X-ray structure analysis of a membrane protein complex. Electron density map at 3 A resolution and a model of the chromophores of the photosynthetic reaction center from Rhodopseudomonas viridis

Crystal structure analysis and refinement at 2.5 A of hexameric C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum. The molecular model and its implications for light-harvesting

The crystal structure of the light-harvesting protein-pigment complex C-phycocyanin from the cyanobacterium Agmenellum quadruplicatum has been determined by Patterson search techniques on the basis of the molecular model of C-phycocyanin from Mastigocladus laminosus. The crystal unit cell (space group P321) contains three (alpha beta)6 hexamers centred on the crystallographic triads. The hexamer at the origin of the unit cell exhibits crystallographic 32 point symmetry. The other two hexamers (independent of the former) show crystallographic 3-fold and local 2-fold symmetry. The 3-fold redundancy of the asymmetric unit of the crystal cell was used in the refinement process, which proceeded by cyclic averaging, model building and energy-restrained crystallographic refinement. Refinement was terminated with a conventional crystallographic R-value of 0.20 with data to 2.5 A resolution. The two independent hexamers of the unit cell are identical within the limits of error at all levels of aggregation. Two trimers, which closely resemble the M. laminosus C-phycocyanin, are aggregated head-to-head to form the hexamer. Both trimers fit complementarily and are held together by polar and ionic interactions. Conservation of the amino acid residues involved in protein-chromophore and intermonomer interactions suggests common structural features for all biliproteins. Most probably, the hexameric aggregation form present in the crystals is closely related to the discs of native phycobilisome rods. All tetrapyrrole chromophores are extended but with different geometries enforced by different protein surroundings. In particular, interactions of the propionic side-chains with arginine residues and of the pyrrole nitrogen atoms with aspartate residues define configuration and conformation of the chromophores. Relative chromophore distances and orientations have been determined and a preferential pathway for the energy transfer suggested. Accordingly, within a hexamer the absorbed energy is funneled to chromophore B84 and then transduced via B84 chromophores along the phycobilisome rods.

Structure and X-ray amino acid sequence of a bacteriochlorophyll A protein from Prosthecochloris aestuarii refined at 1.9 A resolution

The structure of the water-soluble bacteriochlorophyll a protein (Bchl protein) from the green photosynthetic bacterium Prosthecochloris aestuarii has been refined at 1.9 A resolution to a crystallographic residual of 18.9%. The refinement was carried out without knowledge of the amino acid sequence and has led to an "X-ray sequence". The structure consists of seven Bchl molecules enclosed within a protein "bag" and the refinement supports the general conformation of the molecule described previously. The refinement also supports the previous suggestion that the ligands to the seven Bchl magnesiums are, respectively, five histidines, a carbonyl oxygen from the polypeptide backbone of the protein, and a bound water molecule. The conformations of the seven Bchl head-groups are described in detail. In two cases the magnesium atoms are approximately 0.48 A "below" the plane of the conjugated macrocycle while in the other five cases the atoms are, on average, 0.48 A "above" the plane. The acetyl ring substituents are more-or-less coplanar with the dihydrophorbin macrocycle, consistent with a previous resonance Raman study. The conjugated atoms in each of the seven macrocycles have significant departures from strict planarity. These deviations are similar for Bchls 1, 2 and 3 (class I) and are also similar for Bchls 4, 5, 6 and 7 (class II). Ethylchlorophillide also belongs to class II. The out-of-plane deformations for the class I and class II bacteriochlorophylls appear to correspond to two distinct modes of bending or curvature of the dihydrophorbin macrocycle.

Primary donor recovery kinetics in reaction centers from Rhodopseudomonas viridis. The influence of ferricyanide as a rapid oxidant of the acceptor quinones

