A photosystem I reaction center driven by chlorophyll d in oxygenic photosynthesis

A far-red type of oxygenic photosynthesis was discovered in Acaryochloris marina, a recently found marine prokaryote that produces an atypical pigment chlorophyll d (Chl d). The purified photosystem I reaction center complex of A. marina contained 180 Chl d per 1 Chl a with PsaA–F, -L, -K, and two extra polypeptides. Laser excitation induced absorption changes of reaction center Chl d that was named P740 after its peak wavelength. A midpoint oxidation reduction potential of P740 was determined to be +335 mV. P740 uses light of significantly low quantum energy (740 nm = 1.68 eV) but generates a reducing power almost equivalent to that produced by a special pair of Chl a (P700) that absorbs red light at 700 nm (1.77 eV) in photosystem I of plants and cyanobacteria. The oxygenic photosynthesis based on Chl d might either be an acclimation to the far-red light environments or an evolutionary intermediate between the red-absorbing oxygenic and the far-red absorbing anoxygenic photosynthesis that uses bacteriochlorophylls.

Chemical complementation identifies a proton acceptor for redox-active tyrosine D in photosystem II

Through the use of site-directed mutagenesis and chemical rescue, we have identified the proton acceptor for redox-active tyrosine D in photosystem II (PSII). Effects of chemical rescue on the tyrosyl radical were monitored by EPR spectroscopy. We also have acquired the Fourier–transform infrared (FT-IR) spectrum associated with the oxidation of tyrosine D and concomitant protonation of the acceptor. Mutant and isotopically labeled PSII samples are used to assign vibrational lines in the 3,600–3,100 cm−1 region to N-H modes of His-189 in the D2 polypeptide. When His-189 in D2 is changed to a leucine (HL189D2) in PSII, dramatic alterations of both EPR and FT-IR spectra are observed. When imidazole is introduced into HL189D2 samples, results from both EPR and FT-IR spectroscopy argue that imidazole is functionally reconstituted into an accessible pocket and that imidazole acts as a chemical mimic for His-189. Small perturbations of EPR and FT-IR spectra are consistent with access to this pocket in wild-type PSII, as well. Structures of the analogous site in bacterial reaction centers suggest that an accessible pocket, large enough to contain imidazole, is bordered by tyrosine D and His-189 in the D2 polypeptide. These data provide evidence that His-189 in the D2 polypeptide of PSII acts as a proton acceptor for redox-active tyrosine D and that proton transfer to the imidazole ring facilitates the efficient oxidation/reduction of tyrosine D.

Double-level “orthogonal” dynamic combinatorial libraries on transition metal template

Dynamic combinatorial libraries are mixtures of compounds that exist in a dynamic equilibrium and can be driven to compositional self adaptation via selective binding of a specific assembly of certain components to a molecular target. We present here an extension of this initial concept to dynamic libraries that consists of two levels, the first formed by the coordination of terpyridine-based ligands to the transition metal template, and the second, by the imine formation with the aldehyde substituents on the terpyridine moieties. Dialdehyde 7 has been synthesized, converted into a variety of ligands, oxime ethers L11–L33 and acyl hydrazones L44–L77, and subsequently into corresponding cobalt complexes. A typical complex, Co(L22)22+ is shown to engage in rapid exchange with a competing ligand L11 and with another complex, Co(L22)22+ in 30% acetonitrile/water at pH 7.0 and 25°C. The exchange in the corresponding Co(III) complexes is shown to be much slower. Imine exchange in the acyl hydrazone complexes (L44–L77) is strongly controlled by pH and temperature. The two types of exchange, ligand and imine, can thus be used as independent equilibrium processes controlled by different types of external intervention, i.e., via oxidation/reduction of the metal template and/or change in the pH/temperature of the medium. The resulting double-level dynamic libraries are therefore named orthogonal, in similarity with the orthogonal protecting groups in organic synthesis. Sample libraries of this type have been synthesized and showed the complete expected set of components in electrospray ionization MS.

A thermostable endonuclease III homolog from the archaeon Pyrobaculum aerophilum

Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N-glycosylase responsible for the excision of modified pyrimidine bases is the base excision repair (BER) glycosylase endonuclease III, for which functional homologs have been identified and characterized in Escherichia coli, yeast and humans. So far, little is known about how hyperthermophilic Archaea cope with such pyrimidine damage. Here we report characterization of an endonuclease III homolog, PaNth, from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal growth temperature is 100°C. The predicted product of 223 amino acids shares significant sequence homology with several [4Fe-4S]-containing DNA N-glycosylases including E.coli endonuclease III (EcNth). The histidine-tagged recombinant protein was expressed in E.coli and purified. Under optimal conditions of 80–160 mM NaCl and 70°C, PaNth displays DNA glycosylase/β-lyase activity with the modified pyrimidine base 5,6-dihydrothymine (DHT). This activity is enhanced when DHT is paired with G. Our data, showing the structural and functional similarity between PaNth and EcNth, suggests that BER of modified pyrimidines may be a conserved repair mechanism in Archaea. Conserved amino acid residues are identified for five subfamilies of endonuclease III/UV endonuclease homologs clustered by phylogenetic analysis.

