Determination of the amount and the type of quinones present in single crystals from reaction center protein from the photosynthetic bacterium Rhodopseudomonas viridis

Lipidic cubic phase serial femtosecond crystallography structure of a photosynthetic reaction centre

Serial crystallography is a rapidly growing method that can yield structural insights from microcrystals that were previously considered to be too small to be useful in conventional X-ray crystallography. Here, conditions for growing microcrystals of the photosynthetic reaction centre of Blastochloris viridis within a lipidic cubic phase (LCP) crystallization matrix that employ a seeding protocol utilizing detergent-grown crystals with a different crystal packing are described. LCP microcrystals diffracted to 2.25 Å resolution when exposed to XFEL radiation, which is an improvement of 0.15 Å over previous microcrystal forms. Ubiquinone was incorporated into the LCP crystallization media and the resulting electron density within the mobile QB pocket is comparable to that of other cofactors within the structure. As such, LCP microcrystallization conditions will facilitate time-resolved diffraction studies of electron-transfer reactions to the mobile quinone, potentially allowing the observation of structural changes associated with the two electron-transfer reactions leading to complete reduction of the ubiquinone ligand.

Cryo-EM Structure of the Photosynthetic LH1-RC Complex from Rhodospirillum rubrum

Rhodospirillum (Rsp.) rubrum is one of the most widely used model organisms in bacterial photosynthesis. This purple phototroph is characterized by the presence of both rhodoquinone (RQ) and ubiquinone as electron carriers and bacteriochlorophyll (BChl) a esterified at the propionic acid side chain by geranylgeraniol (BChl aG) instead of phytol. Despite intensive efforts, the structure of the light-harvesting-reaction center (LH1-RC) core complex from Rsp. rubrum remains at low resolutions. Using cryo-EM, here we present a robust new view of the Rsp. rubrum LH1-RC at 2.76 Å resolution. The LH1 complex forms a closed, slightly elliptical ring structure with 16 αβ-polypeptides surrounding the RC. Our biochemical analysis detected RQ molecules in the purified LH1-RC, and the cryo-EM density map specifically positions RQ at the QA site in the RC. The geranylgeraniol side chains of BChl aG coordinated by LH1 β-polypeptides exhibit a highly homologous tail-up conformation that allows for interactions with the bacteriochlorin rings of nearby LH1 α-associated BChls aG. The structure also revealed key protein-protein interactions in both N- and C-terminal regions of the LH1 αβ-polypeptides, mainly within a face-to-face structural subunit. Our high-resolution Rsp. rubrum LH1-RC structure provides new insight for evaluating past experimental and computational results obtained with this old organism over many decades and lays the foundation for more detailed exploration of light-energy conversion, quinone transport, and structure-function relationships in this pigment-protein complex.

The Photosynthetic Reaction Center from the Purple Bacterium Rhodopseudomonas viridis

The history and methods of membrane protein crystallization are described. The solution of the structure of the photosynthetic reaction center from the bacterium Rhodopseudomonas viridis is described, and the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Conclusions about the structure of the photosystem II reaction center from plants are drawn, and aspects of membrane protein structure are discussed.

Heterologous production in Wolinella succinogenes and characterization of the quinol:fumarate reductase enzymes from Helicobacter pylori and Campylobacter jejuni

The epsilon-proteobacteria Helicobacter pylori and Campylobacter jejuni are both human pathogens. They colonize mucosal surfaces causing severe diseases. The membrane protein complex QFR (quinol:fumarate reductase) from H. pylori has previously been established as a potential drug target, and the same is likely for the QFR from C. jejuni. In the present paper, we describe the cloning of the QFR operons from the two pathogenic bacteria H. pylori and C. jejuni and their expression in Wolinella succinogenes, a non-pathogenic -proteobacterium. To our knowledge, this is the first documentation of heterologous membrane protein production in W. succinogenes. We demonstrate that the replacement of the homologous enzyme from W. succinogenes with the heterologous enzymes yields mutants where fumarate respiration is fully functional. We have isolated and characterized the heterologous QFR enzymes. The high quality of the enzyme preparation enabled us to determine unequivocally by analytical ultracentrifugation the homodimeric state of the three detergent-solubilized heterotrimeric QFR enzymes, to accurately determine the different oxidation-reduction ('redox') midpoint potentials of the six prosthetic groups, the Michaelis constants for the quinol substrate, maximal enzymatic activities and the characterization of three different anti-helminths previously suggested to be inhibitors of the QFR enzymes from H. pylori and C. jejuni. This characterization allows, for the first time, a detailed comparison of the QFR enzymes from C. jejuni and H. pylori with that of W. succinogenes.

