The influence of axial ligands on the reduction potential of blue copper proteins

 The reduction potentials of blue copper sites vary between 180 and about 1000 mV. It has been suggested that the reason for this variation is that the proteins constrain the distance between the copper ion and its axial ligands to different values. We have tested this suggestion by performing density functional B3LYP calculations on realistic models of the blue copper proteins, including solvent effects by the polarizable continuum method. Constraining the Cu-S_Met bond length to values between 245 and 310 pm (the range encountered in crystal structures) change the reduction potential by less than 70 mV. Similarly, we have studied five typical blue copper proteins spanning the whole range of reduction potentials: stellacyanin, plastocyanin, azurin, rusticyanin, and ceruloplasmin. These studies included the methionine (or glutamine) ligand as well as the back-bone carbonyl oxygen group that is a ligand in azurin and is found at larger distances in the other proteins. The active-site models of these proteins show a variation in the reduction potential of about 140 mV, i.e., only a minor part of the range observed experimentally (800 mV). Consequently, we can conclude that the axial ligands have a small influence on the reduction potentials of the blue copper proteins. Instead, the large variation in the reduction potentials seems to arise mainly from variations in the solvent accessibility of the copper site and in the orientation of protein dipoles around the copper site. Received: 7 April 1999 / Accepted: 26 July 1999     

The phenology and clutch size of UK Blue Tits does not differ with woodland composition

The deciduous tree-herbivorous caterpillar-insectivorous bird food chain is a well-studied system for investigating the impacts of climate change across trophic levels. To date, across Europe, most attention has focused on the impacts of increasing spring temperature on changes to phenology in Oak-dominated (Quercus spp.) woodlands. Paridae species and Pied Flycatcher Ficedula hypoleuca are the most studied secondary consumers, all of which demonstrate an advancement in reproductive phenology with increases in spring temperature. Shifts in climate and phenology may also impact on reproductive investment in clutch size, and the effects of climate on phenology and clutch size may vary depending on woodland composition. To date, the effects of among-habitat variation in phenology and reproductive investment have received little attention. Insectivorous birds inhabiting woodlands that differ in tree composition may differ in the timing of breeding, due to local tree leafing phenology acting as a cue for egg-laying date and/or clutch size. Moreover, for most insectivorous birds, woodland composition within a territory is likely to be the main determinant of food availability for both adults and chicks. Consequently, if warming springs affect the temporal patterns of food availability differently across different woodland compositions, this may affect the optimal average local phenology for nesting birds. Here, using data from 34 long-term (mean 15 years) nest monitoring sites across the UK, we investigate the effect of woodland tree composition and temperature on Blue Tit Cyanistes caeruleus first egg date (FED) and clutch size. We supplemented the nest monitoring data by quantifying woodland composition, at a site level, through modified point counts. We predict that birds breeding in woodlands with greater proportions of late-leafing species, such as Oak and Ash Fraxinus excelsior, will breed later than those breeding in woodlands with greater proportions of early-leafing species, such as Birch Betula spp. and Beech Fagus sylvatica. We found no evidence for differences in Blue Tit FED or clutch size in relation to the proportion of any of the tree species investigated, after controlling for temperature and latitude (FED: −3.4 and 2.2, clutch size: −0.4 and − 0.2 eggs for one-unit increase in temperature and latitude, respectively). In recent decades and across all sites, clutch size has decreased as spring temperatures have increased, a strategy which could allow birds flexibly to adjust their breeding phenology such that nestling demand coincides with peak food availability. The lack of an effect of woodland composition on Blue Tit phenology suggests Blue Tits do not fine-tune their reproductive phenology to the local tree composition. Whether this lack of evidence for phenological divergence is due to an absence of divergent selection on breeding phenology and clutch size or to gene flow is not clear.     

贺兰山岩羊冬春季取食生境的比较

2003年11～12月和2004年4～6月,在贺兰山设定了25条固定样线,采用直接观察法对岩羊冬春季的取食生境选择进行了研究。结果表明,岩羊冬季对12种取食生境生态因子有选择性,偏爱选择位于山地疏林草原带,优势乔木为灰榆,乔木密度〈4株、高度4～6m,灌木密度〉5株、高度〉1．3m,食物质量〉50g,人为干扰距离〈500m,距裸岩距离〈2m的地方取食。而春季对11种取食生境生态因子有选择性,偏爱选择山地疏林草原带,优势乔木为灰榆,乔木密度〈4株、高度〈6m,灌木密度5～10株、高度1．3～1．7m,食物质量〉100g,海拔高度〈2000m,距水源距离〈500m,隐蔽级50％～75％的地点。冬春季岩羊对植被类型、地形特征、优势乔木、乔木密度、乔木高度、灌木密度、灌木距离、食物丰富度、坡向、坡度、距水源距离、人为干扰距离和隐蔽级的选择存在显著差异。主成分分析表明,冬季第1主成分的贡献率达24．493％,其中绝对值较大的权系数出现在植被类型、优势乔木、乔木高度、乔木距离、灌木密度、灌木高度、海拔高度、距水源距离和人为干扰距离等生态因子：春季第1主成分的贡献率达28．777％,其中绝对值较大的权系数出现在植被类型、乔木距离、灌木高度、灌木距离、食物丰富度、海拔高度和人为干扰距离等生态因子。随着北方地区冬春季食物数量和质量的剧烈变化,贺兰山岩羊对取食生境的利用对策也将发生一定程度的改变,与其他分布区的岩羊相比,贺兰山独特的地理位置和特殊生境使其在取食生境选择上存在很大差异。     

