Electron sweep across four b-hemes of cytochrome bc1 revealed by unusual paramagnetic properties of the Qi semiquinone intermediate

Dimeric cytochromes bc are central components of photosynthetic and respiratory electron transport chains. In their catalytic core, four hemes b connect four quinone (Q) binding sites. Two of these sites, Q_i sites, reduce quinone to quinol (QH₂) in a step-wise reaction, involving a stable semiquinone intermediate (SQ_i). However, the interaction of the SQ_i with the adjacent hemes remains largely unexplored. Here, by revealing the existence of two populations of SQ_i differing in paramagnetic relaxation, we present a new mechanistic insight into this interaction. Benefiting from a clear separation of these SQ_i species in mutants with a changed redox midpoint potential of hemes b, we identified that the fast-relaxing SQ_i (SQ_iF) corresponds to the form magnetically coupled with the oxidized heme b_H (the heme b adjacent to the Q_i site), while the slow-relaxing SQ_i (SQ_iS) reflects the form present alongside the reduced (and diamagnetic) heme b_H. This so far unreported SQ_iF calls for a reinvestigation of the thermodynamic properties of SQ_i and the Q_i site. The existence of SQ_iF in the native enzyme reveals a possibility of an extended electron equilibration within the dimer, involving all four hemes b and both Q_i sites. This substantiates the predicted earlier electron transfer acting to sweep the b-chain of reduced hemes b to diminish generation of reactive oxygen species by cytochrome bc₁. In analogy to the Q_i site, we anticipate that the quinone binding sites in other enzymes may contain yet undetected semiquinones which interact magnetically with oxidized hemes upon progress of catalytic reactions.     

Proton pumping in the bc1 complex: A new gating mechanism that prevents short circuits

The Q-cycle mechanism of the bc₁ complex explains how the electron transfer from ubihydroquinone (quinol, QH₂) to cytochrome (cyt) c (or c₂ in bacteria) is coupled to the pumping of protons across the membrane. The efficiency of proton pumping depends on the effectiveness of the bifurcated reaction at the Q_o-site of the complex. This directs the two electrons from QH₂ down two different pathways, one to the high potential chain for delivery to an electron acceptor, and the other across the membrane through a chain containing heme b_L and b_H to the Q_i-site, to provide the vectorial charge transfer contributing to the proton gradient. In this review, we discuss problems associated with the turnover of the bc₁ complex that center around rates calculated for the normal forward and reverse reactions, and for bypass (or short-circuit) reactions. Based on rate constants given by distances between redox centers in known structures, these appeared to preclude conventional electron transfer mechanisms involving an intermediate semiquinone (SQ) in the Q_o-site reaction. However, previous research has strongly suggested that SQ is the reductant for O₂ in generation of superoxide at the Q_o-site, introducing an apparent paradox. A simple gating mechanism, in which an intermediate SQ mobile in the volume of the Q_o-site is a necessary component, can readily account for the observed data through a coulombic interaction that prevents SQ anion from close approach to heme b_L when the latter is reduced. This allows rapid and reversible QH₂ oxidation, but prevents rapid bypass reactions. The mechanism is quite natural, and is well supported by experiments in which the role of a key residue, Glu-295, which facilitates proton transfer from the site through a rotational displacement, has been tested by mutation.     

Possible roles of two quinone molecules in direct and indirect proton pumps of bovine heart NADH-quinone oxidoreductase (complex I)

In many energy transducing systems which couple electron and proton transport, for example, bacterial photosynthetic reaction center, cytochrome bc₁-complex (complex III) and E. coli quinol oxidase (cytochrome bo₃ complex), two protein-associated quinone molecules are known to work together. T. Ohnishi and her collaborators reported that two distinct semiquinone species also play important roles in NADH-ubiquinone oxidoreductase (complex I). They were called SQ_Nf (fast relaxing semiquinone) and SQ_Ns (slow relaxing semiquinone). It was proposed that Q_Nf serves as a “direct” proton carrier in the semiquinone-gated proton pump (Ohnishi and Salerno, FEBS Letters 579 (2005) 4555), while Q_Ns works as a converter between one-electron and two-electron transport processes. This communication presents a revised hypothesis in which Q_Nf plays a role in a “direct” redox-driven proton pump, while Q_Ns triggers an “indirect” conformation-driven proton pump. Q_Nf and Q_Ns together serve as (1e^?/2e^?) converter, for the transfer of reducing equivalent to the Q-pool.     

