Triplet state EPR of reaction centers from the HisL173→LeuL173 mutant of Rhodobacter sphaeroides which contains a heterodimer primary donor

Electron paramagnetic resonance (EPR) spectroscopy has been used to examine the triplet states in reaction centers of Rhodobacter sphaeroides which have undergone a genetic modification affecting the primary donor. Reaction centers containing the His^L173Leu^L173 substitution in the amino acid sequence have a primary donor which consists of a BChl-BPh heterodimer. The triplets formed in this heterodimer reaction center were compared with those formed in the wild-type reaction center which contains the BChl-BChl homodimer. Both reaction centers transfer triplet energy to the carotenoid under illumination at liquid nitrogen temperatures (90 K). However, the intensity of the carotenoid triplet signal is significantly decreased in the Leu^L173 mutant compared with the wild-type reaction center. At 12 K, in wild-type reaction centers only the primary donor triplet is observed. The Leu^L173 mutant exhibits a signal similar to that observed by Bylina et al. (1990) in His^M200Leu^M200 mutant reaction centers from Rb. capsulatus. The values of the zero-field splitting parameters of this triplet are discussed within the context of various models for the primary donor triplet state. No alteration in the ability of the carotenoid to quench the primary donor triplet state results from mutations at these sites.Abbreviations BChl bacteriochlorophyll - BPh bacteriopheophytin - EPR electron paramagnetic resonance - LDAO lauryl-dimethylamine N-oxide     

The structure of the FMO protein from Chlorobium tepidum at 2.2 Å resolution

The bacteriochlorophyll protein, or FMO protein, from Chlorobium tepidum, which serves as a light-harvesting complex and directs light energy from the chlorosomes attached to the cell membrane to the reaction center has been crystallized in a new space group. The crystals belong to the cubic space group P4₃32 and the structure has been refined to a resolution 2.2 Å with a R factor of 19.7%. The electron density maps show that the structure is composed of two sheets that surround seven bacteriochlorophylls as previously reported (Li et al. (1997) J Mol Biol 271: 456–471). The availability of the new data allows a more accurate refinement of the pigment–protein complex including identification of bound solvent molecules. Several structural differences probably contribute to the observed spectroscopic differences between the FMO proteins from Cb. tepidum and Prosthecochloris aestuarii, including differences in the planarity of corresponding tetrapyrroles. A citrate molecule is found on the surface of each protein subunit of the trimer from Cb. tepidum. However, the citrate molecule is over 15 Å from any bacteriochlorophyll. The presence of the citrate probably does not contribute to the function of the protein although it does contribute to the crystallization as it interacts with a crystallographically related trimer. Among the 236 water molecules found in the protein are four that appear to play a special role in the properties of bacteriochlorophyll 2, as this tetrapyrrole is coordinated by one of these water molecules and the waters form a hydrogen-bonded network that leads to the surface of the protein.This revised version was published online in October 2005 with corrections to the Cover Date.     

The spectroscopic and photochemical properties of locked-15,15′-cis-spheroidene in solution and incorporated into the reaction center of Rhodobacter sphaeroides R-26.1

The spectroscopic and photochemical properties of the synthetic carotenoid, locked-15,15-cis-spheroidene, were studied by absorption, fluorescence, circular dichroism, fast transient absorption and electron spin resonance spectroscopies in solution and after incorporation into the reaction center of Rhodobacter (Rb.) sphaeroides R-26.1. HPLC purification of the synthetic molecule reveals the presence of several di-cis geometric isomers in addition to the mono-cis isomer of locked-15,15-cis-spheroidene. In solution, the absorption spectrum of the purified mono-cis sample was red-shifted and showed a large cis-peak at 351 nm compared to unlocked all-trans spheroidene. Molecular modeling and semi-empirical calculations reveal how geometric isomerization and structural factors affect the room temperature spectra. The spectroscopic studies of the purified locked-15,15-mono-cis molecule in solution reveal a more stable manifold of excited states compared to the unlocked spheroidene. Reaction centers of Rb. sphaeroides R-26.1 in which the locked-15,15-cis-spheroidene was incorporated show no difference in either the spectroscopic properties or photochemistry compared to reaction centers in which unlocked spheroidene was incorporated or to Rb. sphaeroides wild type strain 2.4.1 reaction centers which naturally contain spheroidene. The data suggest that the natural selection of a cis-isomer of spheroidene for incorporation into native reaction centers of Rb. sphaeroides wild type strain 2.4.1 is more determined by the structure or assembly of the reaction center protein than by any special quality of the cis-isomer of the carotenoid that would affect its ability to participate in triplet energy transfer or carry out photoprotection.     

