Quantification of protein surfaces, volumes and atom-atom contacts using a constrained Voronoi procedure

MOTIVATION

Geometric representations of proteins and ligands, including atom volumes, atom-atom contacts and solvent accessible surfaces, can be used to characterize interactions between and within proteins, ligands and solvent. Voronoi algorithms permit quantification of these properties by dividing structures into cells with a one-to-one correspondence with constituent atoms. As there is no generally accepted measure of atom-atom contacts, a continuous analytical representation of inter-atomic contacts will be useful. Improved geometric algorithms will also be helpful in increasing the speed and accuracy of iterative modeling algorithms.

RESULTS

We present computational methods based on the Voronoi procedure that provide rapid and exact solutions to solvent accessible surfaces, volumes, and atom contacts within macromolecules. Furthermore, we define a measure of atom-atom contact that is consistent with the calculation of solvent accessible surfaces, allowing the integration of solvent accessibility and inter-atomic contacts into a continuous measure. The speed and accuracy of the algorithm is compared to existing methods for calculating solvent accessible surfaces and volumes. The presented algorithm has a reduced execution time and greater accuracy compared to numerical and approximate analytical surface calculation algorithms, and a reduced execution time and similar accuracy to existing Voronoi procedures for calculating atomic surfaces and volumes.

Fractional simplex designs for interaction screening in complex mixtures

In mixture experiments, one may be interested in estimating not only main effects but also some interactions. Main effects and significant interactions in a mixture may be estimated through appropriate mixture experiments, such as simplex-centroid designs. However, for mixtures with a large number of factors, the run size for these designs becomes impractically large. A subset of a full simplex-centroid design may be used, but the problem remains regarding which factor-level settings should be selected. In this paper, we propose a solution that considers design points with either one or p individual nonzero factor-level settings. These fractional simplex designs provide a means of screening for interactions and of investigating the behavior of many-component mixtures as a whole while greatly reducing the run size compared with full simplex-centroid designs. The means of construction of the design arrays is described, and designs for < or = 31 factors are presented. Some of the proposed methodology is illustrated using generated data.

Impacts of structural photomodification on the toxicity of environmental contaminants: anthracene photooxidation products

The toxicity of polycyclic aromatic hydrocarbons (PHAs) is known to be enhanced by light via photosensitization reactions (production of active oxygen) and photomodification of the chemicals (e.g., oxidation) to more toxic compounds. Anthracene (ANT) toxicity in particular has been found to increase dramatically following photomodification. The objective of this study was to identify the photooxidation products of ANT and assess the toxicity of selected photoproducts. High performance liquid chromatography (HPLC) analysis of anthracene photooxidation revealed a complex array of oxidation products; prevalent among these were anthraquinone (ATQ) and hydroxy-anthraquinones (hATQs). Eleven of these compounds were tested for toxicity using growth inhibition of the duckweed Lemna gibba L. G-3. All but one of the compounds tested were found to be toxic, and when UV radiation was present in the light source toxicity was generally enhanced. The chemicals were also irradiated under SSR prior to toxicity testing. In about half the cases, the ATQ compounds were rapidly photooxidized and the resultant photoproducts were more toxic than the parent compounds. Interestingly, 2-hydroxyanthraquinone, which was not subject to photooxidation, was the most toxic of the compounds tested. As a light stable compound it presents the risk of a persistent environmental hazard.

Photoinduced toxicity of three polycyclic aromatic hydrocarbons (fluoranthene, pyrene, and naphthalene) to the duckweed Lemna gibba L. G-3

The authors recently demonstrated that light dramatically enhances the hazards of three polycyclic aromatic hydrocarbons (PAHs), anthracene, phenanthrene, and benzo[a]pyrene, to the duckweed Lemna gibba L. G-3 (X.-D. Huang, D. G. Dixon, and B. M. Greenberg, 1993, Environ. Toxicol. Chem., 12, 1067-1077). To extend this research, growth and chlorosis were used as end points to assess the photoinduced toxicity of three additional PAHs, fluoranthene, pyrene, and naphthalene, to L. gibba in the presence of simulated solar radiation (a light source with a UV-B: UV-A:visible light ratio equivalent to that of sunlight). The phytotoxicity of these three PAHs was photoactivated, with ultraviolet radiation being the only spectral region that enhanced the harmful effects of the chemicals. Dose-response curves based on chemical concentration and light intensity revealed that the order of phytotoxic strength was fluoranthene > pyrene > naphthalene. To explore whether photomodification (in addition to photosensitization) of fluoranthene, pyrene, and naphthalene could contribute to photoinduced toxicity, the chemicals were irradiated prior to (as opposed to simultaneously with) application to the plans. The rates of photomodification of the three PAHs were rapid enough for the photooxidized compounds to contribute to toxicity, and the photomodified PAHs were more toxic than the parent compounds. As well, toxicity could be correlated to photomodification; impacts increased in parallel with the extent of photomodification.