Probing heme propionate involvement in transmembrane proton transfer coupled to electron transfer in dihemic quinol:fumarate reductase by 13C-labeling and FTIR difference spectroscopy

Quinol:fumarate reductase (QFR) is the terminal enzyme of anaerobic fumarate respiration. This membrane protein complex couples the oxidation of menaquinol to menaquinone to the reduction of fumarate to succinate. Although the diheme-containing QFR from Wolinella succinogenes is known to catalyze an electroneutral process, its three-dimensional structure at 2.2 A resolution and the structural and functional characterization of variant enzymes revealed locations of the active sites that indicated electrogenic catalysis. A solution to this apparent controversy was proposed with the so-called "E-pathway hypothesis". According to this, transmembrane electron transfer via the heme groups is strictly coupled to a parallel, compensatory transfer of protons via a transiently established pathway, which is inactive in the oxidized state of the enzyme. Proposed constituents of the E-pathway are the side chain of Glu C180 and the ring C propionate of the distal heme. Previous experimental evidence strongly supports such a role of the former constituent. Here, we investigate a possible heme-propionate involvement in redox-coupled proton transfer by a combination of specific (13)C-heme propionate labeling and Fourier transform infrared (FTIR) difference spectroscopy. The labeling was achieved by creating a W. succinogenes mutant that was auxotrophic for the heme-precursor 5-aminolevulinate and by providing [1-(13)C]-5-aminolevulinate to the medium. FTIR difference spectroscopy revealed a variation on characteristic heme propionate vibrations in the mid-infrared range upon redox changes of the distal heme. These results support a functional role of the distal heme ring C propionate in the context of the proposed E-pathway hypothesis of coupled transmembrane electron and proton transfer.

The Photosynthetic Reaction Centre from the Purple Bacterium Rhodopseudomonasviridis

We first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. The structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure.

Refined crystal structures of reaction centres from Rhodopseudomonas viridis in complexes with the herbicide atrazine and two chiral atrazine derivatives also lead to a new model of the bound carotenoid

In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled with the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). It has been established by X-ray crystallography that the triazine herbicide terbutryn binds to the QB site. However, the exact description of protein-triazine interactions has had to await the refinement of higher-resolution structures. In addition, there is also interest in the role of chirality in the activity of herbicides. Here, we report the structural characterisation of triazine binding by crystallographic refinement of complexes of the RC either with the triazine inhibitor atrazine (Protein Data Bank (PDB) entry 5PRC) or with the chiral atrazine derivatives, DG-420314 (S(-) enantiomer, PDB entry 6PRC) or DG-420315 (R(+) enantiomer, PDB entry 7PRC). Due to the high quality of the data collected, it has been possible to describe the exact nature of triazine binding and its effect on the structure of the protein at high-resolution limits of 2.35 A (5PRC), 2.30 A (6PRC), and 2.65 A (7PRC), respectively. In addition to two previously implied hydrogen bonds, a third hydrogen bond, binding the distal side of the inhibitors to the protein, and four additional hydrogen bonds mediated by two tightly bound water molecules on the proximal side of the inhibitors, are apparent. Based on the high quality data collected on the RC complexes of the two chiral atrazine derivatives, unequivocal assignment of the structure at the chiral centres was possible, even though the differences in structures of the substituents are small. The structures provide explanations for the relative binding affinities of the two chiral compounds. Although it was not an explicit goal of this work, the new data were of sufficient quality to improve the original model also regarding the structure of the bound carotenoid 1,2-dihydroneurosporene. A carotenoid model with a cis double bond at the 15,15' position fits the electron density better than the original model with a 13,14-cis double bond.

