Crystallization of Arthrobacter sp. strain 1C N-(1-D-carboxyethyl)-L-norvaline dehydrogenase and its complex with NAD+

The novel NAD+-linked opine dehydrogenase from a soil isolate Arthrobacter sp. strain 1C belongs to an enzyme superfamily whose members exhibit quite diverse substrate specificites. Crystals of this opine dehydrogenase, obtained in the presence or absence of co-factor and substrates, have been shown to diffract to beyond 1.8 ? resolution. X-ray precession photographs have established that the crystals belong to space group P21212, with cell parameters a = 104.9, b = 80.0, c = 45.5 ? and a single subunit in the asymmetric unit. The elucidation of the three-dimensional structure of this enzyme will provide a structural framework for this novel class of dehydrogenases to enable a comparison to be made with other enzyme families and also as the basis for mutagenesis experiments directed towards the production of natural and synthetic opine-type compounds containing two chiral centres.     

Decomposition behavior in aggregated data sets

One way to aggregate data is to combine several sets with the same structure, but no overlap in their ranges of values — for instance, aggregating prices before and after a period of hyperinflation. Looking at nonparametric tests on three ‘items’, we compute the relation of the decomposition of the underlying voting profiles of such aggregated sets to those for the original data. We focus on the Basic components, including examples of ‘pure Basic’ sets, computed using Sage. This yields several interesting results about consistency of nonparametric tests with respect to this kind of aggregation, and suggests types of non-uniformity which are not detected by standard tests.     

Ligand-target interaction-based weighting of substructures for virtual screening

A methodology is introduced to assign energy-based scores to two-dimensional (2D) structural features based on three-dimensional (3D) ligand-target interaction information and utilize interaction-annotated features in virtual screening. Database molecules containing such fragments are assigned cumulative scores that serve as a measure of similarity to active reference compounds. The Interaction Annotated Structural Features (IASF) method is applied to mine five high-throughput screening (HTS) data sets and often identifies more hits than conventional fragment-based similarity searching or ligand-protein docking.     

Doping of polyvinylidene difluoride with cobalt nitrate: Structural,electrical, and magnetic properties

Polyvinylidene difluoride (PVDF) doped with a few percentage of cobalt nitrate hexahydrate induces transition into the ferroelectric β‐phase. Infrared spectra show peaks indicative of β‐phase PVDF at 1277 cm^?1 and loss of the α‐phase peak at 790 cm^?1 while polarization measurements show loops consistent with relaxor ferroelectric behavior. Electronic spectroscopy shows that the Co²⁺ ion is in a six‐coordinate environment, and this is confirmed by magnetic susceptibility. Thermal measurements show that the PVDF melts near 155 °C, depending on the Co²⁺ content, and that there are several other thermal features that are associated with the hydrated cobalt nitrate. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Understanding false positives in reporter gene assays: in silico chemogenomics approaches to prioritize cell-based HTS data

High throughput screening (HTS) data is often noisy, containing both false positives and negatives. Thus, careful triaging and prioritization of the primary hit list can save time and money by identifying potential false positives before incurring the expense of followup. Of particular concern are cell-based reporter gene assays (RGAs) where the number of hits may be prohibitively high to be scrutinized manually for weeding out erroneous data. Based on statistical models built from chemical structures of 650 000 compounds tested in RGAs, we created "frequent hitter" models that make it possible to prioritize potential false positives. Furthermore, we followed up the frequent hitter evaluation with chemical structure based in silico target predictions to hypothesize a mechanism for the observed "off target" response. It was observed that the predicted cellular targets for the frequent hitters were known to be associated with undesirable effects such as cytotoxicity. More specifically, the most frequently predicted targets relate to apoptosis and cell differentiation, including kinases, topoisomerases, and protein phosphatases. The mechanism-based frequent hitter hypothesis was tested using 160 additional druglike compounds predicted by the model to be nonspecific actives in RGAs. This validation was successful (showing a 50% hit rate compared to a normal hit rate as low as 2%), and it demonstrates the power of computational models toward understanding complex relations between chemical structure and biological function.     

Two-element dielectric antenna serially excited by optical wavelength multiplexing

A single pulsed laser beam containing multiple wavelengths (wavelength multiplexing) is employed to activate two semiconductor antennas in series. The dielectric nature of the semiconductors permits serial cascading of the antenna elements. Recently observed nonlinear characteristics of the radiated field as a function of the free carrier accelerating (bias) voltage are used to minimize the small interactions between elements. We demonstrate that the temporal electromagnetic radiation distribution of two serial antennas is sensitive to the three-dimensional pattern of the optical excitation source. One can, in turn, vary this distribution continuously by optical means to reconfigure the array.