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a fast in silico simulation of ion flux through the large-pore channel proteins.the psst program (see accompanying article) utilizes the detailed structure of a large-pore channel protein as the sole input for selection of trajectories along which negative and positive ions propagate. in the present study we applied this program to reconstruct the ion flux through five large-pore channel proteins (phoe, ompf, the wt r. blastica general diffusion porin and two of its mutants). the conducting trajectories, one for positive and one for negative particles, are contorted pathway ...200212496073
rhodopseudomonas faecalis sp. nov., a phototrophic bacterium isolated from an anaerobic reactor that digests chicken faeces.five isolates of a previously undescribed species of purple non-sulfur phototrophic bacteria were characterized. they were gram-negative, had mobile, budding vibrioid cells and contained lamellar intracytoplasmic membranes. cultures produced red pigments in the light. live cells of photosynthetic cultures exhibited absorption maxima at 382, 460-464, 494-496, 534-538, 596, 804-806 and 870-874 nm, indicating the presence of bacteriochlorophyll a and carotenoids belonging to the spirilloxanthin ser ...200212508868
[a comparative study of the isocitrate dehydrogenases of chlorobium limicola forma chlorobium thiosulfatophilum and rhodopseudomonas palustris].the carboxylation of 2-oxoglutarate in the reductive tricarboxylic acid cycle in the obligate photolithotroph chlorobium limicola forma thiosulfatophilum and the oxidation of isocitrate in the tricarboxylic acid cycle in the photoheterotroph rhodopseudomonas palustris are catalyzed by isocitrate dehydrogenases. a comparative study of these enzymes isolated from the two bacteria showed that they virtually do not differ in the enzymatic and kinetic properties.200212526196
detergent structure in crystals of the integral membrane light-harvesting complex lh2 from rhodopseudomonas acidophila strain 10050.integral membrane proteins are solubilized by their incorporation into a detergent micelle. the detergent micelle has a critical influence on the formation of a three-dimensional crystal lattice. the bulk detergent phase is not seen in x-ray crystal structures of integral membrane proteins, due to its disordered character. here, we describe the detergent structure present in crystals of the peripheral light-harvesting complex of the purple bacteria rhodopseudomonas acidophila strain 10050 at a m ...200312547211
[phenotypic features and genetic diversity of strains of rhodopseudomonas].14 strains of purple non-sulfur bacteria and 3 type strains of rhodopseudomonas were investigated by phenotypic characterizing, dna-dna hybridizing and dgge analyzing. the characteristics of their morphology, structure and physiology show that 14 strains of isolates have the features of the genus rhodopseudomonas: dividing asymmetrically by budding, lamellar intracytoplasmic membranes, presence of bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series. on the base of their di ...200012548985
[isolation and identification of rhodopseudomonas acidophila from fujian province, china].a strain p301 of gram negative purple nonsulfur bacterium was isolated from the ditch's mud collected in fuzhou, fujian. the cells are rod-shaped. multiplication occur by budding without stalk formation. growth optimum ph is 5.0-5.7. no growth factors required. the cells contain bacteriochlorophyll a. the photosynthetic membrane system consists of parallel lamellae. according to bergery's manual of determinative bacteriology, 8th ed. (1974) and 9th ed. (1994), the strain was identified to be rho ...199812549405
isolation and molecular characterization of pmg160, a mobilizable cryptic plasmid from rhodobacter blasticus.a 3.4-kb cryptic plasmid was obtained from a new isolate of rhodobacter blasticus. this plasmid, designated pmg160, was mobilizable by the conjugative strain escherichia coli s17.1 into rhodobacter sphaeroides, rhodobacter capsulatus, and rhodopseudomonas palustris. it replicated in the latter strains but not in rhodospirillum rubrum, rhodocyclus gelatinosus, or bradyrhizobium species. plasmid pmg160 was stably maintained in r. sphaeroides for more than 100 generations in the absence of selectio ...200312570988
