Interaction of metal ions with humic-like models. Part 5. The crystal and molecular structure of diaquabis(2,6-dihydroxybenzoato)-dioxouranium(VI) octahydrate

The crystal and molecular structure of the complex [UO₂(DHB)₂(H₂O)₂]·8H₂O (DHB = 2,6-di- hydroxybenzoato) has been determined from single- crystal X-ray analysis and refined to a final R value of 0.033 for 3620 observed reflections. The complex crystallizes in the monoclinic system, space group C2/m, with a = 6.704(3), b = 20.171(6), c = 9.454(4) Å and Z = 2. The coordination about the uranyl group, which is linear, involves two bidentate carboxylate groups and two water molecules in trans positions giving rise to an irregular hexagonal bipyramid. Intra- molecular hydrogen bonds between phenolic and carboxylate groups forming six-membered rings allow the molecule to be nearly planar. Spectroscopic (IR, NMR and electronic absorption) data and thermal properties of the compound are also reported.     

Complexes of dibenzylsulfoxide with lanthanide nitrate

A new series of dibenzylsulfoxide (DBSO) compounds of empirical formula [Ln(DBSO)_x(NO₃)₃] are reported, where x = 3 for Ln = Pr; x = 2.5 for Ln = Nd, Sm, Eu, Gd, Er and La; and x=2 for Ln = Dy. The compounds were synthesized from a non-aqueous solvent and isolated as dibenzylsulfoxide salts. Infrared spectral data established coordination by the anion groups and also that coordination of DBSO is through the oxygen. Additional information based on the nature of bonding and geometrical structure was obtained from the electronic absorption spectra, X-ray diffraction analysis, molecular conductivities and molecular weight measurements (as well as magnetic susceptibility measurements). All these physical measurements indicate octahedral coordination. The 20% decrease in the metal ion radius across the lanthanide series and the competition between DBSO and nitrate groups for the coordination site affect the number of DBSO molecules bonded to a tripositive lanthanide ion.     

Isolation and properties of cytochrome c-553, cytochrome c-550, and cytochrome c-549, 554 from Nitrobacter agilis

Three c-type cytochromes isolated from Nitrobacter agilis were purified to apparent homogeneity: cytochrome c-553, cytochrome c-550 and cytochrome c-549, 554. Their amino acid composition and other properties were studied. Cytochrome c-553 was isolated as a partially reduced form and could not be oxidized by ferricyanide. The completely reduced form of the cytochrome had absorption maxima at 419, 524 and 553 nm. It had a molecular weight of 25 000 and dissociated into two polypeptides of equal size of 11 500 during SDS gel electrophoresis. The isoelectric point of cytochrome c-553 was pH 6.8. The ferricytochrome c-550 exhibited an absorption peak at 410 nm and the ferrocytochrome c showed peaks at 416, 521 and 550 nm. The molecular weight of the cytochrome estimated by gel filtration and by SDS gel electrophoresis was 12 500. It had an E_m(7) value of 0.27 V and isoelectric point pH 8.51. The N-terminal sequence of cytochrome c-550 showed a clear homology with the corresponding portions of the sequences of other c-type cytochromes. Cytochrome c-549, 554 possessed atypical absorption spectra with absorption peaks at 402 nm as oxidized form and at 419, 523, 549 and 554 nm when reduced with Na₂S₂O₄. Its molecular weight estimated by gel filtration and SDS polyacrylamide gel electrophoresis was 90 000 and 46 000, respectively. The cytochrome had an isoelectric point of pH 5.6. Cytochrome c-549, 554 was highly autoxidizable.     

Tuning antenna function through hydrogen bonds to chlorophyll a

We describe a molecular mechanism tuning the functional properties of chlorophyll a (Chl-a) molecules in photosynthetic antenna proteins. Light-harvesting complexes from photosystem II in higher plants – specifically LHCII purified with α- or β-dodecyl-maltoside, along with CP29 – were probed by low-temperature absorption and resonance Raman spectroscopies. We show that hydrogen bonding to the conjugated keto carbonyl group of protein-bound Chl-a tunes the energy of its Soret and Q_y absorption transitions, inducing red-shifts that are proportional to the strength of the hydrogen bond involved. Chls-a with non-H-bonded keto C13¹ groups exhibit the blue-most absorption bands, while both transitions are progressively red-shifted with increasing hydrogen-bonding strength – by up 382 & 605 cm⁻¹ in the Q_y and Soret band, respectively. These hydrogen bonds thus tune the site energy of Chl-a in light-harvesting proteins, determining (at least in part) the cascade of energy transfer events in these complexes.     

