Here, we utilized circular dichroism (CD) spectroscopy to examine the molecular mechanisms and binding characteristics of the interaction between MtrC, a unit of OM c-Cyts, in whole Shewanella oneidensis MR-1 cells and hematite nanoparticles. The addition of hematite nanoparticles significantly decreased the intensity of the Soret CD peaks, indicating geometrical changes in the hemes in MtrC associated with their physical contact with hematite. The binding affinity of MtrC estimated using CD spectra changed predominantly depending upon the redox state of MtrC and the concentration of the hematite nanoparticles. In contrast, purified MtrC demonstrated a constant binding affinity following a Langmuir isotherm, with a standard Gibbs free energy of -43 kJ mol^-1, suggesting that the flexibility in the binding affinity of MtrC with hematite was specific in membrane-bound protein complex conditions. Overall, these findings suggest that the binding affinity as well as the heme geometry of OM c-Cyts are flexibly modulated in the membrane complex associated with microbe-mineral interactions.

Structure-function of the cytochrome b6f lipoprotein complex: a scientific odyssey and personal perspective

Structure-function studies of the cytochrome b₆f complex, the central hetero-oligomeric membrane protein complex in the electron transport chain of oxygenic photosynthesis, which formed the basis for a high-resolution (2.5 Å) crystallographic solution of the complex, are described. Structure-function differences between the structure of subunits of the bc complexes, b₆f, and bc₁ from mitochondria and photosynthetic bacteria, which are often assumed to function identically, are discussed. Major differences which suggest that quinone-dependent electron transport pathways can vary in b₆f and bc₁ complexes are as follows: (a) an additional c-type heme, c_n, and bound single copies of chlorophyll a and β-carotene in the b₆f complex; and (b) a cyclic electron transport pathway that encompasses the b₆f and PSI reaction center complexes. The importance of including lipid in crystallization of the cytochrome complex, or with any hetero-oligomeric membrane protein complex, is emphasized, and consequences to structure-function of b₆f being a lipoprotein complex discussed, including intra-protein dielectric heterogeneity and resultant pathways of trans-membrane electron transport. The role of the b₆f complex in trans-membrane signal transduction from reductant generated on the p-side of the electron transport chain to the regulation of light energy to the two photosystems by trans-side phosphorylation of the light-harvesting chlorophyll protein is presented. Regarding structure aspects relevant to plastoquinol-quinone entrance-egress: (i) modification of the p-side channel for plastoquinone access to the iron-sulfur protein would change the rate-limiting step in electron transport; (ii) the narrow niche for entry of plastoquinol into b₆f from the PSII reaction center complex would seem to require close proximity between the complexes.

Whole-cell circular dichroism difference spectroscopy reveals an in vivo-specific deca-heme conformation in bacterial surface cytochromes

Our novel analytical framework to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell revealed that the heme alignment in reduced MtrC is distinct from that in purified system.

We established whole-cell circular dichroism difference spectroscopy to identify the inter-heme interaction in deca-heme cytochrome protein MtrC in whole cell. Our data showed that the heme alignment of reduced MtrC in whole cell is distinct from that in purified one, suggesting the in vivo specific electron transport kinetics.

A map of dielectric heterogeneity in a membrane protein: the hetero-oligomeric cytochrome b6f complex