The cytochrome bc1 complex from Rhodovulum sulfidophilum is a dimer with six quinones per monomer and an additional 6-kDa component

A highly active, large-scale preparation of cytochrome bc1 complex has been obtained from the photosynthetic purple bacterium Rhodovulum (Rhv.) sulfidophilum. It has been characterized using mass spectrometry, quinone and lipid analysis as well as inhibitor binding. About 35 mg of pure complex can be obtained from 1 g of membrane protein. EPR spectroscopy and optical titrations have been used to obtain the redox midpoint potentials of the cofactors. The Em-value of 310 mV for the Rieske protein is the most positive midpoint potential for this protein in a bc1 complex so far. The bc1 complex from Rhv. sulfidophilum is very stable and consists of three subunits and a 6-kDa polypeptide. The complex appears as a dimer in solution and contains six quinone molecules per monomer which are tightly bound. EPR spectroscopy shows that the Q(o) site is highly occupied. High detergent concentrations convert the complex into an inactive, monomeric form that has lost the Rieske protein as well as the quinones and the 6-kDa component.

The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site of the secondary quinone, QB

BACKGROUND

In a reaction of central importance to the energetics of photosynthetic bacteria, light-induced electron transfer in the reaction centre (RC) is coupled to the uptake of protons from the cytoplasm at the binding site of the secondary quinone (QB). In the original structure of the RC from Rhodopseudomonas viridis (PDB entry code 1PRC), the QB site was poorly defined because in the standard RC crystals it was only approximately 30% occupied with ubiquinone-9 (UQ9). We report here the structural characterization of the QB site by crystallographic refinement of UQ9-depleted RCs and of complexes of the RC either with ubiquinone-2 (UQ2) or the electron-transfer inhibitor stigmatellin in the QB site.

RESULTS

The structure of the RC complex with UQ2, refined at 2.45 A resolution, constitutes the first crystallographically reliably defined binding site for quinones from the bioenergetically important quinone pool of biological, energy-transducing membranes. In the UQ9-depleted QB site of the RC structure, refined at 2.4 A resolution, apparently five (and possibly six) water molecules are bound instead of the ubiquinone head group, and a detergent molecule binds in the region of the isoprenoid tail. All of the protein-cofactor interactions implicated in the binding of the ubiquinone head group are also implicated in the binding of the stigmatellin head group. In the structure of the stigmatellin-RC complex, refined at 2.4 A resolution, additional hydrogen bonds stabilize the binding of stigmatellin over that of ubiquinone. The tentative position of UQ9 in the QB site in the original data set (1PRC) was re-examined using the structure of the UQ9-depleted RC as a reference. A modified QB site model, which exhibits greater similarity to the distal ubiquinone-10 (UQ10) positioning in the structure of the RC from Rhodobacter sphaeroides (PDB entry code 1PCR), is suggested as the dominant binding site for native UQ9.

CONCLUSIONS

The structures reported here can provide models of quinone reduction cycle intermediates. The binding pattern observed for the stigmatellin complex, where the ligand donates a hydrogen bond to Ser L223 (where 'L' represents the L subunit of the RC), can be viewed as a model for the stabilization of a monoprotonated reduced intermediate (QBH or QBH-). The presence of Ser L223 in the QB site indicates that the QB site is not optimized for QB binding, but for QB reduction to the quinol.

Influence of M subunit Thr222 and Trp252 on quinone binding and electron transfer in Rhodobacter sphaeroides reaction centres

M subunit Trp252 is the only amino acid residue which is located between the bacteriopheophytin HA and the quinone QA in the photosynthetic reaction centre of Rhodobacter sphaeroides. Oligodeoxynucleotide-directed mutagenesis was employed to elucidate the influence of this aromatic amino acid on the electron transfer between these two chromophores. For this, M subunit Trp252 was changed to tyrosine or phenylalanine, and Thr222, which presumably forms a hydrogen bridge to the indole ring of M subunit Trp252, to valine. In all three mutated reaction centres, the electron-accepting ubiquinone QA is less firmly bound to its binding site than in the wild-type protein. The electron transfer from the reduced bacteriopheophytin HA- to QA proceeds in the wild-type and in the mutant ThrM222Val within 220 ps. However, in the mutants TrpM252Tyr and TrpM252Phe the time constants are 600 ps and 900 ps, respectively. This indicates that M subunit Trp252 participates in the binding of QA and reduction of this quinone.