A slow fluctuation in the molecular conformation of a soya bean trypsin inhibitor

The kinetics of the hydrogen-deuterium exchange reaction in a trypsin inhibitor (Kunitz) from soya bean have been followed by infrared absorption measurements in aqueous solutions at various temperatures and pH values. It was found that, in every case, 49% of the total peptide hydrogen atoms exchange relatively slowly. This amount corresponds to 83 peptide groups per molecule, and this is considered to be equal to the number of peptide NH groups involved in hydrogen bonds with the carbonyls of other peptide groups in the protein molecule in its native form. Each rate constant (k) determined at pH 2.75 for this category of the NH groups is in good agreement with the value expected from an idea that the breaking of the peptide-peptide hydrogen bonds takes place very slowly, and that this is the rate-determining process in the hydrogen-deuterium exchange reaction. Thus, by ultraviolet absorption measurements at 297 nm, the equilibrium constant of the native and denatured forms has been determined in the temperature range from 42 to 53.5 °C, as well as the reaction rate of reaching equilibrium from an off-equilibrium state. From these data the rate constant (k₁) of the denaturation reaction is determined, and the k₁ value is found to be practically equal to the hydrogen exchange rate constant (k). The Arrhenius plot of this rate constant (k) gives a straight line in the 25 to 55 °C region, and this gives a value of 48.6 kcal/mol for the activation energy of the denaturation reaction. The rate of this reaction is found to be very low at 25 °C; its half-life is about eleven days. Infrared absorption spectra observed in the amide I region suggest that the very slow denaturation of this protein is accompanied by a conformation change from an α-helix to a β-form. The number of the peptide groups involved in this α → β change is estimated to be 9 ± 3.     

Electronic transitions and heterogeneity of the bacteriophytochrome Pr absorption band: An angle balanced polarization resolved femtosecond VIS pump–IR probe study

Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump–IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S₀→S₂). Excitation of the S₀→S₂ transition will introduce a more complex photodynamics compared with S₀→S₁ transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.     

Absorption of the flavin dimers

The electronic absorption spectra of the flavomononucleotide (FMN) in aqueous solution and in glycerine-water solution with change of the dye concentration have been measured. The FMN dimer absorption spectrum, monomer absorption spectrum, dimerization constant K and molar fraction of the monomer were calculated. It was found that FMN dimerization constants in aqueous solution were K_a = 118.0 l/mol and in glycerine K_g = 20.5 l/mol. In the region of the monomer absorption band two dimer absorption bands appear, in accordance with the Kasha molecular exciton theory.     

Characterization of cryptomonad phycoerythrin and phycocyanin

Phycoerythrin, a chromoprotein, from the cryptomonad alga Rhodomonas lens is composed of two pairs of nonidentical polypeptides (α₂β₂). This structure is indicated by a molecular weight of 54,300, calculated from osmotic pressure measurements and by sodium dodecyl sulfate (SDS) gel electrophoresis, which showed bands with molecular weights of 9800 and 17,700 in a 1:1 molar ratio. The s_20,w⁰ of 4.3S is consistent with a protein of this molecular weight. Similar results were obtained with another cryptomonad phycoerythrin and a cryptomonad phycocyanin. Electrophoresis after partial cross-linking by dimethyl suberimidate revealed seven bands for the cryptomonad phycocyanin and six bands for cryptomonad phycoerythrin and confirmed the proposed structure. Spectroscopic studies on α and β subunits of cryptomonad phycocyanin and phycoerythrin were carried out on the separated bands in SDS gels. The individual polypeptides possessed a single absorption band with the following maxima: phycoerythrin (R. lens), α at 565 nm, β at 531 nm; phycocyanin (Chroomonas sp.), α at 644 nm, β at 566 nm. Fluorescence polarization was not constant across the visible absorption band regions of phycoerythrin (R. lens and C. ovata) with higher polarizations located at higher wavelengths, as had also been previously shown for cryptomonad phycocyanin (Chroomonas sp.). Combining the absorption spectra and the polarization results indicates that in each case the β subunit contains sensitizing chromophores and the α subunit fluorescing chromophores. The CD spectra of cryptomonad phycocyanin and both phycoerythrins were similar and were related to the spectra of the individual subunits. In Ouchterlony double-diffusion experiments the cryptomonad phycoerythrins and phycocyanins cross-reacted, with spurring, with phycoerythrin isolated from a red alga. The cryptomonad phycoerythrins were immunochemically very similar to each other and to cryptomonad phycocyanin, with little spurring detected.     

