Iron–sulfur protein folds,iron–sulfur chemistry,and evolution

An inventory of unique local protein folds around Fe–S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe–2S]^2+,+ or [4Fe–4S]^2+,+ clusters. In contrast, high-potential Fe–S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe–S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe–S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe–S active sites, protein folds hosting [4Fe–4S]^2+,+ clusters outnumber those with [2Fe–2S]^2+,+ ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe–S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe–S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe–S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe–S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron–sulfur chemistry on the other.     

Is mood chemistry?

The chemical hypothesis of depression suggests that mood disorders are caused by a chemical imbalance in the brain, which can be corrected by antidepressant drugs. However, recent evidence indicates that problems in information processing within neural networks, rather than changes in chemical balance, might underlie depression, and that antidepressant drugs induce plastic changes in neuronal connectivity, which gradually lead to improvements in neuronal information processing and recovery of mood.     

Origin, functions and chemistry of H‐2 regulated odorants

Genes located within the major histocompatibility complex (MHC) of mice are responsible for individual differences in body odor (odortypes). In this review we suggest that the MHC genes themselves are responsible for odor differences among MHC‐congenic mice. Recent studies indicating that volatile carboxylic acids are at least in part responsible for the individual odors and what this finding implies about the pathway from gene to odorant are also reviewed. We suggest that odorants or their precursors are bound directly by MHC products and are released into serum and concentrated in urine. Finally, possible functions of MHC odortypes in mice are enumerated and important future research questions are raised. This revised version was published online in July 2006 with corrections to the Cover Date.     

Australian salt lakes: their history,chemistry, and biota — a review

A vast number of large lakes ( 100 km²) are typically very old features of the Australian landscape; they occupy areas which have changed little tectonically (e.g., they occupy ancient drainage systems in Western Australia or lie in deep depressions such as the Great Artesian Basin: Lake Eyre) and have not been transgressed by the sea since at least the Palaeogene. Other salt lakes, most of which are small ( 50 km²), have been affected morphologically during recurring glacial-interglacial cycles (e.g., lakes associated with gypsum or clay lunettes, sabkhas, pans, lakes near the coast behind barrier dunes as a result of sea-level changes) and their sedimentary records represent comparatively much shorter periods of time. There are also a number of unusually young (< 30 000 years) crater lakes, some of which are the best studied lakes in Australia.The major ions encountered today in Australian salt lakes consist of sodium and chloride although some lakes are also calcium sulphate rich. The origin of these ions is briefly discussed. Sodium carbonate lakes are rare in Australia today. Under past climatic/hydrological conditions the chemistry of a number of lakes was apparently different.The biota of Australian salt lakes is mostly endemic; it is highly diversified as witnessed by the crustacean fauna and is well adapted to the harsh conditions prevailing in saline water. This is the result of a long history of aridity in Australia. The characteristics of this biota are presented together with data on its distribution which is primarily related to climatic conditions.     

Sedimentary chemistry of a small polluted lake,Gallträsk,S. Finland

Macro nutrients N, P, K, Ca, Mg, Na and S as well as heavy metals Pb, Cu, Zn, Co, Cr, Ni, Fe and Mn were analysed from a sediment core representing a 7000-year long history of a lake including the preceding brackish (Litorina Sea) and freshwater (Ancylus Lake) stages. Sediments were also analysed for sedimentary pigments, algal growth potential (AGP) of the interstitial water, phosphorus fractions, pH, specific conductivity and redox potential. The annual accumulation values of several chemical elements were interpreted in light of other paleolimnological data from the same core. In the uppermost sediment stratum the influence of sewage pollution is clearly reflected by increases in total electrolyte content, pH, AGP and sedimentary pigments including myxoxanthophyll. Nickel, copper and manganese only slightly increase in the recent sediment, whilst other heavy metals (especially Cr and Zn) and sulphur, phosphorus, nitrogen and total organic matter are heavily concentrasted in the polluted surface sediment. The interpretation of the chemostratigraphy of the lake accords with evidence of lake development based on biological analyses.     

Quo vadis porphyrin chemistry?

This review summarizes recent developments in the area of porphyrin chemistry in the direction of biological applications. Novel synthetic methodologies are reviewed for porphyrin synthesis, porphyrin analog synthesis, stable porphyrinogens -- calixpyrroles, expanded porphyrins. Unique biological properties of those compounds are desribed with focus on photodynamic therapy (PDT) and molecular recognition properties. Special attentions given to metalloporphyrins with potential to affect heme degradation and CO formation.     

Hematoxylin and related compounds – an annotated bibliography concerning their origin,properties, chemistry,and certain applications

Abstract

This bibliography covers the historical aspects of hematoxylin and its close relative brazilin from their origin in dyewoods to their recently understood chemical reactions and properties. Until the end of the 19th century, dyewoods such as logwood were among the most commercially important natural dyes and investigations over a long period of time led to an extensive literature. The ready oxidation of hematoxylin to hematein, which subsequently can be complexed with metal ions or undergo reactions with acid to give isohematein, has provided a wealth of work for the organic chemist. The elucidation of the structure and subsequent synthesis of hematoxylin has proved to be a major incentive to chemists to discover novel chemical reagents for many years.     