Roles of semiquinone species in proton pumping mechanism by complex I

Complex I (NDH-1) translocates protons across the membrane using electron transfer energy. Two different coupling mechanisms are currently being discussed for complex I: direct (redox-driven) and indirect (conformation-driven). Semiquinone (SQ) intermediates are suggested to be key for the coupling mechanism. Recently, using progressive power saturation and simulation techniques, three distinct SQ species were resolved by EPR analysis of E. coli complex I reconstituted into proteoliposomes. The fast-relaxing SQ (SQ_Nf) signals completely disappeared in the presence of the uncoupler gramicidin D or the potent E. coli complex I inhibitor squamotacin. The slow-relaxing SQ (SQ_Ns) signals were insensitive to gramicidin D, but they were sensitive to squamotacin. The very slow-relaxing SQ (SQ_Nvs) signals were insensitive to both gramicidin D and squamotacin. Interestingly, no SQ_Ns signal was observed in the ΔNuoL mutant, which lacks transporter module subunits NuoL and NuoM. Furthermore, we sought out the effect of using menaquinone (which has a lower redox potential compared to that of ubiquinone) as an electron acceptor on the proton pumping stoichiometry by in vitro reconstitution experiments with ubiquinone-rich or menaquinone-rich double knock-out membrane vesicles, which contain neither complex I nor NDH-2 (non-proton translocating NADH dehydrogenase). No difference in the proton pumping stoichiometry between menaquinone and ubiquinone was observed in the ΔNuoL and D178N mutants, which are considered to lack the indirect proton pumping mechanism. However, the proton pumping stoichiometry with menaquinone decreased by half in the wild-type. The roles and relationships of SQ intermediates in the coupling mechanism of complex I are discussed.     

Discrimination between two possible reaction sequences that create potential risk of generation of deleterious radicals by cytochrome bc1: Implications for the mechanism of superoxide production

In addition to its bioenergetic function of building up proton motive force, cytochrome bc₁ can be a source of superoxide. One-electron reduction of oxygen is believed to occur from semiquinone (SQ_o) formed at the quinone oxidation/reduction Q_o site (Q_o) as a result of single-electron oxidation of quinol by the iron-sulfur cluster (FeS) (semiforward mechanism) or single-electron reduction of quinone by heme b_L (semireverse mechanism). It is hotly debated which mechanism plays a major role in the overall production of superoxide as experimental data supporting either reaction exist. To evaluate a contribution of each of the mechanisms we first measured superoxide production under a broad range of conditions using the mutants of cytochrome bc₁ that severely impeded the oxidation of FeS by cytochrome c₁, changed density of FeS around Q_o by interfering with its movement, or combined these two effects together. We then compared the amount of generated superoxide with mathematical models describing either semiforward or semireverse mechanism framed within a scheme assuming competition between the internal reactions at Q_o and the leakage of electrons on oxygen. We found that only the model of semireverse mechanism correctly reproduced the experimentally measured decrease in ROS for the FeS motion mutants and increase in ROS for the mutants with oxidation of FeS impaired. This strongly suggests that this mechanism dominates in setting steady-state levels of SQ_o that present a risk of generation of superoxide by cytochrome bc₁. Isolation of this reaction sequence from multiplicity of possible reactions at Q_o helps to better understand conditions under which complex III might contribute to ROS generation in vivo.     