Water-soluble chlorophyll protein of Brassica oleracea var. Botrys (cauliflower)

A water-soluble chlorophyll protein was prepared from Brassica oleracea var. Botrys (cauliflower) and purified by (NH₄)₂SO₄ fractionation and by chromatography on a DEAE-cellulose column. The chlorophyll protein contained chlorophylls a and b in the ratio 6:1, and no carotenoids. The molecular weight, determined by means of gel filtration on Sephadex G-100, was 78000. The chlorophyll protein showed absorption peaks at 273, 340, 384, 420, 438, 465, 628, 674 and 700 nm. Since the three bands at 384, 420 and 438 nm all have approximately the same height, the spectrum is different from that of chlorophyll a in organic solvents. The fluorescence of the chlorophyll protein showed a peak at 683 nm, with shoulders at 706 and 745 nm at room temperature, and peaks at 685, 706 and 744 nm at the temperature of liquid N₂. An apo-protein was prepared by removing the chlorophylls with 2-butanone and purified by precipitation with (NH₄)₂SO₄. The apo-protein thus prepared had an absorption band at 273 nm but none at longer wavelengths. The apo-protein could be combined with chlorophylls, forming a chlorophyll protein which had spectral characteristics similar to those of the original.     

Fluorescent BODIPY-labelled GM1 gangliosides designed for exploring lipid membrane properties and specific membrane-target interactions

New fluorophore-labelled G_M1 gangliosides have been synthesised and spectroscopically characterised. Spectroscopically different BODIPY groups were covalently linked, specifically to either the polar or the hydrophobic part of the ganglioside molecule. The absorption and fluorescence spectroscopic properties are reported for 564/571-BODIPY- and 581/591-BODIPY-labelled G_M1. Each of the different BODIPY groups is highly fluorescent and depolarisation experiments provide molecular information about the spatial distribution in lipid bilayers, as well as order and dynamics. From experiments performed on two spectroscopically different BODIPY:s, specific interactions can be revealed by monitoring the rate/efficiency of donor-acceptor electronic energy transfer. Systems of particular interest for applying these probes are e.g. mixtures of lipids, and peptides/proteins interacting with lipid membranes.     

Electronic transitions and heterogeneity of the bacteriophytochrome Pr?absorption band: An angle balanced polarization resolved femtosecond VIS pump–IR probe study

Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump–IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S₀→S₂). Excitation of the S₀→S₂ transition will introduce a more complex photodynamics compared with S₀→S₁ transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.     

Purification and characterization of the blue carotenoprotein from the caparace of the crayfish Procambarus clarkii (Girard)

The isolation, purification and characterization of a blue carotenoprotein isolated from the carapace of the crayfish Procambarus clarkii (Girard) are reported. The molecular weight of the complex has been determined by polyacrylamide gradient gel electrophoresis and gel filtration. Under unfavourable conditions the natural blue complex, designated the α-form (approx. M_r 246 000), dissociated to a purple dimer, the β-form (approx. 41 600). Sodium dodecyl sulphate polyacrylamide gel electrophoresis indicated the β-form to contain two polypeptides, of molecular weight 19 200 and 21 400. The amino-acid composition of the natural protein is described and compared with those of similar carotenoproteins from other crustaceans. The complex contains six carotenoid molecules per molecule of protein (α-form) and the carotenoid has been identified by thin-layer chromatography, light-absorption spectroscopy, HPLC and mass spectrometry as all-trans-astaxanthin (3,3′-dihydroxy-β,β-carotene-4,4′-dione), the three optical isomeric forms, (3R,3′R)-, (3R,3′S) and (3S,3′S), being present in the ratio 20:21:58. The binding of the carotenoid, astaxanthin (absorption maximum in acetone at 470 nm) to the apoprotein results in a marked red spectral shift of about 165 nm, giving rise to absorption maxima at 635 nm and 585 nm for the α- and β-forms, respectively, in 50 mM phosphate buffer (pH 7.5). The λ_max of any sample is dependent upon the relative ratio of α and β forms present.     

