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

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.

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.

On rate limitations of electron transfer in the photosynthetic cytochrome b6f complex

Considering information in the crystal structures of the cytochrome b(6)f complex relevant to the rate-limiting step in oxygenic photosynthesis, it is enigmatic that electron transport in the complex is not limited by the large distance, approximately 26 Å, between the iron-sulfur cluster (ISP) and its electron acceptor, cytochrome f. This enigma has been explained for the respiratory bc(1) complex by a crystal structure with a greatly shortened cluster-heme c(1) distance, leading to a concept of ISP dynamics in which the ISP soluble domain undergoes a translation-rotation conformation change and oscillates between positions relatively close to the cyt c(1) heme and a membrane-proximal position close to the ubiquinol electron-proton donor. Comparison of cytochrome b(6)f structures shows a variation in cytochrome f heme position that suggests the possibility of flexibility and motion of the extended cytochrome f structure that could entail a transient decrease in cluster-heme f distance. The dependence of cyt f turnover on lumen viscosity is consistent with a role of ISP - cyt f dynamics in determination of the rate-limiting step under conditions of low light intensity. Under conditions of low light intensity and proton electrochemical gradient present, for example, under a leaf canopy, it is proposed that a rate limitation of electron transport in the b(6)f complex may also arise from steric constraints in the entry/exit portal for passage of the plastoquinol and -quinone to/from its oxidation site proximal to the iron-sulfur cluster.

Study on energy transfer between carotenoid and chlorophyll a in cytochrome b6f complex from Bryopsis corticulans

The excitation energy transfer between carotenoid and chlorophyll (Chl) in the cytochrome b ( 6 ) f complex from Bryopsis corticulans (B. corticulans), in which the carotenoid is 9-cis-alpha-carotene, was investigated by means of fluorescence excitation and sub-microsecond time-resolved absorption spectroscopies. The presence of efficient singlet excitation transfer from alpha-carotene to Chl a was found with an overall efficiency as high as approximately approximately 24%, meanwhile the Chl a-to-alpha-carotene triplet excitation transfer was also evidenced. Circular dichroism spectroscopy showed that alpha-carotene molecule existed in an asymmetric environment and Chl a molecule had a certain orientation in this complex.

Characterization of the cytochrome b(6)f complex from marine green alga, Bryopsis corticulans

A pure, active cytochrome b(6)f was isolated from the chloroplasts of the marine green alga, Bryopsis corticulans. To investigate and characterize this cytochrome b(6)f complex, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), absorption spectra measurement and HPLC were employed. It was shown that this purified complex contained four large subunits with apparent molecular masses of 34.8, 24, 18.7 and 16.7 kD. The ratio of Cyt (6) to Cyt f was 2.01 : 1. The cytochrome b(6) f was shown to catalyze the transfer of 73 electrons from decylplastoquinol to plastocyanin-ferricyanide per Cyt f per second. alpha-Carotene, one kind of carotenoid that has not been found to present in cytochrome b(6)f complex, was discovered in this preparation by reversed phase HPLC. It was different from beta-carotene usually found in cytochrome b(6)f complex. The configuration of the major alpha-carotene component was assigned to be 9-cis by resonance Raman spectroscopy. Different from the previous reports, the configuration of this alpha-carotene in dissociated state was determined to be all-trans. Besides this carotene, chlorophyll a was also found in this complex. It was shown that the molecular ratios of chlorophyll a, cis and all-trans-alpha-carotene to Cyt f in this complex were 1.2, 0.7 and 0.2, respectively.

Functional implications of pigments bound to a cyanobacterial cytochrome b6f complex

A highly purified cytochrome b(6)f complex from the cyanobacterium Synechocystis sp. PCC 6803 selectively binds one chlorophyll a and one carotenoid in analogy to the recent published structure from two other b(6)f complexes. The unknown function of these pigments was elucidated by spectroscopy and site-directed mutagenesis. Low-temperature redox difference spectroscopy showed red shifts in the chlorophyll and carotenoid spectra upon reduction of cytochrome b(6), which indicates coupling of these pigments with the heme groups and thereby with the electron transport. This is supported by the correlated kinetics of these redox reactions and also by the distinct orientation of the chlorophyll molecule with respect to the heme cofactors as shown by linear dichroism spectroscopy. The specific role of the carotenoid echinenone for the cytochrome b(6)f complex of Synechocystis 6803 was elucidated by a mutant lacking the last step of echinenone biosynthesis. The isolated mutant complex preferentially contained a carotenoid with 0, 1 or 2 hydroxyl groups (most likely 9-cis isomers of beta-carotene, a monohydroxy carotenoid and zeaxanthin, respectively) instead. This indicates a substantial role of the carotenoid - possibly for strucure and assembly - and a specificity of its binding site which is different from those in most other oxygenic photosynthetic organisms. In summary, both pigments are probably involved in the structure, but may also contribute to the dynamics of the cytochrome b(6)f complex.