Redox-linked protonation state changes in cytochrome bc1 identified by Poisson-Boltzmann electrostatics calculations

Cytochrome bc₁ is a major component of biological energy conversion that exploits an energetically favourable redox reaction to generate a transmembrane proton gradient. Since the mechanistic details of the coupling of redox and protonation reactions in the active sites are largely unresolved, we have identified residues that undergo redox-linked protonation state changes. Structure-based Poisson-Boltzmann/Monte Carlo titration calculations have been performed for completely reduced and completely oxidised cytochrome bc₁. Different crystallographically observed conformations of Glu272 and surrounding residues of the cytochrome b subunit in cytochrome bc₁ from Saccharomyces cerevisiae have been considered in the calculations. Coenzyme Q (CoQ) has been modelled into the CoQ oxidation site (Q_o-site). Our results indicate that both conformational and protonation state changes of Glu272 of cytochrome b may contribute to the postulated gating of CoQ oxidation. The Rieske iron-sulphur cluster could be shown to undergo redox-linked protonation state changes of its histidine ligands in the structural context of the CoQ-bound Q_o-site. The proton acceptor role of the CoQ ligands in the CoQ reduction site (Q_i-site) is supported by our results. A modified path for proton uptake towards the Q_i-site features a cluster of conserved lysine residues in the cytochrome b (Lys228) and cytochrome c₁ subunits (Lys288, Lys289, Lys296). The cardiolipin molecule bound close to the Q_i-site stabilises protons in this cluster of lysine residues.     

New interpretation of the redox properties of cytochrome b559 in photosystem II

A model of heme–quinone redox interaction has been developed for cytochrome b559 in photosystem II. The quinone Q_C in the singly protonated form may function as an interacting quinone. The electrostatic effect between the charges on the heme iron of the cytochrome and Q_CH leads to appearance of three forms of the cytochrome with different redox potentials. A simple and effective mechanism of redox regulation of the electron transfer pathways in photosystem II is proposed.     

Direct and mediated electron transfer between intact succinate:quinone oxidoreductase from Bacillus subtilis and a surface modified gold electrode reveals redox state-dependent conformational changes

Succinate:quinone oxidoreductase (SQR) from Bacillus subtilis consists of two hydrophilic protein subunits comprising succinate dehydrogenase, and a di-heme membrane anchor protein harboring two putative quinone binding sites, Q_p and Q_d. In this work we have used spectroelectrochemistry to study the electronic communication between purified SQR and a surface modified gold capillary electrode. In the presence of two soluble quinone mediators the midpoint potentials of both hemes were revealed essentially as previously determined by conventional redox titration (heme b_H, E_m = + 65 mV, heme b_L, E_m = − 95 mV). In the absence of mediators the enzyme still communicated with the electrode, albeit with a reproducible hysteresis, resulting in the reduction of both hemes occurring approximately at the midpoint potential of heme b_L, and with a pronounced delay of reoxidation. When the specific inhibitor 2-n-heptyl-4 hydroxyquinoline N-oxide (HQNO), which binds to Q_d in B. subtilis SQR, was added together with the two quinone mediators, rapid reductive titration was still possible which can be envisioned as an electron transfer occurring via the HQNO insensitive Q_p site. In contrast, the subsequent oxidative titration was severely hampered in the presence of HQNO, in fact it completely resembled the unmediated reaction. If mediators communicate with Q_p or Q_d, either event is followed by very rapid electron redistribution within the enzyme. Taken together, this strongly suggests that the accessibility of Q_p depended on the redox state of the hemes. When both hemes were reduced, and Q_d was blocked by HQNO, quinone-mediated communication via the Q_p site was no longer possible, revealing a redox-dependent conformational change in the membrane anchor domain.     

Determination of the proton environment of high stability Menasemiquinone intermediate in Escherichia coli nitrate reductase A by pulsed EPR