nanodissection and high-resolution imaging of the rhodopseudomonas viridis photosynthetic core complex in native membranes by afm. atomic force microscopy.in photosynthesis, highly organized multiprotein assemblies convert sunlight into biochemical energy with high efficiency. a challenge in structural biology is to analyze such supramolecular complexes in native membranes. atomic force microscopy (afm) with high lateral resolution, high signal-to-noise ratio, and the possibility to nanodissect biological samples is a unique tool to investigate multiprotein complexes at molecular resolution in situ. here we present high-resolution afm of the photo ...200312574504
an artificial antenna complex containing four ru(bpy)3(2+)-type chromophores as light-harvesting components and a ru(bpy)(cn)4(2-) subunit as the energy trap. a structural motif which resembles the natural photosynthetic systems.a cyclam subunit bearing four light-harvesting ru(bpy)3(2+)-type species is connected to a ru(ii) compound having low-lying excited states (energy trap) by hydrogen bonding: the light absorbed by the light-harvesting elements is funnelled to the energy trap with high efficiency.200312585433
the structure and thermal motion of the b800-850 lh2 complex from rps.acidophila at 2.0a resolution and 100k: new structural features and functionally relevant motions.the structure at 100k of integral membrane light-harvesting complex ii (lh2) from rhodopseudomonas acidophila strain 10050 has been refined to 2.0a resolution. the electron density has been significantly improved, compared to the 2.5a resolution map, by high resolution data, cryo-cooling and translation, libration, screw (tls) refinement. the electron density reveals a second carotenoid molecule, the last five c-terminal residues of the alpha-chain and a carboxy modified alpha-met1 which forms t ...200312595263
photobiodegradation of pyridine by rhodopseudomonas palustris ja1.a purple non-sulfur bacterium isolated from dairy effluent was identified as rps. palustris ja1. this organism was able to grow on pyridine as sole source of carbon in a light dependent anaerobic process with a doubling time of 30 h. intermediates of pyridine photobiodegradation were identified as glycine and malonate, produced in stoichiometric molar ratios with simultaneous utilization, yielding biomass.200212597034
the ring structure and organization of light harvesting 2 complexes in a reconstituted lipid bilayer, resolved by atomic force microscopy.the main function of the transmembrane light-harvesting complexes in photosynthetic organisms is the absorption of a light quantum and its subsequent rapid transfer to a reaction center where a charge separation occurs. a combination of freeze-thaw and dialysis methods were used to reconstitute the detergent-solubilized light harvesting 2 complex (lh2) of the purple bacterium rhodopseudomonas acidophila strain 10050 into preformed egg phosphatidylcholine liposomes, without the need for extra che ...200312668456
rhodobacter sphaeroides has a family ii pyrophosphatase: comparison with other species of photosynthetic bacteria.the cytoplasmic pyrophosphatase from rhodobacter sphaeroides was purified and characterized. the enzyme is a homodimer of 64 kda. the n-terminus was sequenced and used to obtain the complete pyrophosphatase sequence from the preliminary genome sequence of rba. sphaeroides, showing extensive sequence similarity to family ii or class c pyrophosphatases. the enzyme hydrolyzes only mg-pp(i) and mn-pp(i) with a k(m) of 0.35 mm for both substrates. it is not activated by free mg (2+), in contrast to t ...200312669192
[calculation of spectra of absorption and circular dichroism of rhodopseudomonas acidophila light harvesting complexes based on roentgen structural data].absorption and circular dichroism spectra of two forms of the peripheral light-harvesting complex from photosynthetic purple bacteria rhodopseudomonas acidophila were calculated. calculations were carried out on the basis of exciton theory for circular aggregates of bacteriochlorophyll molecules and x-ray data for these forms of the complex. it was shown that theoretical spectra fit well experimental ones at the same values of excitation energy, homogeneous and inhomogeneous broadening, and band ...200312723345