In reaction centers from Rhodopseudomonas viridis that contain a single quinone, the decay of the photo-oxidized primary donor, P+, was found to be biphasic when the bound, donor cytochromes were chemically oxidized by ferricyanide. The ratio of the two phases was dependent on pH with an apparent pK of 7.6. A fast phase, which dominated at high pH (t1/2 = 1 ms at pH 9.5), corresponded to the expected charge recombination of P+ and the primary acceptor QA-. A much slower phase dominated at low pH and was shown to arise from a slow reduction of P+ by ferrocyanide in reaction centers where QA- has been rapidly oxidized by ferricyanide. The rate of QA- oxidation was linear with respect to ferricyanide activity and was strongly pH-dependent. The second-order rate constant, corrected for the activity coefficient of ferricyanide, approached a maximum of 2 X 10(8) M-1 X s-1 at low pH, but decreased steadily as the pH was raised above a pK of 5.8, indicating that a protonated state of the reaction center was involved. The slow reduction of P+ by ferrocyanide was also second-order, with a maximum rate constant at low pH of 8 X 10(5) M-1 X s-1 corrected for the activity coefficient of ferrocyanide. This rate also decreased at higher pH, with a pK of 7.4, indicating that ferrocyanide also was most reactive with a protonated form of the reaction center. The oxidation of QA- by ferricyanide was unaffected by the presence of o-phenanthroline, implying that access to QA- was not via the QB-binding site. In reaction centers supplemented with ubiquinone, oxidation of reduced secondary quinone, QB-, by ferricyanide was observed but was substantially slower than that for QA-. It is suggested that Q-B may be oxidized via QA so that the rate is modulated by the equilibrium constant for QA-QB in equilibrium with QAQB-.

Evidence the yeast STE3 gene encodes a receptor for the peptide pheromone a factor: gene sequence and implications for the structure of the presumed receptor

Haploid yeast cells of the a mating type secrete a peptide pheromone, a factor, which acts on cells of the alpha mating type to prepare them for conjugation. We show that the STE3 gene, which is required for mating only by alpha cells and is transcribed only in alpha cells, likely encodes a cell-surface receptor for a factor. This view is based on three findings. First, wild-type Ste3 product is required for response to the pheromone: mutants with any one of five different ste3 mutations are unresponsive to a factor. Second, a hybrid Ste3-beta-galactosidase protein encoded by a STE3-lacZ gene fusion fractionates to the particulate fraction of yeast cell extracts, suggesting that Ste3 is a membrane protein. Finally, the DNA sequence of STE3, which we report here, encodes a protein of 470 amino acid residues that contains seven distinct hydrophobic segments of sufficient length to span a lipid bilayer.

A conformational preference parameter to predict helices in integral membrane proteins

Assignments were made for helical regions in several integral membrane proteins using an algorithm devised to delineate the transmembrane helices in bacteriorhodopsin (Eur. J. Biochem. 182 (1982) 565-575). A new conformational preference parameter for membrane-buried helices was obtained. The use of this parameter to predict helices in membrane proteins is discussed. When applied to the L and M subunits of Rhodopseudomonas sphaeroides, five helices were predicted, which is consistent with the three-dimensional X-ray crystal structure. Data on signal sequences and amino acid exchanges in membrane proteins are also analysed and discussed

Triplet-minus-singlet absorbance difference spectra of reaction centers of Rhodopseudomonas sphaeroides R-26 in the temperature range 24-290 K measured by Magneto-Optical Difference Spectroscopy (MODS)

The recently developed technique of Magneto-Optical Difference Spectroscopy (MODS) [10] has been applied to reaction centers (RC) of the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26. Absorbance changes induced by a magnetic field are measured as a function of wavelength yielding the triplet-minus-singlet (T-S) absorbance difference spectrum. (T-S) spectra thus obtained have been measured from 24-290 K. Going from low to high temperature the (T-S) spectra show the following features: (a) A rapid decrease of positive absorption bands at 809 and 819 nm. (b) A slow appearance of a band shift at 798 nm. (c) A shift of the peak wavelength of the Qy absorbance band of the primary donor P-860 from 992 to 861 nm, and of its Qx band from 603 to 600 nm. The spectra at 24, 66, 116, and 290 K have been analyzed by Gaussian deconvolution. The 800 nm region of the spectrum at 24 K can be decomposed in a combination of two band shifts and an appearing band. The temperature dependence of the spectra in this region is well explained by spectral broadening of the two shifting bands combined with a decrease in intensity of the appearing band when the temperature increases.The two shifting bands in the 800 nm region are identified as the two bands at 803 and 813 nm which together make up the 800 nm band in the absorption spectrum and are assigned to the two accessory RC bacteriochlorophylls (BChls). The band shift of the 813 nm pigment is appreciably larger than that of the 803 nm pigment. The appearing band at 808 nm is attributed to monomeric absorption of (3)P-860, the triplet state being localized on one BChl.We find no evidence for admixture of a charge transfer (CT) state of (3)P-860 with one of the accessory BChls at higher temperature.