The IleL229 → Met mutation impairs the quinone binding to the QB-pocket in reaction centers of Rhodobacter sphaeroides

A spontaneous mutant (R/89) of photosynthetic purple bacterium Rhodobacter sphaeroides R-26 was selected for resistance to 200 M atrazin. It showed increased resistance to interquinone electron transfer inhibitors of o-phenanthroline (resistance factor, RF=20) in UQ_o reconstituted isolated reaction centers and terbutryne in reaction centers (RF=55) and in chromatophores (RF=85). The amino acid sequence of the Q_B binding protein of the photosynthetic reaction center (the L subunit) was determined by sequencing the corresponding pufL gene and a single mutation was found (Ile^L229 Met). The changed amino acid of the mutant strain is in van der Waals contact with the secondary quinone Q_B. The binding and redox properties of Q_B in the mutant were characterized by kinetic (charge recombination) and multiple turnover (cytochrome oxidation and semiquinone oscillation) assays of the reaction center. The free energy for stabilization of Q_AQ_B ^– with respect to Q_A ^–Q_B was G_AB=–60 meV and 0 meV in reaction centers and G_AB=–85 meV and –46 meV in chromatophores of R-26 and R/89 strains at pH 8, respectively. The dissociation constants of the quinone UQ_o and semiquinone UQ_o ^– in reaction centers from R-26 and R/89 showed significant and different pH dependence. The observed changes in binding and redox properties of quinones are interpreted in terms of differential effects (electrostatics and mesomerism) of mutation on the oxidized and reduced states of Q_B.Abbreviations BChl bacteriochlorophyll - Ile isoleucine - Met methionin - P primary donor - Q_A primary quinone acceptor - Q_B secondary quinone acceptor - RC reaction center protein - UQ_o 2,3-dimethoxy-5-methyl benzoquinone - UQ₁₀ ubiquinone 50 This work is dedicated to the memory of Randall Ross Stein (1954–1994) and is, in a small way, a testament to the impact which Randy's ideas have had on the development of the field of competitive herbicide binding.     

Effects of zwitterionic detergents on the electronic structure of the primary donor and the charge recombination kinetics of P+Q A − in native and mutant reaction centers from Rhodobacter sphaeroides

The effects of detergents on the electronic structure of the oxidized primary donor P⁺ and the time constant _AP of the P⁺Q _A ^– charge recombination at ambient temperatures have been investigated in native and mutant reaction centers (RCs) from Rhodobacter sphaeroides. It is shown that N-lauryl-N,N-dimethyl-3-ammonio-1-propane sulfonate (SB12) induces a transition to a second distinct conformation of the RC. In the case of the wild type and the mutant FY(M197), in which a hydrogen bond is introduced to the 2-acetyl group of the dimer half of P that is associated with the M-subunit of the RC, the conformational change causes a more asymmetric spin density distribution between the two bacteriochlorophyll moieties of P⁺ in favor of the L-half. For both types of RCs the time constant _AP depends on the SB12/RC ratio as does the position of the long-wavelength band of P, _max. The increase of _AP by 30 ms and the shift of _max from 866 nm to 851 nm are indicative for the conformational change. In addition, a smaller linear increase of _AP with increasing SB12/RC ratio is superimposed on the variation of _AP due to the conformational change. Similar effects of SB12 on the optical spectra as well as on _AP are also observed for the two heterodimer mutants HL(L173) and HL(M202), in which one of the bacteriochlorophylls of P is replaced by a bacteriopheophytin. There are no clear indications for a correlation of _AP with the localization of the positive charge in P⁺. Furthermore, it is concluded from the dependence of _AP on the SB12/RC ratio that the single-site mutations do not affect the standard free energy difference of the two conformations to a measurable extent.     