some properties of glycine aminotransferase purified from rhodopseudomonas palustris no. 7 concerning extracellular porphyrin production.glycine aminotransferase (ec 2.6.1.4; glyat) was presumed to be an enzyme concerning the supply of glycine for the extracellular porphyrin production by rhodopseudomonas palustris no. 7. glyat was purified from strain no. 7 as an electrophoretically homogenous protein. the enzyme was a monomer protein with the molecular weight of about 42,000. from the absorption spectrum of the enzyme (350 nm, 410 nm), it was indicated that the enzyme had pyridoxal phosphate as a prosthetic group. the enzyme sh ...200312784618
influence of carotenoid molecules on the structure of the bacteriochlorophyll binding site in peripheral light-harvesting proteins from rhodobacter sphaeroides.in the lh2 proteins from rhodobacter (rb.) sphaeroides, the hydrogen bonds between the bacteriochlorophyll (bchl) molecules and their proteic binding sites exhibit a strong variance with respect to carotenoid content and type. in the absence of the carotenoid molecule, such as in the lh2 from rb. sphaeroides r26.1, the void in the protein structure induces a significant reorganization of the binding site of both bchl molecules responsible for the 850 nm absorption, which is not observed when the ...200312795622
afm imaging of bacteria in liquid media immobilized on gelatin coated mica surfaces.immobilization of particulates, especially biomolecules and cells, onto surfaces is critical for imaging with the atomic force microscope (afm). in this paper, gelatin coated mica surfaces are shown to be suitable for immobilizing and imaging both gram positive, staphylococcus aureus, and gram negative, escherichia coli, bacteria in both air and liquid environments. gelatin coated surfaces are shown to be superior to poly-l-lysine coated surfaces that are commonly used for the immobilization of ...200312801673
multichannel carotenoid deactivation in photosynthetic light harvesting as identified by an evolutionary target analysis.a new channel of excitation energy deactivation in bacterial light harvesting was recently discovered, which leads to carotenoid triplet population on an ultrafast timescale. here we show that this mechanism is also active in lh2 of rhodopseudomonas acidophila through analysis of transient absorption data with an evolutionary target analysis. the algorithm offers flexible testing of kinetic network models with low a priori knowledge requirements. it applies universally to the simultaneous fittin ...200312829499
in most bradyrhizobium groups sequence comparison of 16s-23s rdna internal transcribed spacer regions corroborates dna-dna hybridizations.in an extension of a previous small-scale test to assess the use of 16s-23s rdna internal transcribed spacer (its) sequences for rapid grouping of bradyrhizobia, we have sequenced the its region of 32 isolates of bradyrhizobium that had previously been studied using aflp and dna-dna hybridizations. we also included representatives of afipia and rhodopseudomonas. our results indicate that its sequences are very diverse among bradyrhizobia. nevertheless, for most of the bradyrhizobia, the grouping ...200312866847
phytoplankton successions under ice cover in four lakes located in north-eastern sweden: effects of liming.phytoplankton successions under ice cover (january-march) were determined in four oligotrophic lakes (burtjärn, aspen, vialamptjärn and storkorstjärn) located in north-eastern sweden. the total phosphorus concentration in the lakes was less than 10 micrograms/l. lake burtjärn (reference lake) had a similar hydrology as lake aspen. storkorstjärn and vialamptjärn were of similar hydrology and had heavily colored water (> 100 mgpt/l). aspen as well as vialamptjärn became continuously limed with cal ...200312879750