Escherichia coli nitrate reductase A (NarGHI) is a membrane-bound enzyme that couples quinol oxidation at a periplasmically oriented Q-site (Q_D) to proton release into the periplasm during anaerobic respiration. To elucidate the molecular mechanism underlying such a coupling, endogenous menasemiquinone-8 intermediates stabilized at the Q_D site (MSQ_D) of NarGHI have been studied by high-resolution pulsed EPR methods in combination with ¹H₂O/²H₂O exchange experiments. One of the two non-exchangeable proton hyperfine couplings resolved in hyperfine sublevel correlation (HYSCORE) spectra of the radical displays characteristics typical from quinone methyl protons. However, its unusually small isotropic value reflects a singularly low spin density on the quinone carbon α carrying the methyl group, which is ascribed to a strong asymmetry of the MSQ_D binding mode and consistent with single-sided hydrogen bonding to the quinone oxygen O1. Furthermore, a single exchangeable proton hyperfine coupling is resolved, both by comparing the HYSCORE spectra of the radical in ¹H₂O and ²H₂O samples and by selective detection of the exchanged deuterons using Q-band ²H Mims electron nuclear double resonance (ENDOR) spectroscopy. Spectral analysis reveals its peculiar characteristics, i.e. a large anisotropic hyperfine coupling together with an almost zero isotropic contribution. It is assigned to a proton involved in a short ∼1.6 Å in-plane hydrogen bond between the quinone O1 oxygen and the Nδ of the His-66 residue, an axial ligand of the distal heme b_D. Structural and mechanistic implications of these results for the electron-coupled proton translocation mechanism at the Q_D site are discussed, in light of the unusually high thermodynamic stability of MSQ_D.     

A reevaluation of the events leading to the electrogenic reaction and proton translocation in the ubiquinol-cytochrome c oxidoreductase of Rhodopseudomonas sphaeroides

Chromatophore membranes from Rhodopseudomonas sphaeroides activated by light display a carotenoid band shift (phase III) that occurs in response to the electrogenic event (charge separation) in the ubiquinol-cytochrome c oxidoreductase. The rate of formation of this electrogenic event has previously been shown to be strongly dependent on the initial redox state of a bound ubiquinone species (designated Q_z) associated with the oxidoreductase. When Q_z is reduced (quinol form; Q_zH₂) the electrogenic event takes place in less than 5 ms. When Q_z is oxidized (quinone form; Q_z) it is much slower; under these conditions the fact that it occurs has been ignored. In this report, we address this issue and describe events that lead to the generation of carotenoid band shift phase III when the total population of Q_z of the chromatophore is oxidized before flash activation. The following characteristics are apparent: (1) When oxidized Q_z is present before activation, the half-time of formation of carotenoid band-shift phase III is 10–20-times slower than when Q_zH₂ is present before activation. (2) When oxidized Q_z is present, the measured full extent of phase III generated by a single-turnover flash is diminished by about one-half of that observed when Q_zH₂ is present before activation. (3) The rate of formation of the carotenoid band shift phase III when Q_z is initially oxidized corresponds closely to the rate of completion of the flash-activated electron-transfer cycle. This can be seen under two different conditions: (a) as the partial reduction of cytochrome c₁ + c₂ (at redox potentials of 200–300 mV) or (b) as the partial reduction of flash-oxidized bacteriochlorophyll dimer, (BChl)₂⁺ (at redox potentials above 300 mV). (4) At the higher redox potentials (above 300 mV), antimycin-sensitive proton binding shares a common, rate-limiting step with the carotenoid band shift phase III and (BChl)₂⁺ reduction. (5) However, proton binding at redox potentials above 300 mV is not observed at all unless valinomycin (K⁺) is present. Thus, proton binding occurs only when the carotenoid band shift is collapsed in milliseconds, whereas, conversely, the carotenoid band shift is stably generated when proton binding is not observed. These and other observations are the basis of a reevaluation of our current views on the coupling of electron transfer and proton translocation in photosynthetic bacteria.     

Is the Redox State of the ci Heme of the Cytochrome b6f Complex Dependent on the Occupation and Structure of the Qi Site and Vice Versa?