The cytochrome b₆f complex, a member of the cytochrome bc family that mediates energy transduction in photosynthetic and respiratory membranes, is a hetero-oligomeric complex that utilizes two pairs of b-hemes in a symmetric dimer to accomplish trans-membrane electron transfer, quinone oxidation–reduction, and generation of a proton electrochemical potential. Analysis of electron storage in this pathway, utilizing simultaneous measurement of heme reduction, and of circular dichroism (CD) spectra, to assay heme–heme interactions, implies a heterogeneous distribution of the dielectric constants that mediate electrostatic interactions between the four hemes in the complex. Crystallographic information was used to determine the identity of the interacting hemes. The Soret band CD signal is dominated by excitonic interaction between the intramonomer b-hemes, b_n and b_p, on the electrochemically negative and positive sides of the complex. Kinetic data imply that the most probable pathway for transfer of the two electrons needed for quinone oxidation–reduction utilizes this intramonomer heme pair, contradicting the expectation based on heme redox potentials and thermodynamics, that the two higher potential hemes b_n on different monomers would be preferentially reduced. Energetically preferred intramonomer electron storage of electrons on the intramonomer b-hemes is found to require heterogeneity of interheme dielectric constants. Relative to the medium separating the two higher potential hemes b_n, a relatively large dielectric constant must exist between the intramonomer b-hemes, allowing a smaller electrostatic repulsion between the reduced hemes. Heterogeneity of dielectric constants is an additional structure–function parameter of membrane protein complexes.

The Q cycle of cytochrome bc complexes: a structure perspective

Aspects of the crystal structures of the hetero-oligomeric cytochrome bc(1) and b(6)f ("bc") complexes relevant to their electron/proton transfer function and the associated redox reactions of the lipophilic quinones are discussed. Differences between the b(6)f and bc(1) complexes are emphasized. The cytochrome bc(1) and b(6)f dimeric complexes diverge in structure from a core of subunits that coordinate redox groups consisting of two bis-histidine coordinated hemes, a heme b(n) and b(p) on the electrochemically negative (n) and positive (p) sides of the complex, the high potential [2Fe-2S] cluster and c-type heme at the p-side aqueous interface and aqueous phase, respectively, and quinone/quinol binding sites on the n- and p-sides of the complex. The bc(1) and b(6)f complexes diverge in subunit composition and structure away from this core. b(6)f Also contains additional prosthetic groups including a c-type heme c(n) on the n-side, and a chlorophyll a and β-carotene. Common structure aspects; functions of the symmetric dimer. (I) Quinone exchange with the bilayer. An inter-monomer protein-free cavity of approximately 30Å along the membrane normal×25Å (central inter-monomer distance)×15Å (depth in the center), is common to both bc(1) and b(6)f complexes, providing a niche in which the lipophilic quinone/quinol (Q/QH(2)) can be exchanged with the membrane bilayer. (II) Electron transfer. The dimeric structure and the proximity of the two hemes b(p) on the electrochemically positive side of the complex in the two monomer units allow the possibility of two alternate routes of electron transfer across the complex from heme b(p) to b(n): intra-monomer and inter-monomer involving electron cross-over between the two hemes b(p). A structure-based summary of inter-heme distances in seven bc complexes, representing mitochondrial, chromatophore, cyanobacterial, and algal sources, indicates that, based on the distance parameter, the intra-monomer pathway would be favored kinetically. (III) Separation of quinone binding sites. A consequence of the dimer structure and the position of the Q/QH(2) binding sites is that the p-side QH(2) oxidation and n-side Q reduction sites are each well separated. Therefore, in the event of an overlap in residence time by QH(2) or Q molecules at the two oxidation or reduction sites, their spatial separation would result in minimal steric interference between extended Q or QH(2) isoprenoid chains. (IV) Trans-membrane QH(2)/Q transfer. (i) n/p-side QH(2)/Q transfer may be hindered by lipid acyl chains; (ii) the shorter less hindered inter-monomer pathway across the complex would not pass through the center of the cavity, as inferred from the n-side antimycin site on one monomer and the p-side stigmatellin site on the other residing on the same surface of the complex. (V) Narrow p-side portal for QH(2)/Q passage. The [2Fe-2S] cluster that serves as oxidant, and whose histidine ligand serves as a H(+) acceptor in the oxidation of QH(2), is connected to the inter-monomer cavity by a narrow extended portal, which is also occupied in the b(6)f complex by the 20 carbon phytyl chain of the bound chlorophyll.