augmentation of h2 photoproduction in rhodopseudomonas palustris by n-heterocyclic aromatic compounds.increases of 23- (5.6 mmol acetylene reduced mg dry wt(-1)) and 16- (4 mmol acetylene reduced mg dry wt(-1)) fold in nitrogenase activity and 12- (671 microl h2 mg dry wt(-1) h(-1)) and 6- (349 microl mg dry wt(-1) h(-1)) fold in h2 photoproduction in rhodopseudomonas palustris ja1 over 24 h were achieved with pyrazine 2-carboxylate (3 mm) and 3-picoline (3 mm), respectively, and were higher than earlier reports of enhancement (1.5 to 5-fold) in biological h2 production using various alternative ...200312882311
effects of photosynthetic reaction center h protein domain mutations on photosynthetic properties and reaction center assembly in rhodobacter sphaeroides.purple bacterial photosynthetic reaction center (rc) h proteins comprise three cellular domains: an 11 amino acid n-terminal sequence on the periplasmic side of the inner membrane; a single transmembrane alpha-helix; and a large c-terminal, globular cytoplasmic domain. we studied the roles of these domains in rhodobacter sphaeroides rc function and assembly, using a mutagenesis approach that included domain swapping with blastochloris viridis rc h segments and a periplasmic domain deletion. all ...200312885224
construction of a genetically engineered microorganism for co2 fixation using a rhodopseudomonas/escherichia coli shuttle vector.the co2 fixation ability of rhodopseudomonas palustris dh was enhanced by introducing the recombinant plasmid pmg-cbbm containing the form ii ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) gene (cbbm) isolated from rps. palustris no. 7. sequencing of a 3.0-kb psti fragment containing the cbbm gene revealed an open reading frame encoding 461 amino acids, homologous to known cbbm genes, with a ribosome binding site upstream of cbbm and a terminator downstream of cbbm, without promoter. ...200312900023
changing concepts in the systematics of bacterial nitrogen-fixing legume symbionts.as of february 2003, bacteria that form nitrogen-fixing symbiotic associations with legumes have been confirmed in 44 species of 12 genera. phylogenies of these taxa containing legume symbionts based on the comparative analysis of 16s rdna sequences show that they are not clustered in one lineage but are distributed in the classes alphaproteobacteria and betaproteobacteria, and dispersed over the following nine monophyletic groups, being intermingled with other taxa that do not contain legume sy ...200312949698
biogeography of the purple nonsulfur bacterium rhodopseudomonas palustris.the biogeography of the purple nonsulfur bacterium rhodopseudomonas palustris on a local scale was investigated. thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by box-pcr genomic dna fingerprinting. cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were rep ...200312957900
spatial distribution of rhodopseudomonas palustris ecotypes on a local scale.the number, spatial distribution, and significance of genetically distinguishable ecotypes of prokaryotes in the environment are poorly understood. oda et al. (y. oda, b. star, l. a. huisman, j. c. gottschal, and l. j. forney, appl. environ. microbiol. 69:xxx-xxx, 2003) have shown that rhodopseudomonas palustris ecotypes were lognormally distributed along a 10-m transect and that multiple strains of the species could coexist in 0.5-g sediment samples. to extend these observations, we investigate ...200312957901
tuning heme redox potentials in the cytochrome c subunit of photosynthetic reaction centers.the photosynthetic reaction center (rc) from rhodopseudomonas viridis contains four cytochrome c hemes. they establish the initial part of the electron transfer (et) chain through the rc. despite their chemical identity, their midpoint potentials cover an interval of 440 mv. the individual heme midpoint potentials determine the et kinetics and are therefore tuned by specific interactions with the protein environment. here, we use an electrostatic approach based on the solution of the linearized ...200312975370
porphyrin synthesis by rhodopseudomonas speroides. 195313093645
factors determining the viability of selected microorganisms in inorganic media. 195413174488
the photosynthetic metabolism of acetone by rhodopseudomonas gelatinosa. 195413174528
hematin compounds in photosynthetic bacteria. 195413221572
enzymatic activities affecting cytochromes in photosynthetic bacteria. 195413221573
comparative studies on bacterial cytochromes. 195513239624