Oxidoreductases of the cytochrome bc₁/b₆f family transfer electrons from a liposoluble quinol to a soluble acceptor protein and contribute to the formation of a transmembrane electrochemical potential. The crystal structure of cyt b₆f has revealed the presence in the Q_i site of an atypical c-type heme, heme c_i. Surprisingly, the protein does not provide any axial ligand to the iron of this heme, and its surrounding structure suggests it can be accessed by exogenous ligand. In this work we describe a mutagenesis approach aimed at characterizing the c_i heme and its interaction with the Q_i site environment. We engineered a mutant of Chlamydomonas reinhardtii in which Phe⁴⁰ from subunit IV was substituted by a tyrosine. This results in a dramatic slowing down of the reoxidation of the b hemes under single flash excitation, suggesting hindered accessibility of the heme to its quinone substrate. This modified accessibility likely originates from the ligation of the heme iron by the phenol(ate) side chain introduced by the mutation. Indeed, it also results in a marked downshift of the c_i heme midpoint potential (from +100 mV to −200 mV at pH 7). Yet the overall turnover rate of the mutant cytochrome b₆f complex under continuous illumination was found similar to the wild type one, both in vitro and in vivo. We propose that, in the mutant, a change in the ligation state of the heme upon its reduction could act as a redox switch that would control the accessibility of the substrate to the heme and trigger the catalysis.The cytochrome b₆f complex of oxygenic photosynthesis is the integral membrane protein, the quinol:plastocyanin oxido-reductase activity of which allows the linear electron flow between the two photosystems (PSI and PSII).⁴ The turnover of the cytochrome b₆f complex depends on the steady state of its redox partners, the liposoluble plastoquinol (PQH₂ reduced and protonated plastoquinone PQ) formed by the PSII, and the hydrosoluble plastocyanin oxidized by the PSI. In the Q_o site, exposed to the lumenal side, the quinol is oxidized, and this oxidation is coupled to the release of two protons into the lumen. The two electrons provided by the quinol are transferred along two bifurcated pathways, the high and low potential chains. The high potential chain involves two lumenal redox partners, the membrane-anchored flexible Rieske [2Fe-2S] cluster and the cytochrome f, which ultimately interacts with the soluble plastocyanin. In the low potential chain, electrons are transferred to the stroma via the low and high potential b hemes (b_L and b_H) of the transmembrane b₆ subunit. Two turnovers of the cyt b₆f complex lead to the reduction of the low potential chain, thereby allowing the reduction of a quinone molecule in the stromal Q_i pocket. This mechanism, which recycles reducing equivalents, is referred to as the “Q cycle,” initially described by Mitchell (1) and modified later by Crofts et al. and others (2, 3).Although this quinol:cytochrome oxidoreductase activity is involved in both the respiratory and photosynthetic electron transfer chains, recent x-ray data (4–6) have evidenced major structural differences between the b₆f complex and its mitochondrial counterpart the bc₁ complex (for reviews see Refs. 7–10). Indeed an additional heme localized in close contact with heme b_H stands as another putative electron carrier as proposed earlier by Lavergne (11). Since it was brought to light by the x-ray studies, knowledge of the basic properties of this heme, named c_i in reference to the Q_i site (5) or c_n in reference to its proximity to the negatively charged side of the membrane (4), has significantly improved. The proteins involved in the assembly machinery of the heme have been identified in Chlamydomonas reinhardtii and Arabidopsis thaliana (12, 13). Consistent with the structure, according to which the only axial ligand could be a water molecule interacting with the proponiate chain of the b_H heme, the spectroscopic properties of this heme are those of a high spin heme (14, 15). Evidences for a high spin heme covalently bound to the cytochrome b subunit were also found in Heliobacterium modesticaldum and Heliobacillus mobilis (16).In the b₆f complex from the oxygenic photosynthetic chain, EPR (15) and structural data (17) have shown that NQNO (2-n-nony l-4-hydroxyquinoline N-oxide), an inhibitor of the Q_i pocket (18, 19), can act as an axial ligand to c_i. This ligation is accompanied by a significant change in the redox properties of c_i, because, in the presence of NQNO, at least two titrations waves were observed (13, 14), one with a midpoint potential (E_m) similar to that observed in the absence of NQNO and the other with a midpoint potential downshifted by ∼250 mV. This, together with the widespread range of redox potential found for heme c_i (11, 14, 15, 20), points to a structural plasticity of the c_i ligand network.This plasticity may arise from the unusual coordination properties of the heme c_i. As a matter of fact, the x-ray models of the complex from C. reinhardtii and Mastigocladus laminosus evidenced a water or hydroxyl molecule as a fifth ligand. The sixth position of coordination is directed toward the Q_i pocket and appears as free. Nevertheless, the side chain of Phe⁴⁰ of subunit IV protrudes above the heme plane, leaving little space for any axial ligand to the heme c_i. Besides, modeling a quinone analogue in the electron density found in the Q_i pocket of structures obtained in presence of Tridecyl- Stigmatellin or NQNO implies a steric clash with the native position of the Phe⁴⁰ aromatic ring.⁵ The Phe⁴⁰ residue of subunit IV therefore stands as a key residue for the plasticity of the site, making it an ideal mutagenesis target when attempting to alter the possible interactions between c_i and the quinone or quinol (4, 5) (Fig. 1). Here we present the consequences of the substitution of Phe⁴⁰ by a tyrosine on the properties and function of the c_i heme.Open in a separate windowFIGURE 1.A view of the Q_i site from the dimer interface. The coordinates are from the Protein Data Bank 1Q90 model. The Van der Waal''s surface of the peptide chains was drawn with Pymol. Phe⁴⁰ is in van der Waal''s contact with the plane of the c_i, heme.     