Ubiquinol oxidation in the cytochrome bc1 complex: Reaction mechanism and prevention of short-circuiting

This review is focused on the mechanism of ubiquinol oxidation by the cytochrome bc1 complex (bc1). This integral membrane complex serves as a "hub" in the vast majority of electron transfer chains. The bc1 oxidizes a ubiquinol molecule to ubiquinone by a unique "bifurcated" reaction where the two released electrons go to different acceptors: one is accepted by the mobile redox active domain of the [2Fe-2S] iron-sulfur Rieske protein (FeS protein) and the other goes to cytochrome b. The nature of intermediates in this reaction remains unclear. It is also debatable how the enzyme prevents short-circuiting that could happen if both electrons escape to the FeS protein. Here, I consider a reaction mechanism that (i) agrees with the available experimental data, (ii) entails three traits preventing the short-circuiting in bc1, and (iii) exploits the evident structural similarity of the ubiquinone binding sites in the bc1 and the bacterial photosynthetic reaction center (RC). Based on the latter congruence, it is suggested that the reaction route of ubiquinol oxidation by bc1 is a reversal of that leading to the ubiquinol formation in the RC. The rate-limiting step of ubiquinol oxidation is then the re-location of a ubiquinol molecule from its stand-by site within cytochrome b into a catalytic site, which is formed only transiently, after docking of the mobile redox domain of the FeS protein to cytochrome b. In the catalytic site, the quinone ring is stabilized by Glu-272 of cytochrome b and His-161 of the FeS protein. The short circuiting is prevented as long as: (i) the formed semiquinone anion remains bound to the reduced FeS domain and impedes its undocking, so that the second electron is forced to go to cytochrome b; (ii) even after ubiquinol is fully oxidized, the reduced FeS domain remains docked to cytochrome b until electron(s) pass through cytochrome b; (iii) if cytochrome b becomes (over)reduced, the binding and oxidation of further ubiquinol molecules is hampered; the reason is that the Glu-272 residue is turned towards the reduced hemes of cytochrome b and is protonated to stabilize the surplus negative charge; in this state, this residue cannot participate in the binding/stabilization of a ubiquinol molecule.

Composition of the heme centers in chromaffin granule cytochrome b(561)

Electron paramagnetic resonance and circular dichroism spectra of cytochrome b(561) from chromaffin granule membranes indicated a 2:1 stoichiometry of high- and low-potential hemes. Recombinant bovine cytochrome b(561) expressed in a baculovirus system retained native spectroscopic characteristics and represents a promising model for further study.

On the spatial organization of hemes and chlorophyll in cytochrome b(6)f. A linear and circular dichroism study

The organization of chromophores in the cytochrome b(6) f from Chlamydomonas reinhardtii has been studied spectroscopically. Linear dichroism (LD) measurements, performed on the complex co-reconstituted into vesicles with photosynthetic reaction centers as an internal standard, allow the determination of the orientations of the chromophore with respect to the membrane plane. The orientations of the b(H)- and b(L)-hemes are comparable to those determined crystallographically on the cytochrome bc(1). The excitonic CD signal, resulting from the interaction between b-hemes, is similar to that reported for the cytochrome bc(1). LD and CD data are consistent with the differences between the b(6) f and bc(1) leaving the orientation of the b-hemes unaffected. By contrast, the LD data yield a different orientation for the heme f as compared either to the heme c(1) in the crystallographic structures or to the heme f as studied by electron paramagnetic resonance. This difference could either result from incorrect assumptions regarding the orientations of the electronic transitions of the f-heme or may point to the possibility of a redox-dependent movement of cytochrome f. The chlorophyll a was observed in a well defined orientation, further corroborating a specific binding site for it in the b(6) f complex.