On the solvatochromic properties of the oxalate-bridged complexes [(BuCO2)3M2]2(μ-O2C2O2) where M = Mo or W

The room temperature electronic absorption spectra of the oxalate bridged MM quadruply bonded complexes [(^tBuCO₂)₃M₂]₂(μ-O₂C₂O₂), where M = Mo or W have been recorded in H₂O, THF:H₂O mixtures, THF, CH₂Cl₂, toluene, DMSO, aniline, toluene saturated with N,N-dimethylaniline and ethanol. The strong absorptions in the visible region of the electronic absorption spectra assignable to the metal-to-ligand (bridge) charge transfer are shown to be highly solvent dependent. Those samples prepared in H₂O, CH₂Cl₂ and toluene are shown to comprise of a suspension of microcrystalline particles ranging in size from 100 nm to 5 μm. Individual particles were found by scanning electron microscopy to have an aspect ratio of ∼10:1, all being needle shaped. The spectra in THF, EtOH, aniline, DMSO and toluene-N,N-dimethylaniline all show similar vibronic progressions and are attributed to discrete solvated molecular species. The spectra recorded in aniline are notably red-shifted which is proposed to arise from a combination of hydrogen bonding and Lewis base stabilization of the photoexcited state.     

Some Properties of Phytochrome Isolated From Dark-grown Oat Seedlings (Avena sativa L.)

Phytochrome was partially purified from etiolated seedlings of Avena sativa L. Several properties of the red-absorbing (P_R) and far-red absorbing (P_FR) forms of the pigment were compared. The 2 forms could not be shown to differ with respect to their sedimentation velocity in sucrose density gradients, elution volume from Sephadex G-200 columns, binding properties on calcium phosphate, or electrophoretic mobility. P_FR, however, was more labile than P_R during precipitation with 50% ammonium sulfate. Sephadex G-200 elution diagrams obtained with fresh phytochrome preparations revealed 2 components of different molecular weights, 1 roughly 180,000, and 1 roughly 80,000. Native phytochrome had an absorption spectrum in vivo showing an absorption maximum for P_R of 667 nm. Both the large and small forms of phytochrome mentioned above can be maintained with an absorption maximum for P_R of 667 nm. However, allowing them to remain for several hours as P_FR, even at 4°, shifted this peak to 660 nm. The protein conformational change during phytochrome transformation may be quite small, though the various comparative techniques used do not strictly rule out a fairly large one. The need for maintaining the pigment as P_R during all steps of purification, but particularly during ammonium sulfate precipitation is underscored.     

A carotenoid-protein from cyanobacteria

Easily solubilized carotenoid-containing proteins have been found in aqueous extracts from three genera of cyanobacteria. The three proteins have been purified, and the absorption spectra have been determined to be virtually identical with absorption maxima at 495 and 465 nm. During the purification the orange protein spontaneously changed to a red protein with a single, broad absorption maximum at 505 nm. The orange protein showed a molecular weight of 47 000 on gel filtration while that of the red protein was 26 700. Sodium dodecyl sulfate polacrylamide gel electrophoresis indicated a single polypeptide of M_r 16 000 in both the red and orange forms, but this method removed the chromophore from the proteins. The main carotenoid component of the complex was determined to be 3′-hydroxy-4-keto-ββ-carotenoid or 3′-hydroxyechinenone. The number of carotenoid molecules per molecule of orange protein of molecular weight 47 000 was between 20 and 40. The stoichiometry of carotenoid to protein seemed reasonably constant.     