the synthesis of porphyrins and bacteriochlorophyll by cell suspensions of rhodopseudomonas spheroides. 195613293156
the effect of x-rays on the survival of bacteria and yeast. i. a comparative study of the dose-survival curves of azotobacter agile, escherichia coli, pseudomonas fluorescens, rhodopseudomonas spheroides, and saccharomyces cerevisiae irradiated in the resting state. 195613331870
some mutational changes in the photosynthetic pigment system of rhodopseudomonas spheroides. 195613346032
studies in carotenogenesis. 23. the nature of the carotenoids in the photosynthetic bacterium rhodopseudomonas spheroides (athiorhodaceae). 195613373799
ph-induced changes of the infrared absorption spectra of purple bacteria. 195613373840
an assay of iron protoporphyrin based on the reduction of nitrate by a variant strain of staphylococcus aureus; synthesis of iron protoporphyrin by suspensions of rhodopseudomonas spheroides. 195613376883
relative biological efficiency of 1000-kvp and 250-kvcp x-rays. ii. supplemental determinations based on the dose-survival curves of escherichia coli and rhodopseudomonas spheroides. 195613379621
a note on the porphyrins excreted by the blue-green mutant of rhodopseudomonas spheroides. 195613405969
the biology of photosynthetic bacterium which lacks colored carotenoids. 195613405970
the dark anaerobic metabolism of acetone and acetate by the photosynthetic bacterium rhodopseudomonas gelatinosa. 195713475293
some effects of ultraviolet on respiration in purple bacteria. 195813534435
the carotenoids of rhodopseudomonas. i. carotenoids of the green mutant. 195813534716
the carotenoids of rhodopseudomonas. ii. a comparative study of mutants and the wild type. 195813534717
biosynthesis of delta-aminolaevulic acid by extracts of rhodopseudomonas spheroides. 195813535752
[development of facultative anaerobic purple bacteria and its relation to oxidation-reduction of the environment]. 195713540934
endogenous photosensitization in a carotenoidless mutant of rhodopseudomonas speroides.endogenous photosensitization in a carotenoidless mutant of rhodopseudomonas spheroides has been studied. when this mutant is exposed to visible light and oxygen there is a short lag period followed by exponential killing of the cells. the killing process obeys the bunsen-roscoe law of reciprocity and is temperature-independent. the chlorophyll content of the cells does not affect the rate of killing until a certain low threshold has been reached. exposure of photosynthetically grown cells to ai ...195813563800
intermediates in the biosynthesis of porphyrins from porphobilinogen by rhodopseudomonas spheroides. 195813566079
action of a non-ionic detergent on chromatophores of rhodopseudomonas spheroides. 195813572382
the enzymatic synthesis of delta-aminolevulinic acid. 195813598764
enzymatic synthesis of sigma-aminolevulinic acid. 195813627809
the biosynthesis of porphyrins from porphobilinogen by rhodopseudomonas spheroides. 195913651129
some enzymic reactions concerned in the metabolism of acetoacetyl-coenzyme a in athiorhodaceae. 196113691001
role of h2o2 in the photooxidative killing of blue-green mutants of rhodopseudomonas spheroides. 196113694000
noncyclic photophosphorylation in photosynthetic bacteria. 196113729856
observations on a b-type cytochrome from rhodopseudomonas spheroides. 196113731175
the lack of diphosphofructose aldolase in two photosynthetic organisms: anacystis nidulans and rhodopsudomonas spheroides. 196113741386
inhibitory effect of light on oxygen-uptake by cell-free extracts and particulate fractions of rhodopseudomonas palustris. 196113751778
the formation of isocitratase by the athiorhodaceae. 196013753189
carboxylic acids metabolism and its relation to porphyrin biosynthesis in rhodopseudomonas spheroides under light-anaerobic conditions. 196113755908
the intracellular concentration of succinic acid in photosynthetic bacteria. 196113759249
the formation of ribulose 1:5-diphosphate carboxylase by growing cultures of athiorhodaceae. 196013759251
the synthesis of enzymes concerned in bacteriochlorophyll formation in growing cultures of rhodopseudomonas spheroides. 196013759252
[preliminary observations on the microbial flora of thermal waters of viterbo in the nature of sulfobacteria]. 195913792401