Relative orientation of the hemes of the cytochrome bc(1) complexes from Rhodobacter sphaeroides, Rhodospirillum rubrum, and beef heart mitochondria. A linear dichroism study

The orientation of the chromophores in the cytochrome bc(1) of Rhodospirillum rubrum, Rhodobacter sphaeroides, and beef heart mitochondria is reported. The combination of redox-resolved absorption spectrophotometry and linear dichroism experiments at low temperature allows the determination of the orientation of the three hemes with respect to the membrane plane. The orientations of the b(H)-and b(L)-hemes of the R. sphaeroides and beef heart mitochondrial complexes are similar to those determined by crystallographic studies of the mitochondrial cytochrome bc(1). On the other hand the orientations of the b-hemes of the R. rubrum complex lead to the conclusion that the b(H)-heme is more perpendicular to the membrane plane than the b(L)-heme. This could be explained by a specific organization of the b-hemes due to subunit composition of the complex or, alternatively, to a different spatial position of the heme transitions with respect to the porphyrin macrocycle compared with the other complexes. Moreover, our results demonstrate a different orientation of the heme c(1) of the three studied complexes in comparison to crystallographic studies. This difference may arise from the above hypothesis on the transitions of the heme or from flexibility of this subunit in function of its redox state.

The chemistry and mechanics of ubihydroquinone oxidation at center P (Qo) of the cytochrome bc1 complex

The emerging X-ray structures of the cytochrome bc1 complexes from bovine and chicken heart mitochondria support the protonmotive Q-cycle as the overall electron- and proton-pathway within the cytochrome bc1 complex. The energy conserving reaction within this reaction scheme is the unique bifurcation of electron flow into a high potential and a low potential pathway occurring at the ubihydroquinone-oxidation center (center P or Qo). This step is prerequisite for the 'recycling' of every second electron across the membrane onto the ubiquinone-reduction center, which results in vectorial proton translocation. It has been shown that during steady-state the step controlling this reaction is the first deprotonation of ubihydroquinone and not, as proposed earlier, the formation of a highly unstable semiquinone species. Ubiquinone has not yet been detected at the ubihydroquinone-oxidation center of the protein structures now available, but the pocket seems spacious enough to accommodate two ubiquinone molecules. This is in line with recent enzymological studies, which have shown that not only two ubiquinones, but also two inhibitor molecules can bind to center P. The most striking result from the structures is that the hydrophilic domain of the 'Rieske' protein can be found in two different positions which seem to allow electron transfer between the iron-sulfur cluster and either ubiquinone binding at center P or heme c1. This provides strong support for the 'catalytic switch' model proposed earlier based on detailed analysis of inhibitor binding to cytochrome bc1 complex in different redox states.

Molecular genetic identification of a pathway for heme binding to cytochrome b6

Heme binding to cytochrome b6 is resistant, in part, to denaturing conditions that typically destroy the noncovalent interactions between the b hemes and their apoproteins, suggesting that one of two b hemes of holocytochrome b6 is tightly bound to the polypeptide. We exploited this property to define a pathway for the conversion of apo- to holocytochrome b6, and to identify mutants that are blocked at one step of this pathway. Chlamydomonas reinhardtii strains carrying substitutions in either one of the four histidines that coordinate the bh or bl hemes to the apoprotein were created. These mutations resulted in the appearance of distinct immunoreactive species of cytochrome b6, which allowed us to specifically identify cytochrome b6 with altered bh or bl ligation. In gabaculine-treated (i.e. heme-depleted) wild type and site-directed mutant strains, we established that (i) the single immunoreactive band, observed in strains carrying the bl site-directed mutations, corresponds to apocytochrome b6 and (ii) the additional band present in strains carrying bh site-directed mutations corresponds to a bl-heme-dependent intermediate in the formation of holocytochrome b6. Five nuclear mutants (ccb strains) that are defective in holocytochrome b6 formation display a phenotype that is indistinguishable from that of strains carrying site-directed bh ligand mutants. The defect is specific for cytochrome b6 assembly, because the ccb strains can synthesize other b cytochromes and all c-type cytochromes. The ccb strains, which define four nuclear loci (CCB1, CCB2, CCB3, and CCB4), provide the first evidence that a b-type cytochrome requires trans-acting factors for its heme association.