The influence of hydrogen bonds on electron transfer rate in photosynthetic RCs

Hydrogen bonds formed between photosynthetic reaction centers (RCs) and their cofactors were shown to affect the efficacy of electron transfer. The mechanism of such influence is determined by sensitivity of hydrogen bonds to electron density rearrangements, which alter hydrogen bonds potential energy surface. Quantum chemistry calculations were carried out on a system consisting of a primary quinone Q_A, non-heme Fe²⁺ ion and neighboring residues_. The primary quinone forms two hydrogen bonds with its environment, one of which was shown to be highly sensitive to the Q_A state. In the case of the reduced primary quinone two stable hydrogen bond proton positions were shown to exist on [Q_A-His^M219] hydrogen bond line, while there is only one stable proton position in the case of the oxidized primary quinone. Taking into account this fact and also the ability of proton to transfer between potential energy wells along a hydrogen bond, theoretical study of temperature dependence of hydrogen bond polarization was carried out. Current theory was successfully applied to interpret dark P⁺/Q_A⁻ recombination rate temperature dependence.     

Redox potential of the non-heme iron complex in bacterial photosynthetic reaction center

In bacterial photosynthetic reaction centers (bRC), the electron is transferred from the special pair (P) via accessory bacteriochlorophyll (B_A), bacteriopheopytin (H_A), the primary quinone (Q_A) to the secondary quinone (Q_B). Although the non-heme iron complex (Fe complex) is located between Q_A and Q_B, it was generally supposed not to be redox-active. Involvement of the Fe complex in electron transfer (ET) was proposed in recent FTIR studies [A. Remy and K. Gerwert, Coupling of light-induced electron transfer to proton uptake in photosynthesis, Nat. Struct. Biol. 10 (2003) 637-644]. However, other FTIR studies resulted in opposite results [J. Breton, Steady-state FTIR spectra of the photoreduction of Q_A and Q_B in Rhodobacter sphaeroides reaction centers provide evidence against the presence of a proposed transient electron acceptor X between the two quinones, Biochemistry 46 (2007) 4459-4465]. In this study, we calculated redox potentials of Q_A/B (E_m(Q_A/B)) and the Fe complex (E_m(Fe)) based on crystal structure of the wild-type bRC (WT-bRC), and we investigated the energetics of the system where the Fe complex is assumed to be involved in the ET. E_m(Fe) in WT-bRC is much less pH-dependent than that in PSII. In WT-bRC, we observed significant coupling of ET with Glu-L212 protonation upon oxidation of the Fe complex and a dramatic E_m(Fe) downshift by 230 mV upon formation of Q_A⁻ (but not Q_B⁻) due to the absence of proton uptake of Glu-L212. Changes in net charges of the His ligands of the Fe complex appear to be the nature of the redox event if we assume the involvement of the Fe complex in the ET.     

Hybrid fusions show that inter-monomer electron transfer robustly supports cytochrome bc1 function in vivo

Electronic connection between Q_o and Q_i quinone catalytic sites of dimeric cytochrome bc₁ is a central feature of the energy-conserving Q cycle. While both the intra- and inter-monomer electron transfers were shown to connect the sites in the enzyme, mechanistic and physiological significance of the latter remains unclear. Here, using a series of mutated hybrid cytochrome bc₁-like complexes, we show that inter-monomer electron transfer robustly sustains the function of the enzyme in vivo, even when the two subunits in a dimer come from different species. This indicates that minimal requirement for bioenergetic efficiency is to provide a chain of cofactors for uncompromised electron flux between the catalytic sites, while the details of protein scaffold are secondary.     