Linear dichroism of biomolecules: which way is up?

Understanding the organization of molecules in naturally occurring ordered arrays (e.g. membranes, protein fibres and DNA strands) is of great importance to understanding biological function. Unfortunately, few biophysical techniques provide detailed structural information on these non-crystalline systems. UV, visible and IR linear dichroism have the potential to provide such information. Recent advances in technology and simulations allow this potential to be fulfilled, and can now provide a detailed understanding of the molecular mechanisms of such fundamental biological processes as amyloid fibre formation and membrane protein folding.

Spectroscopic studies on electron transfer between plastocyanin and cytochrome b6f complex

This paper reports the results of the research on the interaction between the highly active cytochrome b(6)f complex and plastocyanin, both isolated from the same source - spinachia oleracea plants. An equilibrium constant K between the cytochrome f of the cytochrome b(6)f complex and plastocyanin has been estimated by two independent spectroscopic techniques: steady-state absorption spectroscopy and stopped-flow. The second-order rate constants k2 for forward and backward electron transfer between cytochrome f and plastocyanin have been found between 1.4-2 x 10(7) and 8-10 x 10(6) M(-1)s(-1), respectively, giving the value of an equilibrium constant of about 2+/-0.4 or a difference in redox potential between plastocyanin and cytochrome f of cytochrome b(6)f complex of ca. 17 mV. The value of K=1.7+/-0.3 has been estimated from steady-state experiments in which the initial and final concentrations of participating components after mixing have been estimated via differential spectra analysis or spectra deconvolution. We propose a method of evaluation of the final plastocyanin concentration after the electron transfer reaction between cytochrome bf complex and plastocyanin that overcomes the interference by the strong chlorophyll absorption in the spectral region where oxidised plastocyanin has its low extinction absorption band. The data from both experiments, in the system devoid of quinol being the electron donor to cytochrome b(6), suggest that in case of electron transfer from cytochrome f to plastocyanin electron transfer can either bypass cytochrome f or the Rieske iron-sulfur protein can be reduced prior to its movement to the quinol binding site of cytochrome b(6). The role of the Rieske protein in forward and backward electron transfer reactions is discussed.

An atypical haem in the cytochrome b6f complex

Photosystems I and II (PSI and II) are reaction centres that capture light energy in order to drive oxygenic photosynthesis; however, they can only do so by interacting with the multisubunit cytochrome b(6)f complex. This complex receives electrons from PSII and passes them to PSI, pumping protons across the membrane and powering the Q-cycle. Unlike the mitochondrial and bacterial homologue cytochrome bc(1), cytochrome b(6)f can switch to a cyclic mode of electron transfer around PSI using an unknown pathway. Here we present the X-ray structure at 3.1 A of cytochrome b(6)f from the alga Chlamydomonas reinhardtii. The structure bears similarities to cytochrome bc(1) but also exhibits some unique features, such as binding chlorophyll, beta-carotene and an unexpected haem sharing a quinone site. This haem is atypical as it is covalently bound by one thioether linkage and has no axial amino acid ligand. This haem may be the missing link in oxygenic photosynthesis.

Functional insensitivity of the cytochrome b6f complex to structure changes in the hinge region of the Rieske iron-sulfur protein

Structure analysis of the cytochrome bc1 complex in the presence and absence of Qp quinol analog inhibitors implied that a large amplitude motion of the Rieske iron-sulfur protein (ISP) is required to mediate electron transfer from ubiquinol to cytochrome c1. Studies of the functional consequences of mutagenesis of an 8-residue ISP "hinge" region in the bc1 complex showed it to be sensitive to structure perturbation, implying that optimum flexibility and length are required for the large amplitude motion. Mutagenesis-function analysis carried out on the ISP hinge region of the cytochrome b6 f complex using the cyanobacterium Synechococcus sp. PCC 7002 showed the following. (i) Of three petC genes, only that in the petCA operon codes for functional ISP. (ii) The function of the complex was insensitive to changes in the hinge region that increased flexibility, decreased flexibility by substitutions of 4-6 Pro residues, shortened the hinge by a 1-residue deletion, or elongated it by insertion of 4 residues. The latter change increased sensitivity to Qp inhibitors, whereas deletion of 2 residues resulted in a loss of inhibitor sensitivity and a decrease in activity, indicating a minimum hinge length of 7 residues required for optimum binding of ISP at the Qp site. Thus, in contrast to the bc1 complex, the function of the b6 f complex was insensitive to sequence changes in the ISP hinge that altered its length or flexibility. This implies that either the barriers to motion or the amplitude of ISP motion required for function is smaller than in the bc1 complex.