On the depletion and reconstitution of both QA and metal in reaction centers of the photosynthetic bacterium Rb. sphaeroides R-26

Four possible ways to prepare QA-depleted, Fe-depleted and QA-reconstituted RCs were studied: (1) first depleting the Fe, then depleting QA and finally reconstituting QA (D-Fe, D-Q, R-Q), (2) first depleting QA, then depleting the Fe and finally reconstituting QA (D-Q, D-Fe, R-Q), (3) first depleting QA, then reconstituting QA and finally depleting Fe (D-Q, R-Q, D-Fe), (4) first depleting QA, then depleting the Fe and reconstituting QA in the same step (D-Q, D-Fe-R-Q). Our results showed that: method (1) results in the irreversible loss of photochemical activity; method (2) and (3) result in low recovery of the photochemical activity and poor yield of Fe-depleted, QA-reconstituted RCs; method (4) gives surprisingly good results. This method allows for the first time to prepare the QA-depleted, Fe-depleted, QA-reconstituted RCs with high recovery of the photochemical activity and good yield. The sample has 98% of photochemical activity (yield of P(+) QA (-)) compared with that of the native RCs and shows strong polarization of the EPR signal of QA (-) under continuous illumination at 5K. The decay halftime of I(-) is slow (∼5 ns) compared with that of the native RCs, but it is the same as that measured for the RCs from which only iron is removed. These results indicate that the depletion of iron and the reconstitution of QA have been successful. Reconstitution of the QA-depleted, Fe-depleted and QA-reconstituted RCs with Zn(2+) gives also the spin-polarized QA (-), and yields the same decay of I(-) (halftime 200 ps) as that of the native RCs.

Contribution of vitamin K1 to the electron spin polarization in spinach photosystem I

The electron spin polarized (ESP) electron paramagnetic resonance (EPR) signal observed in spinach photosystem I (PSI) particles was examined in preparations depleted of vitamin K1 by solvent extraction and following biological reconstitution by the quinone. The ESP EPR signal was not detected in the solvent-extracted PSI sample but was restored upon reconstitution with either protonated or deuterated vitamin K1 under conditions that also restored electron transfer to the terminal PSI acceptors. Reconstitution using deuterated vitamin K1 resulted in a line narrowing of the ESP EPR signal, supporting the conclusion that the ESP EPR signals in the reconstituted samples arise from a radical pair consisting of the oxidized PSI primary donor, P700+, and reduced vitamin K1.

The photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis

We first describe the history and methods of membrane protein crystallization, and show how the structure of the photosynthetic reaction centre from the purple bacterium Rhodopseudomonas viridis was solved. The structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Finally we draw conclusions on the structure of the photosystem II reaction centre from plants and discuss the aspects of membrane protein structure.

Structure of Rhodopseudomonas sphaeroides R-26 reaction center

The molecular replacement method has been successfully used to provide a structure for the photosynthetic reaction center of Rhodopseudomonas sphaeroides at 3.7 A resolution. Atomic coordinates derived from the R. viridis reaction center were used in the search structure. The crystallographic R-factor is 0.39 for reflections between 8 and 3.7 A. Validity of the resulting model is further suggested by the visualization of amino acid side chains not included in the R. viridis search structure, and by the arrangements of the reaction centers in the unit cell. In the initial calculations quinones or pigments were not included; nevertheless, in the resulting electron density map, electron density for both quinones QA and QB appears along with the bacteriochlorophylls and bacteriopheophytins. Kinetic analysis of the charge recombination shows that the secondary quinone is fully functional in the R. sphaeroides crystal.

Structure of the protein subunits in the photosynthetic reaction centre of Rhodopseudomonas viridis at 3Å resolution

The molecular structure of the photosynthetic reaction centre from Rhodopseudomonas viridis has been elucidated using X-ray crystallographic analysis. The central part of the complex consists of two subunits, L and M, each of which forms five membrane-spanning helices. We present the first description of the high-resolution structure of an integral membrane protein.