Crystal structure of the C-terminal globular domain of oligosaccharyltransferase from Archaeoglobus fulgidus at 1.75 Å resolution

Protein N-glycosylation occurs in the three domains of life. Oligosaccharyltransferase (OST) transfers glycan to asparagine in the N-glycosylation sequon. The catalytic subunit of OST is called STT3 in eukaryotes, AglB in archaea, and PglB in eubacteria. The genome of a hyperthermophilic archaeon, Archaeoglobus fulgidus, encodes three AglB paralogs. Two of them are the shortest AglBs across all domains of life. We determined the crystal structure of the C-terminal globular domain of the smallest AglB to identify the minimal structural unit. The Archaeoglobus AglB lacked a β-barrel-like structure, which had been found in other AglB and PglB structures. In agreement, the deletion in a larger Pyrococcus AglB confirmed its dispensability for the activity. By contrast, the Archaeoglobus AglB contains a kinked helix bearing a conserved motif, called DK/MI motif. The lysine and isoleucine residues in the motif participate in the Ser/Thr recognition in the sequon. The Archaeoglobus AglB structure revealed that the kinked helix contained an unexpected insertion. A revised sequence alignment based on this finding identified a variant type of the DK motif with the insertion. A mutagenesis study of the Archaeoglobus AglB confirmed the contribution of this particular type of the DK motif to the activity. When taken together with our previous results, this study defined the classification of OST: one group consisting of eukaryotes and most archaea possesses the DK-type Ser/Thr pocket, and the other group consisting of eubacteria and the remaining archaea possesses the MI-type Ser/Thr pocket. This classification provides a useful framework for OST studies.     

The rate of Q(x)→Q(y) relaxation in bacteriochlorophylls of reaction centers from Rhodobacter sphaeroides determined by kinetics of the ultrafast carotenoid bandshift

Transient absorption changes induced by excitation of isolated reaction centers (RCs) from Rhodobacter sphaeroides with 600nm laser pulses of 20fs (full width at half maximum) were monitored in the wavelength region of 420-560nm. The spectral features of the spectrum obtained are characteristic for an electrochromic band shift of the single carotenoid (Car) molecule spheroidene, which is an integral constituent of these RCs. This effect is assigned to an electrochromic bandshift of Car due to the local electric field of the dipole moment formed by electronic excitation of bacteriochlorophyll (BChl) molecule(s) in the neighborhood of Car. Based on the known distances between the pigments, the monomeric BChl (B(B)) in the inactive B-branch is inferred to dominate this effect. The excitation of B(B) at 600nm leads to a transition into the S(2) state (Q(x) band), which is followed by rapid internal conversion to the S(1) state (Q(y) band), thus leading to a change of strength and orientation of the dipole moment, i.e., of the electric field acting on the Car molecule. Therefore, the time course of the electrochromic bandshift reflects the rate of the internal conversion from S(2) to S(1) of B(B). The evaluation of the kinetics leads to a value of 30fs for this relaxation process. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

The 1.6 Å resolution structure of Fe-superoxide dismutase from the thermophilic cyanobacterium Thermosynechococcus elongatus

The iron-containing superoxide dismutase (FeSOD) from the thermophilic cyanobacterium Thermosynechococcus elongatus has been isolated. The protein crystallizes readily and we have determined the structure to 1.6 A resolution. This is the first structural characterization of an FeSOD isolated from a cyanobacterium and one of the highest resolution FeSOD structures determined to date. The activity of the T. elongatus FeSOD has been measured both at 25 degrees C and 50 degrees C and it has been spectroscopically characterized. The T. elongatus FeSOD EPR spectra at pH 5.1, 7.5 and 10.0 are similar. This indicates that no change in the geometry of the Fe(III) site occurs over a wide range of pH. This is in contrast to the other FeSODs described in the literature.     

Crystal structure determination at 1.4 Å resolution of ferredoxin from the green alga Chlorella fusca

Background: [2Fe–2S] ferredoxins, also called plant-type ferredoxins, are low-potential redox proteins that are widely distributed in biological systems. In photosynthesis, the plant-type ferredoxins function as the central molecule for distributing electrons from the photolysis of water to a number of ferredox-independent enzymes, as well as to cyclic photophosphorylation electron transfer. This paper reports only the second structure of a [2Fe–2S] ferredoxin from a eukaryotic organism in its native form.Results: Ferredoxin from the green algae Chlorella fusca has been purified, characterised, crystallised and its structure determined to 1.4 Å resolution – the highest resolution structure published to date for a plant-type ferredoxin. The structure has the general features of the plant-type ferredoxins already described, with conformational differences corresponding to regions of higher mobility. Immunological data indicate that a serine residue within the protein is partially phosphorylated. A slightly electropositive shift in the measured redox potential value, -325 mV, is observed in comparison with other ferredoxins.Conclusions: This high-resolution structure provides a detailed picture of the hydrogen-bonding pattern around the [2Fe–2S] cluster of a plant-type ferredoxin; for the first time, it was possible to obtain reliable error estimates for the geometrical parameters. The presence of phosphoserine in the protein indicates a possible mechanism for the regulation of the distribution of reducing power from the photosynthetic electron-transfer chain.     

Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-Å resolution

The three-dimensional structure of the saccharopine reductase enzyme from the budding yeast Saccharomyces cerevisiae was determined to 1.7-A resolution in the apo form by using molecular replacement. The enzyme monomer consists of three domains: domain I is a variant of the Rossmann fold, domain II folds into a alpha/beta structure containing a mixed seven-stranded beta-sheet as the central core, and domain III has an all-helical fold. Comparative fold alignment with the enzyme from Magnaporthe grisea suggests that domain I binds to NADPH, and domain II binds to saccharopine and is involved in dimer formation. Domain III is involved in closing the active site of the enzyme once substrates are bound. Structural comparison of the saccharopine reductase enzymes from S. cerevisiae and M. grisea indicates that domain II has the highest number of conserved residues, suggesting that it plays an important role in substrate binding and in spatially orienting domains I and III.     

Crystal structure of bullfrog M ferritin at 2.8 Å resolution: analysis of subunit interactions and the binuclear metal center

Ferritins concentrate and store iron as a mineral in all bacterial, plant, and animal cells. The two ferritin subunit types, H or M (fast) and L (slow), differ in rates of iron uptake and mineralization and assemble in vivo to form heteropolymeric protein shells made up of 24 subunits; H/L subunit ratios reflect cell specificity of H and L subunit gene expression. A diferric peroxo species that is the initial reaction product of Fe(II) in H-type ferritins, as well as in ribonucleotide reductase (R2) and methane monooxygenase hydroxylase (MMOH), has recently been characterized, exploiting the relatively high accumulation of the peroxo intermediate in frog H-subunit type recombinant ferritin with the M sequence. The stability of the diferric reaction centers in R2 and MMOH contrasts with the instability of diferric centers in ferritin, which are precursors of the ferric mineral. We have determined the crystal structure of the homopolymer of recombinant frog M ferritin in two crystal forms: P4(1)2(1)2, a = b = 170.0 A and c = 481.5 A; and P3(1)21, a = b = 210.8 A and c = 328.1 A. The structural model for the trigonal form was refined to a crystallographic R value of 19.0% (Rfree = 19.4%); the two structures have an r.m.s.d. of approximately 0.22 A for all C alpha atoms. Comparison with the previously determined crystal structure of frog L ferritin indicates that the subunit interface at the molecular twofold axes is most variable, which may relate to the presence of the ferroxidase site in H-type ferritin subunits. Two metal ions (Mg) from the crystallization buffer were found in the ferroxidase site of the M ferritin crystals and interact with Glu23, Glu58, His61, Glu103, Gln137 and, unique to the M subunit, Asp140. The data suggest that Gln137 and Asp140 are a vestige of the second GluxxHis site, resulting from single nucleotide mutations of Glu and His codons and giving rise to Ala140 or Ser140 present in other eukaryotic H-type ferritins, by additional single nucleotide mutations. The observation of the Gln137xxAsp140 site in the frog M ferritin accounts for both the instability of the diferric oxy complexes in ferritin compared to MMOH and R2 and the observed kinetic variability of the diferric peroxo species in different H-type ferritin sequences.     