Characterisation of the thiol–disulphide chemistry of desmopressin by LC, μ-LC, LC-ESI-MS and Maldi-Tof

Summary. To date, the majority of therapeutic peptides and proteins have to be administered via parenteral routes, which are painful and inconvenient. In order to gain sufficient high blood concentrations after oral application, various barriers in the gastrointestinal tract have to be overcome. Apart from a poor membrane uptake and intense enzymatic degradation, this study will demonstrate that thiol–disulphide reactions are an underestimated essential part of the presystemic metabolism. Glutathione, integrative part of the antioxidant defence system in the gastrointestinal tract, may play an important role in the inactivation of orally given peptides and proteins. In order to verify this hypothesis, desmopressin which bears a single disulphide bond was used as model peptide drug. Desmopressin was incubated with GSH in various concentrations, and the extent of thiol/disulphide exchange reactions between the peptide drug and GSH was investigated in dependence on pH and ratio of reactants determined as a function of time via HPLC, LC-MS and Maldi-Tof-MS analyses. Results showed that desmopressin is degraded by 1% reduced glutathione at pH 4 and pH 5.5. In presence of 0.01%, 0.1% and 1% of reduced glutathione 6.1%, 19.4% and 52.1% of desmopressin, respectively, were degraded. The masses of the conjugates after deconvolution measured by liquid chromatography and electrospray ionisation mass spectrometric detection were m/z 1069.67, m/z 1376.50, m/z 1683.40 and m/z 2138. These molecular masses, confirmed by Maldi-Tof-MS analysis, correspond with the masses of conjugates expected in theory. Under defined conditions, these results reveal that thiol–disulphide exchange reactions have a considerable impact on the alteration of peptide drugs and proteins.     

Electrophilic oxygen-atom transfer chemistry of α-azohydroperoxides

The ionic oxidations of alkenes, sulfides, and amines by α-azohydroperoxides are discussed. The reactivity and selectivity of cyclic α-azohydroperoxide 1 are similar to those of flavin 4a-hydroperoxide model compounds in heteroatom-oxidation. The α-azohydroperoxides show similar selectivity in epoxidation to that of peracids. The lack of a general acid catalysis requirement in aprotic medium as well as Hammett-type studies suggests a mechanism of oxygen-atom transfer that involves nucleophilic attack of the substrate on the terminal oxygen with concomitant transfer (hydrogen-bonding) of the hydroperoxy proton to the azo function. ¹⁷O NMR data on enriched samples of α-azohydroperoxides show a solvent dependence that appears to correlate with kinetic data. However, solvent effects and intermolecular acid catalysis of the oxidations are generally minor effects. The intramolecular acid catalytic effects are of greater magnitude. α-Azohydroperoxides that contain phenolic groups show approximately 100-fold increased reactivity over those of electronically similar analogs. For α-azohydroperoxide ionic oxidations, selectivity appears to be essentially invariant, at a maximum value, and independent of reactivity.     

Characterisation of the enigmatic,endemic red algaGelidium allanii (Gelidiales) from northern New Zealand — morphology,distribution, agar chemistry

Gelidium allanii Chapman is endemic to northern New Zealand with a highly localised distribution. This species has remained little known, having been collected from only one locality for more than 40 years. We compare this species with other New Zealand members of the Gelidiaceae, in particularGelidium caulacantheum andPterocladia capillacea, presenting new data on morphology, distribution and agar chemistry to more fully characteriseG. allanii.G. allanii possesses a very distinctive, highly pyruvated agar. New Zealand records of two Australian speciesG. australe andG. asperum are examined and it is concluded that there is no evidence for their occurrence in New Zealand.Author for correspondence     

Sulfur chemistry,biofilm, and the (in)direct attack mechanism — a critical evaluation of bacterial leaching

It has been shown (a) that bacterial leaching of metal sulfides apparently requires the attachment of leach bacteria to metal sulfides, (b) that exopolymerbound iron compounds are responsible for or at least considerably increase the rate of the biological attack over the chemical rate, (c) that the primary attacking agent in leaching environments is the ferric iron hexahydrate ion, (c) that thiosulfate is the first intermediate sulfur compound, giving rise to a variety of other compounds including polythionate-containing periplasmic granula, and (d) that we have no idea about the actual concentrations of protons, ferrous/ferric and/or other cations, and sulfur compounds in the reaction space between the bacterium and the sulfide surface.     

Hematology, serum chemistry, and serology of Galápagos penguins (Spheniscus mendiculus) in the Galápagos Islands, Ecuador

The Galápagos penguin (Spheniscus mendiculus) is an endangered species endemic to the Galápagos Islands, Ecuador. In 2003 and 2004, 195 penguins from 13 colonies on the islands of Isabela and Fernandina in the Galápagos archipelago were examined. Genetic sexing of 157 penguins revealed 62 females and 95 males. Hematology consisted of packed cell volume (n = 134), white blood cell differentials (n = 83), and hemoparasite blood smear evaluation (n = 114). Microfilariae were detected in 22% (25/114) of the blood smears. Female penguins had significantly higher eosinophil counts than males. Serum chemistry on 83 penguins revealed no significant differences between males and females. Birds were seronegative to avian paramyxovirus type 1-3, avian influenza virus, infectious bursal disease virus, Marek's disease virus (herpes), reovirus, avian encephalomyelitis virus, and avian adenovirus type 1 and 2 (n = 75), as well as to West Nile virus (n = 87), and Venezuelan, western and eastern equine encephalitis viruses (n = 26). Seventy-five of 84 (89%) penguins had antibodies to Chlamydophila psittaci but chlamydial DNA was not detected via polymerase chain reaction in samples from 30 birds.