Purification and properties of thiosulfate reductase from Desulfovibrio gigas

Thiosulfate reductase of the dissimilatory sulfate-reducing bacterium Desulfovibrio gigas has been purified 415-fold and its properties investigated. The enzyme was unstable during the different steps of purification as well as during storage at-15°C. The molecular weight of thiosulfate reductase estimated from the chromatographic behaviour of the enzyme on Sephadex G-200 was close to 220 000. The absorption spectrum of the purified enzyme exhibited a protein peak at 278 nm without characteristic features in the visible region. Thiosulfate reductase catalyzed the stoichiometric production of hydrogen sulfide and sulfite from thiosulfate, and exhibited tetrathionate reductase activity. It did not show sulfite reductase activity. The optimum pH of thiosulfate reduction occurred between pH 7.4 and 8.0 and its K _m value for thiosulfate was calculated to be 5·10^-4 M. The sensitivity of thiosulfate reductase to sulfhydryl reagent and the reversal of the inhibition by cysteine indicated that one or more sulfhydryl groups were involved in the catalytic activity. The study of electron transport between hydrogenase and thiosulfate reductase showed that the most efficient coupling was obtained with a system containing cytochromes c ₃ (M _r =13000) and c ₃ (M _r =26000).     

The relationship between absorption of sulfur dioxide (SO2) and inhibition of photosynthesis in several plants

Photosynthetic rate, transpiration rate and SO₂ absorption rate were simultaneously measured under exposure to SO₂ (0.1–1.0 μl l ^?1) for 5 or 8 hr in six species belonging to C₄ or C₃ plants (Zea mays, Sorghum vulgare, Amaranthus tricolor, Oryza sativa, Avena sativa andHelianthus annuus). Distinct interspecific differences were found as to the extent of inhibition of photosynthetic rate. Calculation of diffusive resistance to H₂O(r) and SO₂(r′) showed that the ratio of r′/r was 1.9 irrespective of species and coincided well with the theoretical value based on molecular diffusion. Thus it was made clear that the absorption of SO₂ was dependent upon the gas exchange capacity of leaf blade. Using the ratio of r′/r the rate of SO₂ absorption could be calculated from transpiration rate and was compared with the inhibition rate of photosynthesis. In three C₄ species, the inhibition of photosynthesis increased linearly with the amount of SO₂ absorbed during a 5-hour period. The pattern of inhibition of photosynthesis inA. sativa andH. annuus among C₃ species was similar to that of C₄ species until the amount of SO₂ absorbed reached 60 mg-SO₂ m^?2 above which the inhibition abruptly increased. The inhibition of photosynthesis inO. sativa was exceptionally severe even with only a small amount of SO₂ absorbed.     

RNA-free DNA Extraction Protocol from PinusTissues for Molecular Biology or HPCE/HPLC Analyses

A simple method for extracting DNA from various in vitro or ex vitro Pinus tissues is described. Good yield and high quality RNA-free DNA ready to use in molecular biology assays or analytical analysis was obtained. DNA quality was measured analyzing absorption spectra between 200 and 300 nm, A_260/280 ratio and HPCE. This protocol was tested with no modification in a wide range of Pinus tissues from recalcitrant in vitro callus to mature field scions improving the results obtained with previous protocols. As the protocol is simple, almost universal and inexpensive it may be used for routine isolation from Pinus tissues. An isolation troubleshooting table was included to facilitate the setting up of reported protocol to other plant species.     

Optical and electrochemical properties and the calculated structure of pentacoordinate aluminum 8-hydroxyquinoline

In this study we report on the characterization of a series of pentacoordinate aluminum 8-hydroxyquinolines, AlQ₂X (X = F, Cl, Br), composed of two 8-hydroxyquinoline (8-HQ) groups and one halogen ligand. These were prepared by reacting 8-hydroxyquinoline and dialkylaluminum halide stoichiometrically. The λ_maxs of absorption and emission were in the range of 385-388 and 515-516 nm, respectively, which were similar to AlQ₃. The molar absorptivity of AlQ₂X is similar regardless of the X group but emission efficiency of AlQ₂X is 2-3 fold higher than that of AlQ₃ when X = F or Br, but not when X = Cl. This result can be attributed to decreased quenching of energy due to a less steric environment by reducing quinolinate content. The overall molecular orbital structures and the absorption spectra of AlQ₂X and AlQ₃ are very similar due to a single quinolinate unit. The value of the potential difference of AlQ₂Xs between anodic and cathodic waves (ΔE = 3.12 V) is close to the estimated HOMO-LUMO energy gap (the optical band gap, ΔE_optical ∼ 1240/λ_max), 3.19 eV. Detailed optical and electrochemical properties of AlQ₂X are discussed.