Tuning of Hemes b Equilibrium Redox Potential Is Not Required for Cross-Membrane Electron Transfer

In biological energy conversion, cross-membrane electron transfer often involves an assembly of two hemes b. The hemes display a large difference in redox midpoint potentials (ΔE_{m_}b), which in several proteins is assumed to facilitate cross-membrane electron transfer and overcome a barrier of membrane potential. Here we challenge this assumption reporting on heme b ligand mutants of cytochrome bc₁ in which, for the first time in transmembrane cytochrome, one natural histidine has been replaced by lysine without loss of the native low spin type of heme iron. With these mutants we show that ΔE_{m_}b can be markedly increased, and the redox potential of one of the hemes can stay above the level of quinone pool, or ΔE_{m_}b can be markedly decreased to the point that two hemes are almost isopotential, yet the enzyme retains catalytically competent electron transfer between quinone binding sites and remains functional in vivo. This reveals that cytochrome bc₁ can accommodate large changes in ΔE_{m_}b without hampering catalysis, as long as these changes do not impose overly endergonic steps on downhill electron transfer from substrate to product. We propose that hemes b in this cytochrome and in other membranous cytochromes b act as electronic connectors for the catalytic sites with no fine tuning in ΔE_{m_}b required for efficient cross-membrane electron transfer. We link this concept with a natural flexibility in occurrence of several thermodynamic configurations of the direction of electron flow and the direction of the gradient of potential in relation to the vector of the electric membrane potential.     

Carboxylate shifts steer interquinone electron transfer in photosynthesis

Understanding the mechanisms of electron transfer (ET) in photosynthetic reaction centers (RCs) may inspire novel catalysts for sunlight-driven fuel production. The electron exit pathway of type II RCs comprises two quinone molecules working in series and in between a non-heme iron atom with a carboxyl ligand (bicarbonate in photosystem II (PSII), glutamate in bacterial RCs). For decades, the functional role of the iron has remained enigmatic. We tracked the iron site using microsecond-resolution x-ray absorption spectroscopy after laser-flash excitation of PSII. After formation of the reduced primary quinone, Q_A⁻, the x-ray spectral changes revealed a transition (t_½ ≈ 150 μs) from a bidentate to a monodentate coordination of the bicarbonate at the Fe(II) (carboxylate shift), which reverted concomitantly with the slower ET to the secondary quinone Q_B. A redox change of the iron during the ET was excluded. Density-functional theory calculations corroborated the carboxylate shift both in PSII and bacterial RCs and disclosed underlying changes in electronic configuration. We propose that the iron-carboxyl complex facilitates the first interquinone ET by optimizing charge distribution and hydrogen bonding within the Q_AFeQ_B triad for high yield Q_B reduction. Formation of a specific priming intermediate by nuclear rearrangements, setting the stage for subsequent ET, may be a common motif in reactions of biological redox cofactors.     

Characterizing the effects of the protein environment on the reduction potentials of metalloproteins

The reduction potentials of electron transfer proteins are critically determined by the degree of burial of the redox site within the protein and the degree of permanent polarization of the polypeptide around the redox site. Although continuum electrostatics calculations of protein structures can predict the net effect of these factors, quantifying each individual contribution is a difficult task. Here, the burial of the redox site is characterized by a dielectric radius R _p (a Born-type radius for the protein), the polarization of the polypeptide is characterized by an electret potential ? _p (the average electrostatic potential at the metal atoms), and an electret-dielectric spheres (EDS) model of the entire protein is then defined in terms of R _p and ? _p. The EDS model shows that for a protein with a redox site of charge Q, the dielectric response free energy is a function of Q ², while the electret energy is a function of Q. In addition, R _p and ? _p are shown to be characteristics of the fold of a protein and are predictive of the most likely redox couple for redox sites that undergo different redox couples.     