Isolation of membrane protein subunits in their native state: evidence for selective binding of chlorophyll and carotenoid to the b(6) subunit of the cytochrome b(6)f complex

Cytochrome (cyt) b-c complexes play a central role in electron transfer chains and are almost ubiquitous in nature. Although similar in their basic structure and function, the cyt b(6)f complex of photosynthetic membranes and its counterpart, the mitochondrial cyt bc(1) complex, show some characteristic differences which cannot be explained by the high resolution structure of the cyt bc(1) complex alone. Especially the presence of a chlorophyll molecule is a striking feature of all cyt b(6)f complex preparations described so far, imposing questions as to its structural and functional role. To allow a more detailed characterization, we here report the preparation of native subunits cyt b(6) and IV starting from a monomeric cyanobacterial cyt b(6)f complex. Spectroscopical and reversed-phase HPLC analyses of the purified cyt b(6) subunit showed that it contained not only two b-type hemes, but also one chlorophyll a molecule and a cyanobacterial carotenoid, echinenone. Evidence for selective binding of both pigments to this subunit is presented and their putative function is discussed.

Helical membrane protein folding, stability, and evolution

Helical membrane protein folding and oligomerization can be usefully conceptualized as involving two energetically distinct stages-the formation and subsequent side-to-side association of independently stable transbilayer helices. The interactions of helices with the bilayer, with prosthetic groups, and with each other are examined in the context of recent evidence. We conclude that the two-stage concept remains useful as an approach to simplifying discussions of stability, as a framework for folding concepts, and as a basis for understanding membrane protein evolution.

Structure and function of cytochrome bc complexes

The cytochrome bc complexes represent a phylogenetically diverse group of complexes of electron-transferring membrane proteins, most familiarly represented by the mitochondrial and bacterial bc1 complexes and the chloroplast and cyanobacterial b6f complex. All these complexes couple electron transfer to proton translocation across a closed lipid bilayer membrane, conserving the free energy released by the oxidation-reduction process in the form of an electrochemical proton gradient across the membrane. Recent exciting developments include the application of site-directed mutagenesis to define the role of conserved residues, and the emergence over the past five years of X-ray structures for several mitochondrial complexes, and for two important domains of the b6f complex.

The cytochrome b(6)f complex: structural studies and comparison with the bc(1) complex

Electron crystallography of the chloroplastic b(6)f complex allowed the calculation of projection maps of crystals negatively stained or embedded in glucose. This gives insights into the overall structure of the extra- and transmembrane domains of the complex. A comparison with the structure of the bc(1) complex, the mitochondrial homologue of the b(6)f complex, suggests that the transmembrane domains of the two complexes are very similar, confirming the structural homology deduced from sequence analysis. On the other hand, the extramembrane organisation of the c-type cytochrome and of the Rieske protein seems quite different. Nevertheless, the same type of movement of the Rieske protein is observed in the b(6)f as in the bc(1) complex upon the binding of the quinol analogue stigmatellin. Crystallographic data also suggest movements in the transmembrane domains of the b(6)f complex, which would be specific of the b(6)f complex.

Conformational changes in the cytochrome b6f complex induced by inhibitor binding

Binding of stigmatellin, an inhibitor of the Q(o) site of the bc-type complexes, has been shown to induce large conformational changes of the Rieske protein in the respiratory bc(1) complex (Kim, H., Xia, D., Yu, C. A., Xia, J. Z., Kachurin, A. M., Zhang, L., Yu, L., and Deisenhofer, J. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 8026-8033; Iwata, S., Lee, J. W., Okada, K., Lee, J. K., Iwata, M., Rasmussen, B., Link, T. A., Ramaswamy, S., and Jap, B. K. (1998) Science 281, 64-71; Zhang, Z., Huang, L., Shulmeister, V. M., Chi, Y. I., Kim, K. K., Hung, L. W., Crofts, A. R., Berry, E. A., and Kim, S. H. (1998) Nature 392, 677-684). Such a movement seems necessary to shuttle electrons from the membrane-soluble quinol to the extramembrane heme of cytochrome c(1). To see whether similar changes occur in the related photosynthetic b(6)f complex, we have studied the effect of the binding of stigmatellin to the eukaryotic b(6)f complex by electron crystallography. Comparison of projection maps of thin three-dimensional crystals prepared with or without stigmatellin, and either negatively stained or embedded in glucose, reveals a similar type of movement to that observed in the bc(1) complex and suggests also the occurrence of conformational changes in the transmembrane region.

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.