Improving the accuracy of macromolecular structure refinement at 7 Å resolution

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Highlights? Improved models by DEN refinement at 7 Å ? Best method is DEN refinement with initial segmented rigid-body refinement ? R_free has predictive power at 7 Å     

Effect of temperature and surface potential on the electrogenic proton uptake in the QB site of the Rhodobacter sphaeroides photosynthetic reaction center: QA −. B −. → QAQBH2 transition

Direct electrometry was used to study the light-induced voltage changes in the Rhodobacter sphaeroides chromatophores adsorbed to a phospholipid-impregnated nitrocellulose film. After the second laser flash, a fast increase in the voltage associated with charge separation was followed by a slower increase attributed to the proton uptake in the Q_B site of the photosynthetic reaction centers. Kinetics and relative amplitudes of these voltage changes attributed to the Q_A ^–. _B ^–. Q_AQ_BH₂ transition, were measured as a function of pH and temperature between +4 and +40 °C. The kinetics can be approximated by a single exponent above +23 °C (100 µs at +25 °C, pH 7.2), whereas below this temperature, it was a good fit of two exponential approximation (65 µs and 360 µs with similar contributions at +10 °C, pH 7.2). The faster component diminished with an apparent pK 8.5, whereas the slower one was maintained at a constant level until pH 9.5 and then decreased. The calculated activation energy from the temperature dependence of the slower component (55 – 65 kJ/mol) was much higher than that of the faster component (< 10 kJ/mol). The two voltage components can be attributed to the transfer of the first (faster component) and the second (slower component) proton from the reaction center surface to Q_B. We suggested that higher activation energy of the slower component was due to a conformational change in the reaction center kinetically coupled to the second proton transfer to Q_BH^–.The faster component diminished in the presence of 1 M KCl, with an apparent pK 7.5. To explain this observation, we assume that: (i) the midpoint potential of the Q_A/Q_A ^–. redox pair was higher in 1 M KCl because of the reduced surface potential of chromatophores; (ii) the midpoint potential of the Q_B ^–./Q_BH^–. redox pair was insensitive to the surface potential change; (iii) the equilibrium constant of the reaction Q_A ^–.Q_B ^–. Q_AQ_BH^– decreased at high ionic strength.     

Molecular structure of troponin C from chicken skeletal muscle at 3Å resolution

Troponin C is the Ca²⁺-binding subunit of the troponin complex and is involved in the calcium control of muscle contraction. The X-ray structure of chicken TnC has been determined at 3Å resolution using a single heavy atom derivative and application of a novel phase improvement and phase extension procedure. The protein has an unusual dumbbell-shape with a length of about 70A. The N- and C-domains are connected by a single long α-helix of about 9 turns. Two metal binding sites (the Ca²⁺-Mg²⁺ sites) in the C-domain are occupied by metal ions in the crystals and the helix-loop-helix Ca²⁺ -binding folds are very similar to those in other known Ca²⁺ -binding proteins. In contrast, the Ca²⁺ -specific sites in the N-domain appear unoccupied and the two putative Ca²⁺ -binding folds have a vastly different structural arrangement. The conformational rearrangements in the N-domain upon Ca²⁺ binding are believed to be the trigger for a cascade of protein-protein interaction alterations which lead to muscle contraction.     

The Efficiency of Energy Transfer from Quantum Dots to Photosynthetic Reaction Centers of Rhodobacter sphaeroides in the Temperature Range of 100–310 K

Biophysics - The temperature dependence of the efficiency of energy transfer from polymer coated CdSe/CdS/ZnS quantum dots bearing terminal carboxyl groups to the reaction centers of purple...     

Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 Å resolution

Journal of Structural and Functional Genomics -     

The fine structure of the salivary glands of the desert locust Schistocerca gregaria Forskål

Summary This paper describes the structure of the salivary glands of Schistocerca gregaria as seen under the electron microscope and the light microscope. The salivary glands consist of a number of acini located on both sides of the pro-, meso-, and metathoracic segments of the locust. Each acinus is drained by a duct which unites with others from the same side to form a lateral collecting duct. The ducts from the two sides join in the head capsule and open into a salivary cup on the labium. Each acinus consists of parietal cells, zymogenic cells, duct cells, tracheoblasts, sheath cells and pigment cells. The parietal and zymogenic cells are the main sites for the production of the salivary gland secretions, which pass through microvilli from the zymogenic cells to the lumen of the ducts within the acinus. Outside the acinus each duct is composed of highly specialized cells with infolded basement membranes extending about a third of the way across the cell. The cytoplasm between the membranes contains elongated mitochondria and glycogen granules. The apical border of the cell is thrown into microvilli which are closely aggregated under the cuticle lining the duct. These cells have all the features of cells previously described in vertebrates and invertebrates which are known to absorb water and/or ions. Absorption of water from the gut could allow the excretion of hypertonic saliva by the locust.