Guideline values for sediments contaminated with dioxins and furans.

There is a growing volume of data reporting contamination of aquatic sediments with dioxins and furans. Despite a great deal of research and investigation into the occurrence and effects of these chemicals no standards or reference values currently exist to assist putting these data into an operational pollution control context, or to help decision making in relation to remediation actions. This paper uses information from the literature to propose an approach to deriving sediment guideline values for these substances, which could be used to aid such operational decisions.

Three-dimensional structure of cytochrome c' from two Alcaligenes species and the implications for four-helix bundle structures.

The three-dimensional structures of two cytochromes c' have been determined in order to analyse the common features of proteins of this family and their relationship with other four-helix bundle structures. The structure of cytochrome c' from Alcaligenes sp was determined by molecular replacement supplemented with the iron anomalous scattering and the use of a single isomorphous heavy-atom derivative, and was refined using synchrotron data to 1.8 A resolution. The final model, comprising 956 protein atoms (one monomer) and 89 water molecules, has a final R value of 0.188 for all data in the range 20.0-1.8 A resolution (14 673 reflections). The structure of the cytochrome c' from Alcaligenes denitrificans is isomorphous and essentially identical (r.m.s. deviation for all atoms 0.36 A). Although its amino-acid sequence has not been determined chemically, only four differences from that of Alcaligenes sp cytochrome c' were identified by the X-ray analysis. The final model for Alcaligenes denitrificans cytochrome c', comprising 953 protein atoms and 75 water molecules, gave a final R factor of 0.167 for all data in the range 20.0-2.15 A (8220 reflections). The cytochrome c' monomer forms a classic four-helix bundle, determined by the packing of hydrophobic side chains around the enclosed haem group. There are very few cross-linking hydrogen bonds between the helices, the principal side-chain hydrogen bonding involving one of the haem propionates and a conserved Arg residue. The cytochrome c' dimer is created by a crystallographic twofold axis. Monomer-monomer contacts primarily involve the two A helices, with size complementarity of side chains in a central solvent-excluded portion of the interface and hydrogen bonding at the periphery. Both species have a pyroglutamic acid N-terminal residue. The haem iron is five-coordinate, 0.32 A out of the haem plane towards the fifth ligand, His120. The unusual magnetic properties of the Fe atom may be linked to a conserved basic residue, Arg124, adjacent to His120.

Quantitative structure-activity relationships as a tool to assess the comparative toxicity of organic chemicals.

Quantitative structure-activity relationships of toxicity are discussed as a means of assessing the value of the Microtox test which uses the light-emitting bacterium Vibrio fisheri (Photobacterium phosphoreum) as a replacement for toxicity testing in higher species. The Microtox test is found to be a good surrogate for testing in fish, for compounds acting by the narcosis mechanism. However, for reactive chemicals the Microtox test significantly underestimates the potential hazard. It should not therefore be used in isolation for such chemicals, but rather as part of a battery of tests.

Use of iron anomalous scattering with multiple models and data sets to identify and refine a weak molecular replacement solution: structure analysis of cytochrome c' from two bacterial species.

The structure of cytochrome c' from two bacterial species, Alcaligenes sp and Alcaligenes denitrificans, have been determined from X-ray diffraction data to 3.0 A resolution using the anomalous scattering of the single Fe atom in each to identify and refine a weak molecular-replacement solution. Molecular-replacement studies, with the program AMORE, used two isomorphous data sets (from the two species), two independent search models (the cytochromes c' from Rhodospirillum molischianum and Rhodospirillum rubrum), both with and without side chains, and two different resolution ranges (10.0-4.0 and 15.0-3.5A) to generate a large number of potential solutions. No single solution stood out and none appeared consistently. The Fe-atom position in each structure was then determined from its anomalous-scattering contribution and all molecular- replacement solutions were discarded which did not (i) place the Fe atom correctly and (ii) orient the molecule such that a crystallographic twofold axis generated a dimer like those of the two search models. Finally, electron-density maps phased solely by the Fe-atom anomalous scattering were calculated. As these were combined and subjected to solvent flattening and histogram matching (with the program SQUASH), correlation with the remaining molecular-replacement solutions identified one as correct and enabled it to be improved and subjected to preliminary refinement. The correctness of the solution is confirmed by parallel isomorphous-replacement studies.

Crystallization and preliminary X-ray diffraction studies on cytosolic (class 1) aldehyde dehydrogenase from sheep liver.

The cytosolic (Class 1) aldehyde dehydrogenase (AlDH) from sheep liver has been crystallized in a form suitable for X-ray diffraction studies. The crystals, grown by vapour diffusion using 6.5 to 7.5% methoxypolyethylene glycol 5000 as precipitant, at pH 6.5, are orthorhombic with cell dimensions a = 80.7, b = 92.5, c = 151.6 A, space-group P2(1)2(1)2(1), and one dimer in the asymmetric unit. The crystals diffract to at least 2.8 A resolution. Although unmodified AlDH crystallized readily, a key factor in obtaining diffraction-quality crystals was the covalent attachment of an active site reporter group, provided by 3,4-dihydro-3-methyl-6-nitro-2H-1,3-benzoxazin-2-one.

QSAR studies of comparative toxicity in aquatic organisms.

This study investigated the relationships between the toxicities of common organic pollutants to the fathead minnow (Pimephales promelas), to Daphnia magna, to Tetrahymena pyriformis and in the Microtox test, which uses the luminescent bacterium Photobacterium phosphoreum. The toxicity data were compiled from the literature, with the exception of 40 experimentally determined Microtox data. Encouraging correlations are seen, indicating significant relationships between fish toxicities and those to lower organisms. When the toxicities of individual chemical classes are studied, further improvement is often seen in the correlations. Analysis of significant outliers from the inter-species relationships has led to the suggestion that the fathead minnow may be more susceptible to chemicals that are metabolised to reactive intermediates (such as the aldehydes). The fish may, however, be less susceptible to other chemical classes such as ketones and alcohols.

Octanol:water partition coefficients (P): measurement, estimation, and interpretation, particularly for chemicals with P greater than 10(5).

Methods for measurement and estimation of octanol:water partition coefficients are discussed with particular reference to high values (log P greater than 5). A novel experimental method for P measurement is described and preliminary results presented. The use of high performance liquid chromatography capacity factors for estimating P values has been investigated; better correlations between the two parameters have been found if HPLC results at different methanol:water liquid phases are extrapolated to pure water, but even this procedure does not always give reliable P values. The interpretation of high log P values in terms of fish bioconcentration is discussed and the correlations of molecular connectivity and molecular weight with fish bioconcentration are presented.