SOME NEW STRUCTURAL ASPECTS AND OLD CONTROVERSIES CONCERNING THE CYTOCHROME b6f COMPLEX OF OXYGENIC PHOTOSYNTHESIS

The cytochrome b6f complex functions in oxygenic photosynthetic membranes as the redox link between the photosynthetic reaction center complexes II and I and also functions in proton translocation. It is an ideal integral membrane protein complex in which to study structure and function because of the existence of a large amount of primary sequence data, purified complex, the emergence of structures, and the ability of flash kinetic spectroscopy to assay function in a readily accessible ms-100 mus time domain. The redox active polypeptides are cytochromes f and b6 (organelle encoded) and the Rieske iron-sulfur protein (nuclear encoded) in a mol wt = 210,000 dimeric complex that is believed to contain 22-24 transmembrane helices. The high resolution structure of the lumen-side domain of cytochrome f shows it to be an elongate (75 A long) mostly beta-strand, two-domain protein, with the N-terminal alpha-amino group as orthogonal heme ligand and an internal linear 11-A bound water chain. An unusual electron transfer event, the oxidant-induced reduction of a significant fraction of the p (lumen)-side cytochrome b heme by plastosemiquinone indicates that the electron transfer pathway in the b6f complex can be described by a version of the Q-cycle mechanism, originally proposed to describe similar processes in the mitochondrial and bacterial bc1 complexes.

Cytochrome b-245 of the neutrophil superoxide-generating system contains two nonidentical hemes. Potentiometric studies of a mutant form of gp91phox

Analysis of potentiometric titrations of the cytochrome b-245 from a X+ chronic granulomatous disease patient with an Arg54 --> Ser mutation in gp91phox indicates that the mutant form of the cytochrome contains two nonidentical hemes with midpoint potentials of Em7 = -220 and Em7 = -300 mV. In the light of this information, reanalysis of redox titrations of wild-type cytochrome b-245 implies that it probably also contains two separate heme centers with midpoint potentials of Em7 = -225 and Em7 = -265 mV. The effect of the Arg54 --> Ser substitution is to reduce the midpoint potential of one of the heme centers by approximately 35 mV and suggests possible interaction between Arg54 and a heme propionate side chain.

Electron transfer and spectral alpha-band properties of the di-heme protein cytochrome c4 from Pseudomonas stutzeri

Cytochrome c4 is a 190-residue protein active in the aerobic and anaerobic respiration of several bacteria. We have isolated Pseudomonas stutzeri (ATCC no. 11607) cytochrome c4 by an optimized growth procedure following factorial design. The ultraviolet/visible spectra of reduced cytochrome c4 have a composite alpha/beta band which can be resolved into six components. One of these seems to be specific for the high-potential heme group. The kinetics for full oxidation and reduction with the two inorganic redox couples, [Co(terpy)2]2+/3+ and [Co(bipy)3]2+/3+, is formally compatible with either bi- or tri-exponential kinetics. The former would be in line with weak interaction between the heme groups, the latter with notable interaction effects. Arguments in favour of the latter and a cooperative two-electron transfer pattern are given. All phases are approximately proportional to the Co-complex concentration, implying that intramolecular electron transfer in this time range is unlikely. The rate constants are in the range (0.7-80) x 10(4) M-1 s-1 at pH = 7.6 (Tris) and 0.1 M NaCl and very little dependent on the ionic strength in the range 0.1-0.3 M. The reduction potentials could be calculated from the forward and reverse rate constant ratios. The values are 241 +/- 5 and 328 +/- 2 mV (Nernst hydrogen electrode) if bi-exponential kinetics is used and interaction between the heme groups disregarded. The intrinsic microscopic reduction potential values are closer when the tri-exponential, cooperative model is used as this model transfers 30-40 mV to electrostatically dominated interaction potentials. The overall electron transfer pattern can be related to the recently determined crystal structure of the P. stutzeri cytochrome c4.