Interactions of the bacteriochlorophylls in antenna bacteriochlorophyll-protein complexes of photosynthetic bacteria

Several models have been proposed for the arrangements of the bacteriochlorophylls in the antenna complexes of purple photosynthetic bacteria, but none of the models has accounted fully for the spectroscopic properties of the bacteriochlorophyll-protein complexes. We suggest a model involving strong exciton interactions within a bacteriochlorophyll dimer, and weaker interactions of each dimer with other, relatively distant dimers. The model is shown to account for the spectroscopic properties of the complexes, and to be consistent with other available information.

Chlorophyll-protein complexes

Recent advances in the studies on chlorophyll-protein complexes of higher plants are summarized in this article. Special emphasis is laid on the isolation, pigment composition and the absorption and fluorescence properties of the complexes.

Electron donors and acceptors in photosynthetic reaction centers

A review is given of primary and associated electron transport reactions in various division of photosynthetic bacteria and in the two photosystems of plant photosynthesis. Two types of electron acceptor chains are distinguished: type 'Q', found in purple bacteria, Chloroflexus and system II of oxygenic photosynthesis and type 'F', found in green sulfur bacteria, Heliobacterium and photosystem I. Secondary donor reactions are discussed in relation to plant photosystem II.

What role does sulpholipid play within the thylakoid membrane?

Sulphoquinovosyldiacylglycerol is a negatively charged lipid which exists in the thylakoid membrane. It is proposed that a large proportion of this acidic lipid does not form a part of the bulk lipid matrix but is closely associated with protein complexes where it is tightly bound and participates in either optimising catalytic activities, or maintaining the complexes in a functional conformation. Experimental evidence for this proposal is emerging from studies with isolated photosystem 2, and coupling factor complexes.

Inhibitors of photosystem II and the topology of the herbicide and QB binding polypeptide in the thylakoid membrane

The folding through the thylakoid membrane of the D-1 herbicide binding polypeptide and of the homologous D-2 subunit of photosystem II is predicted from comparison of amino acid sequences and hydropathy index plots with the folding of the subunits L and M of a bacterial photosystem. As the functional amino acids involved in Q and Fe binding in the bacterial photosystem of R. viridis, as indicated by the X-ray structure, are conserved in the homologous D-1 and D-2 subunits of photosystem II, a detailed topology of the binding niche of QB and of herbicides on photosystem II is proposed. The model is supported by the observed amino acid changes in herbicide tolerant plants and algae. These changes are all in the binding domain on the matrix side of the D-1 polypeptide, and turn out to be of functional significance in the QB binding.New inhibitors of QB function are described. Their chemical structure, i.e. pyridones, quinolones, chromones and benzodiones, contains the features of the phenolic type herbicides. Their essential elements, π-charges at particular atoms, QSAR and steric requirements for optimal inhibitory potency are discussed and compared with the "classical" herbicides of the urea/triazine type.

Structural aspects of vectorial electron transfer in photosynthetic reaction centers

Structural aspects of photosynthetic reaction centers in bacteria and plants are discussed in relation with the ability of these structures to perform a photoinduced electron transfer from one side of the membrane to the other. A comparison is made with recently synthesized artificial models. Functional similarities between the acceptor sides of bacterial and of Photosystem-II centers are utilized to hypothesize on their structure.

Vibronic coupling to electron transfer and the structure of the R. Viridis reaction center

This paper points out that the orientations of the porphyrins, bacteriochlorophyll and bacteriopheophytin, in the reaction centers of Rhodopseudomonas viridis, as shown by the new X-ray determined structure, have a peculiar orientation towards each other: electron donors are broadside toward the acceptors and acceptors are edgeon toward donors. Vibronic coupling which is the mechanism of converting free-energy loss in electron transport to vibrational energy is examined as a possible explanation. Preliminary calculations do not support this as an explanation of the orientations but suggest strongly that the non-heme iron atom has the function of promoting vibronic coupling in the electron transfer from bacteriopheophytin to menaquinone. It is further suggested that the system of electron transport from the special pair of bacteriochlorophyll to the bacteriopheophytin is arranged to keep virbonic coupling to a minimum to match the very small electronic free-energy loss in this region.

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.