Redox-coupled proton transfer in the active site of cytochrome cbb3

Cytochrome cbb₃ is a distinct member of the superfamily of respiratory heme-copper oxidases, and is responsible for driving the respiratory chain in many pathogenic bacteria. Like the canonical heme-copper oxidases, cytochrome cbb₃ reduces oxygen to water and couples the released energy to pump protons across the bacterial membrane. Homology modeling and recent electron paramagnetic resonance (EPR) studies on wild type and a mutant cbb₃ enzyme [V. Rauhamäki et al. J. Biol. Chem. 284 (2009) 11301-11308] have led us to perform high-level quantum chemical calculations on the active site. These calculations bring molecular insight into the unique hydrogen bonding between the proximal histidine ligand of heme b₃ and a conserved glutamate, and indicate that the catalytic mechanism involves redox-coupled proton transfer between these residues. The calculated spin densities give insight in the difference in EPR spectra for the wild type and a recently studied E383Q-mutant cbb₃-enzyme. Furthermore, we show that the redox-coupled proton movement in the proximal cavity of cbb₃-enzymes contributes to the low redox potential of heme b₃, and suggest its potential implications for the high apparent oxygen affinity of these enzymes.     

The proton pumping mechanism of the bc1 complex

The bc₁ complex is a proton pump of the mitochondrial electron transport chain which transfers electrons from ubiquinol to cytochrome c. It operates via the modified Q cycle in which the two electrons from oxidation of ubiquinol at the Q_o center are bifurcated such that the first electron is passed to Cytc via an iron sulfur center and c₁ whereas the second electron is passed across the membrane by b_L and b_H to reduce ubiquinone at the Q_i center. Proton pumping occurs because oxidation of ubiquinol at the Q_o center releases protons to the P-side and reduction of ubiquinone at the Q_i center takes up protons from the N-side. However, the mechanisms which prevent the thermodynamically more favorable short circuit reactions and so ensure precise bifurcation and proton pumping are not known. Here we use statistical thermodynamics to show that reaction steps that originate from high energy states cannot support high flux even when they have large rate constants. We show how the chemistry of ubiquinol oxidation and the structure of the Q_o site can result in free energy profiles that naturally suppress flux through the short circuit pathways while allowing high rates of bifurcation. These predictions are confirmed through in-silico simulations using a Markov state model.     

Acetate in mixotrophic growth medium affects photosystem II in Chlamydomonas reinhardtii and protects against photoinhibition

Chlamydomonas reinhardtii is a photoautotrophic green alga, which can be grown mixotrophically in acetate-supplemented media (Tris–acetate–phosphate). We show that acetate has a direct effect on photosystem II (PSII). As a consequence, Tris–acetate–phosphate-grown mixotrophic C. reinhardtii cultures are less susceptible to photoinhibition than photoautotrophic cultures when subjected to high light. Spin-trapping electron paramagnetic resonance spectroscopy showed that thylakoids from mixotrophic C. reinhardtii produced less ¹O₂ than those from photoautotrophic cultures. The same was observed in vivo by measuring DanePy oxalate fluorescence quenching. Photoinhibition can be induced by the production of ¹O₂ originating from charge recombination events in photosystem II, which are governed by the midpoint potentials (E_m) of the quinone electron acceptors. Thermoluminescence indicated that the E_m of the primary quinone acceptor (Q_A/Q_A⁻) of mixotrophic cells was stabilised while the E_m of the secondary quinone acceptor (Q_B/Q_B⁻) was destabilised, therefore favouring direct non-radiative charge recombination events that do not lead to ¹O₂ production. Acetate treatment of photosystem II-enriched membrane fragments from spinach led to the same thermoluminescence shifts as observed in C. reinhardtii, showing that acetate exhibits a direct effect on photosystem II independent from the metabolic state of a cell. A change in the environment of the non-heme iron of acetate-treated photosystem II particles was detected by low temperature electron paramagnetic resonance spectroscopy. We hypothesise that acetate replaces the bicarbonate associated to the non-heme iron and changes the environment of Q_A and Q_B affecting photosystem II charge recombination events and photoinhibition.