Biodegradation of Reactive Blue 59 by isolated bacterial consortium PMB11

Morphologically different, three bacterial strains, capable of decolorizing Reactive Blue 59 were isolated from dye effluent contaminated soil sample, collected from Ichalkaranji, India. The individual bacterial strains viz. Bacillus odysseyi SUK3, Morganella morganii SUK5 and Proteus sp. SUK7 decolorized Reactive Blue 59 (50 mg l(-1)) completely within 60, 30, 24 h, respectively, while the bacterial consortium PMB11 of these strains required 3 h for the complete decolorization. The decolorization was confirmed by UV-Vis spectroscopy. Further, the biodegradation of Reactive Blue 59 in to different metabolites was confirmed by High performance liquid chromatography and Fourier transform infrared spectroscopy analysis. Significant increase in the activity of aminopyrine N-demethylase (AND) in the individual as well consortium cells, obtained after decolorization showed involvement of AND in the decolorization process. Phytotoxicity studies, revealed the nontoxic nature of the degraded metabolites of Reactive Blue 59 indicating effectiveness of bacterial consortium PMB11 for the treatment of textile effluent containing Reactive Blue 59.     

Structural and spectroscopic comparison of five-coordinate cobalt(II) and nickel(II) thiolato complexes with the related four-coordinate complexes

Five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co and Ni) (L1 = hydrotris(3,5-diisopropyl-1-pyrazolyl)borate anion and HSMeIm = 2-mercapto-1-methylimidazole), were synthesized. These complexes were compared with the corresponding Cu(II) and Zn(II) complexes with the same ligands and were also compared with the related four-coordinate complexes [L1M(SC₆F₅)] (HSC₆F₅ = pentafluorobenzenthiol). All the complexes were characterized by X-ray crystallography and UV-Vis absorption, IR, ¹H NMR, and other spectroscopic techniques. All five-coordinate thiolato complexes, [L1M(SMeIm)] (M = Co, Ni, and Cu), form a distorted square pyramidal structure with a high spin state, and only [L1Zn(SMeIm)] takes a four-coordinate structure with a distorted tetrahedral configuration. The N21-M-S bond angles of the obtained five-coordinate complexes were proportional to the corresponding d value, which comes from between the equatorial basal plane with N4S ligand donor sets and metal ion. These observations and M-S bond distances affect on UV-Vis and far-IR spectral behavior.     

Screening for dioxin-degrading basidiomycetes from temperate and tropical forests

A total of 500 strains of basidiomycetes isolated from temperate forests in Japan and 379 strains from tropical forests in Indonesia were subjected to a laboratory screening for dioxin-degrading ability. At first, about 200 fungal strains were selected by their ability to decolorize Remazol Brilliant Blue R dye as an indicator of ligninolytic activities. Next, for excluding the factor of dioxin sorption by mycelia, we prepared two series of living cultures exposed either long-term or short-term to 2,7-dichlorodibenzo-p-dioxin (2,7-DCDD), and compared the decreases in the remaining amounts of this model compound. We chose Bjerkandera adusta strain VH57 as a promising new candidate for dioxin degradation, because it gave 40% difference in 2,7-DCDD levels between the two treatments after 30 days of exposure.     

Spontaneous alternation in marine crabs: Invasive versus native species

Organisms ranging from paramecia to humans tend to explore places that have been least recently explored, which is referred to as spontaneous alternation. Although organisms rely on different sources of information in alternating between places, the emergent behavioral pattern is likely advantageous during exploration and foraging. Under this rationale, continuous spontaneous alternation performance of the invasive green crab, Carcinus maenas was assessed and compared with the native blue crab, Callinectes sapidus in a plus-maze submerged in seawater. For the first time spontaneous alternation behavior was demonstrated in Crustacea (i.e., C. maenas) and significant interspecific differences in alternation performance were observed between the invasive versus the native species. Carcinus maneas exhibited a pronouncedly higher spontaneous alternation performance than C. sapidus. Carcinus maneas on average alternated at levels higher than chance, which was not the case for C. sapidus. These observations point to an additional behavioral mechanism that might result in the competitive success of green crabs over blue crabs in areas where they co-occur. Most of the subjects exhibited asymptotic alternation performance from the onset; there was no improvement in their performance over the course of the experimental session. This finding implies the innate nature of this behavioral policy.     