Potency of Michael reaction acceptors as inducers of enzymes that protect against carcinogenesis depends on their reactivity with sulfhydryl groups

Induction of phase 2 enzymes and elevations of glutathione are major and sufficient strategies for protecting mammals and their cells against the toxic and carcinogenic effects of electrophiles and reactive forms of oxygen. Inducers belong to nine chemical classes and have few common properties except for their ability to modify sulfhydryl groups by oxidation, reduction, or alkylation. Much evidence suggests that the cellular “sensor” molecule that recognizes the inducers and signals the enhanced transcription of phase 2 genes does so by virtue of unique and highly reactive sulfhydryl functions that recognize and covalently react with the inducers. Benzylidene-alkanones and -cycloalkanones are Michael reaction acceptors whose inducer potency is profoundly increased by the presence of ortho- (but not other) hydroxyl substituent(s) on the aromatic ring(s). This enhancement correlates with more rapid reactivity of the ortho-hydroxylated derivatives with model sulfhydryl compounds. Proton NMR spectroscopy provides no evidence for increased electrophilicity of the β-vinyl carbons (the presumed site of nucleophilic attack) on the hydroxylated inducers. Surprisingly, these ortho-hydroxyl groups display a propensity for extensive intermolecular hydrogen bond formation, which may raise the reactivity and facilitate addition of mercaptans, thereby raising inducer potencies.

Manganese oxide minerals: Crystal structures and economic and environmental significance

Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry.

Estudo da remediação de um aquífero contaminado com sulfato e metais através de barreira reativa permeável orgânica.

Este trabalho teve como objetivo geral estudar a viabilidade técnica de utilizar bagaço de cana como meio reativo de barreiras reativas permeáveis (BRP) para remoção de sulfato e metais de águas subterrâneas contaminadas. O estudo baseou-se em investigação experimental, por meio de ensaios laboratoriais de coluna, e em modelagem matemática, para a qual utilizaram-se também alguns dados obtidos em um estudo de caso de uma unidade industrial contaminada com sulfato e metais. Neste local contaminado, as características hidrogeológicas e topográficas propiciam a utilização de uma barreira reativa permeável como técnica de remediação. Barreiras reativas permeáveis são uma alternativa para remediação de águas subterrâneas que vem progredindo rapidamente na última década, a partir de ensaios de bancada e coluna em laboratório para implementação em escala real em campo. Três colunas bióticas foram montadas utilizando bagaço de cana como meio reativo e um material de base poroso constituído de areia e cascalho para fornecer adequada condutividade hidráulica, com a proporção de 1:28 em massa seca. Também foi adicionado ao meio reativo um inóculo bacteriano composto por esterco bovino dissolvido. Uma quarta coluna, sem inóculo e contendo um agente biocida, compôs o experimento branco (abiótico). Uma solução sintética foi introduzida nas colunas simulando condições da água subterrânea do estudo de caso, com velocidade de Darcy em torno de 2,0x10-7 m/s composta por sulfato e metais (zinco e níquel) com concentrações de 6.000 mg/L e 15 mg/L, respectivamente. Os resultados das análises da fase líquida das colunas bióticas apresentaram: (i) média da taxa de remoção de sulfato durante todo o tempo do experimento de 49 mg/L/dia; (ii) as concentrações de Zn e Ni diminuíram de 15 mg/L para valores não detectáveis pela técnica analítica utilizada (< 0,01 mg/L); (iii) aumento do pH de 5.5-5.8 para valores entre 6,8-8,0; (iv) redução do valor do potencial de óxido redução (Eh) para valores de até -200mV. Não foram observadas reduções das concentrações de metais e sulfato na fase líquida da coluna abiótica e os valores de pH e Eh permaneceram dentro das faixas iniciais. Análises nas fases sólidas das colunas bióticas por MEV e EDS após o término do experimento identificaram a presença de Ni, Zn, S e Mn, indicando a precipitação desses metais em forma de sulfetos. Estes elementos não foram detectados na fase sólida da coluna abiótica. Assim, pôde-se inferir que toda a remoção de sulfato verificada nas colunas bióticas pode ser atribuída a redução bacteriana de sulfato. A partir das condições experimentais dos ensaios, foi realizada a modelagem e o dimensionamento da BRP. Para a estimativa da cinética de redução de sulfato, aplicou-se a solução analítica de Van Genuchten para transporte de contaminantes com degradação, obtendo-se uma taxa de decaimento de primeira ordem de 0,01 dia-1. A determinação da espessura e tempo de residência da barreira foi realizada considerando que a concentração de sulfato na saída da barreira fosse menor ou igual a 250 mg/L. O resultado do dimensionamento de uma BRP preenchida com bagaço de cana e areia nas proporções de 1:28 em massa seca resultaria em uma BRP de 7,1 m de espessura, com tempo de residência de 950 dias, no local de estudo de caso. Caso fosse utilizado o dobro da proporção de bagaço de cana e areia em massa seca (1:14), a implantação da BRP apresentar-se-ia viável, com espessura aproximada de 4 m. Através destes resultados, pôde ser comprovada a hipótese de que bagaço de cana como substrato e esterco bovino como inóculo compõem um meio reativo viável para a redução de sulfato e precipitação de metais em uma BRP.