Toward a predictive understanding of slow methyl group dynamics in proteins.

The development of the most recent generation of molecular mechanics force fields promises an increasingly predictive understanding of the protein dynamics-function relationship. Based on extensive validation against various types of experimental data, the AMBER force field ff99SB was benchmarked in recent years as a favorable force field for protein simulations. Recent improvements of the side chain and backbone potentials, made by different groups, led to the ff99SB-ILDN and ff99SBnmr1 force fields, respectively. The combination of these potentials into a unified force field, termed ff99SBnmr1-ILDN, was used in this study to perform a microsecond time scale molecular dynamics simulation of free ubiquitin in explicit solvent for validation against an extensive set of experimental NMR methyl group residual dipolar couplings. Our results show a high level of consistency between the experimental data and the values predicted from the molecular dynamics trajectory reflecting a systematically improved performance of ff99SBnmr1-ILDN over the original ff99SB force field. Moreover, the unconstrained ff99SBnmr1-ILDN MD ensemble achieves a similar level of agreement as the recently introduced EROS ensemble, which was constructed based on a large body of NMR data as constraints, including the methyl residual dipolar couplings. This suggests that ff99SBnmr1-ILDN provides a high-quality representation of the motions of methyl-bearing protein side chains, which are sensitive probes of protein-protein and protein-ligand interactions

Risk, Uncertainty and Precaution in Science: The Threshold of the Toxicological Concern Approach in Food Toxicology

ISSN:1353-3452ISSN:1471-554

Monitoring aromatic surfactants and their biodegradation intermediates in raw and treated sewages by solid-phase extraction and liquid Chromatography

On the basis of solid-phase extraction, a simple procedure for determining simultaneously two aromatic surfactant classes, i.e., linear alkylbenzene sulfonates (LAS) and nonylphenol polyethoxylates (NPEO), as well as their biodegradation intermediates in raw and treated sewages is presented. This procedure involved passing 10 and 100 mL of an influent and effluent water sample, respectively, through a 1-g graphitized carbon black (GCB) extraction cartridge. By exploiting the presence of positively charged active centers on the GCB surface, we succeeded in fractionating the complex mixture of the analytes considered by differential elution. The first fraction contained NPEO and nonylphenol (NP). The second fraction contained the carboxylated biotransformation products of NPEO, i.e., nonylphenoxy carboxylic acids (NPEC). Finally, the last fraction contained LAS and their metabolites, i.e., carboxylic sulfophenyl acids (SPC). By suitably adjusting the chromatographic conditions, any group of analytes was subfractionated and quantified by liquid chromatography with fluorometric detection. Recoveries of all compounds of interest ranged between 89 % and 99%. This procedure was empolyed for 1 year to assess monthly the concentrations of the analytes considered in raw and treated sewages of a mechanical-biological treatment plant. © 1994 American Chemical Society