rhodopseudomonas spheroides: high catalase and blue-green double mutants. 196013810590
[aerobiosis and the hemoprotein content of photosynthetic bacteria]. 195913810591
an intermediate stage in the hydrogen peroxide-induced synthesis of catalase in rhodopseudomonas spheroides. 196013810592
kinetics of hydrogen peroxide destruction in rhodopseudomonas spheroides: roles of catalase and other enzymes. 196013810593
permeability barriers and the assay of catalase in intact cells. 195913810594
physiology of induced catalase synthesis in rhodopseudomonas spheroides. 196013810595
protein synthesis in the induced formation of catalase in rhodopseudomonas spheroides. 196013810596
purified catalase from rhodopseudomonas spheroides. 195913810597
the induced synthesis of catalase in rhodopseudomonas spheroides. 196013810598
function of carotenoids in photosynthetic bacteria. 195913818963
the effect of dark, aerobic growth on the photosensitivity of carotenoidless rhodopseudomonas spheroides. 196013818964
absorption spectrum changes observed on illumination of aerobic suspensions of photosynthetic bacteria. 196013832061
reactions of carotenoid pigments in photosynthetic bacteria. 196013832062
carbohydrate metabolism in rhodopseudomonas sphreoides. 196013836488
energy transfer between carotenoids and bacteriochlorophyll in chromatophores of purple bacteria. 195913850395
the lethal effects of x-irradiation and of hydrogen peroxide on wild-type and on a high-catalase mutant of rhodopseudomonas spheroides. 196213859441
enzymes of the beta-hydroxy-beta-methylglutaryl-coenzyme a cycle in rhodopseudomonas spheroides. 196213876813
protein synthesis and viability in x-irradiated rhodopseudomonas spheroides. 196213879849
high-catalase mutant rhodopseudomonas spheroides. characterization of the catalase. 196213879850
[studies on the products of assimilation of carbon c-14 by rhodo-pseudomonas issatchenkoi bacteria]. 196213887076
studies on the biosynthesis of porphyrin and bacteriochlorophyll by rhodopseudomonas spheroides. 2. the effects of ethionine and threonine. 196213898422
studies on the biosynthesis of porphyrin and bacteriochlorophyll by rhodopseudomonas spheroides. 1. the effect of growth conditions. 196213898423
studies on the biosynthesis of prophyrin and bacteriochlorophyll by rhodoseudomonas spheroides. 3. the effect of threonine on the biosynthesis of homoserine and methionine. 196213898424
further mutational changes in the photosynthetic pigment system of rhodopseudomonas spheroides. 196213901878
the fatty acids of rhodopseudomonas particles. 196213904320
pulse-labeled ribonucleic acid of rhodopseudomonas spheroides in the presence and absence of massive catalase formation. 196213905705
carotenoid pigment conversion in rhodopseudomonas spheroides. 196213912201
observations on the relationship between the formation of photopigments and the synthesis of protein in rhodopseudomonas spheroides. 196213913484
the kinetics of the synthesis of photopigments in rhodopseudomonas spheroides. 196213913485
gamma,delta-dioxovalerate aminotransferase activity in rhodopseudomonas spheroides. 196313938132
studies on the electron-transfer systems in photosynthetic bacteria. i. the light-induced absorption-spectrum changes and the effect of phenylmercuric acetate. 196313938786
studies on the electron-transfer systems in photosynthetic bacteria. ii. the effect of heptylhydroxyquinoline-n-oxide and antimycin a on the photosynthetic and respiratory electron-transfer systems. 196313938787
nuclear envelope-chloroplast relationships in algae.in ochromonas danica and two related species (chrysophyceae) and in rhodomonas lens and cryptomonas sp. (cryptophyceae), the chloroplast is surrounded by an outer double-membraned envelope which lies outside the usual double-membraned chloroplast envelope. at the borders of the area where the chloroplast lies adjacent to the nucleus, this outer envelope is continuous with the outer membrane of the nuclear envelope as a double-membraned outfolding, so that the entire chloroplast in these species ...196213947685
observations on the respiratory system of rhodospirillum rubrum. 196213954901
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