Picosecond kinetics of the initial photochemical electron-transfer reaction in bacterial photosynthetic reaction centers

The absorption changes that occur in reaction centers of the photosynthetic bacterium Rhodopseudomonas sphaeroides during the initial photochemical electron-transfer reaction have been examined. Measurements were made between 740 and 1300 nm at 295 and 80 K by using a pulse-probe technique with 610-nm, 0.8-ps flashes. An excited singlet state of the bacteriochlorophyll dimer P* was found to give rise to stimulated emission with a spectrum similar to that determined previously for fluorescence from reaction centers. The stimulated emission was used to follow the decay of P*; its lifetime was 4.1 +/- 0.2 ps at 295 K and 2.2 +/- 0.1 ps at 80 K. Within the experimental uncertainty, the absorption changes associated with the formation of a bacteriopheophytin anion, Bph-, develop in concert with the decay of P* at both temperatures, as does the absorption increase near 1250 nm due to the formation of the cation of P, P+. No evidence was found for the formation of a bacteriochlorophyll anion, Bchl-, prior to the formation of Bph-. This is surprising, because in the crystal structure of the Rhodopseudomonas viridis reaction center [Deisenhofer, J., Epp, O., Miki, K., Huber, R., & Michel, H. (1984) J. Mol. Biol. 180, 385-398] a Bchl is located approximately in between P and the Bph. It is possible that Bchl- (or Bchl+) is formed but, due to kinetic or thermodynamic constraints, is never present at a sufficient concentration for us to observe. Alternatively, a virtual charge-transfer state, such as P+Bchl-Bph or PBchl+Bph-, could serve to lower the energy barrier for direct electron transfer between P* and the Bph.

Aqueous micellar systems in membrane protein crystallization. Partial miscibility of a nonionic surfactant in the presence of salt or polyethylene glycol

The effects of NaCl and polyethylene glycol (PEG) 4000 on the lower consolution boundary (LCB) of a nonionic surfactant (C8E5) were studied and compared. Micellar systems were NaCl and PEG 4000 are present are often used in membrane protein crystallization. While sodium chloride shifts the surfactant LCB to lower temperatures without a significant change in the shape of the boundary, PEG produces a large solubility change strongly depending on the surfactant concentration. The salt effect is explained by a reduced interaction of the micellar oligooxyethylene chains with the water and the PEG effect by an unfavourable configurational interaction between the C8E5 micelles and PEG molecules.

Characterization of bacterial photosynthetic reaction center crystals from Rhodopseudomonas sphaeroides R-26 by X-ray diffraction

An orthorhombic crystal form (P2(1)2(1)2(1)) of the reaction center from the photosynthetic bacterium Rhodopseudomonas sphaeroides R-26 has been characterized. The crystals were grown from polyethylene glycol; the unit cell dimensions are a = 142.2 A, b = 139.6 A, and c = 78.7 A; and they contain one reaction center in each crystallographic asymmetric unit. The crystals diffract to at least 3.0 A resolution, and are suitable for detailed structural studies.

Membrane-linked energy transductions. Bioenergetic functions of sodium: H+ is not unique as a coupling ion

The concept is developed according to which Na+, like H+, can play the role of a coupling ion in energy-transducing biomembranes. This idea is based on observations that (i) Na+ can be extruded from the cell by primary pumps (Na-motive NADH-quinone reductase, decarboxylase or ATPase), and (ii) the downhill Na+ flux into the cell can be coupled with the performance of all the three types of membrane-linked work i.e. chemical (ATP synthesis), osmotic (accumulation of solutes) and mechanical (motility). Marine alkalotolerant Vibrio alginolyticus represents the first example of such a complete sodium cycle pattern. Simplified versions of the sodium cycle or some of its constituents are found in the cytoplasmic membrane of a great variety of taxa including anaerobic, aerobic and photosynthetic bacteria, cyanobacteria and animals; this fact indicates that Na+ energetics should be regarded as a common case, rather than a rare exception applied to some natural niches only.

The Rhodopseudomonas viridis photosynthetic membrane: arrangement in situ

The organization of photosynthetic membranes in the cytoplasm of the photosynthetic bacterium Rh. viridis has been examined by several techniques for electron microscopy. Thin sections of membrane stacks show that the regular lattice of membrane subunits reported in other studies can be observed in thin section. Tilting of sections in the electron microscope shows that the regular lattices of several membranes overlap in a way that suggests they are in register with each other. This observation can be confirmed by freeze-fracture images in which a regular arrangement of membrane lattices can be observed, each perfectly aligned. Analysis of the spacings of membrane pairs shows that the photosynthetic membranes of Rh. viridis are very closely apposed. The mean diameter of two membranes is 160A, and the average space between two such membranes is only 42A. When a recently developed atomic level model of Rh. viridis reaction center is superimposed against these spacings, each reaction center extends from the surface of its respective membrane far enough to make contact with an apposing membrane. The limited free space between membranes and regular alignment of lattices has a number of implications for how this membrane is organized to carry out the process of energy transfer.