Nickel(II)-substituted azurin I from Alcaligenes xylosoxidans as characterized by resonance Raman spectroscopy at cryogenic temperature

Metal-substituted blue copper proteins (cupredoxins) have been successfully used to study the effect of metal-ion identity on their active-site properties, specifically the coordination geometry and metal–ligand bond strengths. In this work, low-temperature (77 K) resonance Raman (RR) spectra of the blue copper protein Alcaligenes xylosoxidans azurin I and its Ni(II) derivative are reported. A detailed analysis of all observed bands is presented and responsiveness to metal substitution is discussed in terms of structural and bonding changes. The native cupric site exhibits a RR spectrum characteristic of a primarily trigonal planar (type 1) coordination geometry, identified by the ν(Cu–S)_Cys markers at 373, 399, 409, and 430 cm⁻¹. Replacement of Cu(II) with Ni(II) results in optical and RR spectra that reveal (1) a large hypsochromic shift in the main (Cys)S → M(II) charge-transfer absorption from 622 to 440 nm, (2) greatly reduced metal–thiolate bonding interaction, indicated by substantially lower ν(Ni–S)_Cys stretching frequencies, (3) elevation of the cysteine ν(C _β –S) stretching, amide III, and ρ _s(C _β H₂) scissors vibrational modes, and (4) primarily four-coordinated, trigonally distorted tetrahedral geometry of the Ni(II) site that is marked by characteristic ν(Ni–S)_Cys stretching RR bands at 347, 364, and 391 cm⁻¹. Comparisons of the electronic and vibrational properties between A. xylosoxidans azurin I and its closely structurally related azurin from Pseudomonas aeruginosa are made and discussed. For cupric azurins, the intensity-weighted average M(II)–S(Cys) stretching frequencies are calculated to be ν(Cu–S)_iwa = 406.3 and 407.6 cm⁻¹, respectively. These values decreased to ν(Ni–S)_iwa = 359.3 and 365.5 cm⁻¹, respectively, after Ni(II) → Cu(II) exchange, suggesting that the metal–thiolate interactions are similar in the two native proteins but are much less alike in their Ni(II)-substituted forms.     

Development of a generic approach to native metalloproteomics: application to the quantitative identification of soluble copper proteins in Escherichia coli

A combination of techniques to separate and quantify the native proteins associated with a particular transition metal ion from a cellular system has been developed. The procedure involves four steps: (1) labeling of the target proteins with a suitable short-lived radioisotope (suitable isotopes are ⁶⁴Cu, ⁶⁷Cu, ¹⁸⁷W, ⁹⁹Mo, ⁶⁹Zn, ⁵⁶Mn, ⁶⁵Ni); (2) separation of intact soluble holoproteins using native isoelectric focusing combined with blue native polyacrylamide gel electrophoresis into native–native 2D gel electrophoresis; (3) spot visualization and quantification using autoradiography; and (4) protein identification with tandem mass spectrometry. The method was applied to the identification of copper proteins from a soluble protein extract of wild-type Escherichia coli K12 using the radioisotope ⁶⁴Cu. The E. coli protein CueO, which has previously been only identified as a multicopper oxidase following homologous overexpression, was now directly detected as a copper protein against a wild-type background at an expression level of 0.007% of total soluble protein. The retention of the radioisotope by the copper proteins throughout the separation process corroborates the method to be genuinely native. The procedure developed here can be applied to cells of any origin, and to any metal having suitable radioisotopes. The finding that the periplasmic protein CueO is the only major form of soluble protein bound copper in E. coli strengthens the view that the bacterial periplasm contains only a few periplasmic copper proteins, and that the cytosol is devoid of copper proteins. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Biosorption of reactive and basic dyes using fermentation waste <Emphasis Type="Italic">Corynebacterium glutamicum</Emphasis>: the effects of pH and salt concentration and characterization of the binding sites

A low cost biosorbent, Corynebacterium glutamicum, was studied for the sorption of Reactive Red 4 (RR 4) and Methylene Blue (MB). The equilibrium isotherm data were well described by the Langmuir model. pH edge experiments showed that pH of the solution was an important controlling parameter in the sorption process. In the case of RR 4, with increases in the pH from 2 to 10, the uptake decreased from 52 to 1 mg/g; conversely, the uptake of MB increased and the maximum MB uptake was obtained at pH ≥ 9. An increase in the salt concentration strongly influenced the uptake of MB, but had no effect on that of RR 4. In order to identify the binding sites for the dye molecules, the biosorbent was potentiometrically titrated, the results of which showed the presents of four major functional group types on the biomass surface, which were confirmed by FTIR analysis. It was found that positively charged amine groups (Biomass-NH₃ ⁺) were the likely binding sites for anionic RR 4, and negatively charged carboxyl (Biomass-COO⁻) and phosphate groups (Biomass-HPO₄ ⁻) played a role in the electrostatic attraction of cationic MB.