Paralog-selective ligands for bcl-2 proteins

There is considerable current interest in molecules that bind intra- or extracellular protein surfaces and inhibit protein-protein interactions. Previously we have reported that miniature proteins based on pancreatic-fold polypeptides can recognize even shallow alpha-helix binding clefts with high affinity and selectivity against unrelated proteins. One such miniature protein, PPBH3-1, binds the anti-apoptotic protein paralogs Bcl-2 and Bcl-XL with nanomolar affinity and a DeltaDeltaG = 1.2 kcal.mol-1 preference for Bcl-XL. Here we describe the directed evolution of PPBH3-1 into two new miniature proteins, PPBH3-5 and PPBH3-6, whose paralog specificity is reversed relative to PPBH3-1. PPBH3-5 and PPBH3-6 bind Bcl-2 with nanomolar affinity and a DeltaDeltaG = 0.9-1.3 kcal.mol-1 preference for Bcl-2 over Bcl-XL. Experiments with Bcl-XL variants suggest that PPBH3-5 and PPBH3-6 achieve high paralog specificity by exploiting subtle structural or electrostatic differences in the Bcl-2 and Bcl-XL molecular landscapes. PPBH3-5 and PPBH3-6 may have unique applications as early examples of nonnatural ligands that interact selectively with Bcl-2 proteins.     

Crystallographic studies on the reaction of isopenicillin N synthase with an unsaturated substrate analogue

Isopenicillin N synthase (IPNS) catalyses conversion of the linear tripeptide delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine (ACV) to isopenicillin N (IPN), the central step in biosynthesis of the beta-lactam antibiotics. The unsaturated substrate analogue delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-vinylglycine (ACvG) has previously been incubated with IPNS and single product was isolated, a 2-alpha-hydroxymethyl isopenicillin N (HMPen), formed via a monooxygenase mode of reactivity. ACvG has now been crystallised with IPNS and the structure of the anaerobic IPNS:Fe(II):ACvG complex determined to 1.15 A resolution. Furthermore, by exposing the anaerobically grown crystals to high-pressure oxygen gas, a structure corresponding to the bicyclic product HMPen has been obtained at 1.60 A resolution. In light of these and other IPNS structures, and recent developments with related dioxygenases, the [2 + 2] cycloaddition mechanism for HMPen formation from ACvG has been revised, and a stepwise radical mechanism is proposed. This revised mechanism remains consistent with the observed stereospecificity of the transformation, but fits better with apparent constraints on the coordination geometry around the active site iron atom.     

A Claisen rearrangement route to the vineomycins

Anthrarufin is converted by a high yield route involving sequential Claisen rearrangements to an intermediate (3) suitable for the synthesis of vineomycins     

Sliding backshorts for planar circuits

The Superconductor-Insulator-Superconductor (SIS) tunnel junction is an extremely sensitive heterodyne detector at millimeter and submillimeter wavelengths. The large inherent capacitance associated with this device results in a substantial impedance mismatch with typical antennas and, therefore, requires a tuning circuit for optimum results. At frequencies where waveguide dimensions are realizable, impedance matching can be accomplished by embedding the detector in a waveguide circuit with adjustable waveguide backshorts. At higher frequencies, where waveguide dimensions become prohibitively small, a planar transmission line embedding circuit provides a reasonable alternative. Typically, such planar circuits offer no post-fabrication adjustability, resulting in demanding materials and design requirements. An adjustable planar embedding circuit based on coplanar transmission lines with movable noncontacting shorting elements has been developed. The shorting elements each consist of a thin metallic plate with an optimized arrangement of rectangular holes, placed along the insulated metallic transmission line to provide a periodic variation of the line impedance. A scadel (1–5 GHz) has shown that a large reflection coefficient, |s ₁₁|–0.5 dB, can be achieved with these sliding elements. A low frequency tuning circuit incorporating these shorting elements has been tested to demonstrate practical tuning ranges.     

Validation of a headspace trap gas chromatography and mass spectrometry method for the quantitative analysis of volatile compounds from degraded rapeseed oil

Due to lipid oxidation, off‐flavors, characterized by a fishy odor, are emitted during the heating of rapeseed oil in a fryer and affect the flavor of rapeseed oil even at low concentrations. Thus, there is a need for analytical methods to identify and quantify these products. To study the headspace composition of degraded rapeseed oil, and more specifically the compounds responsible for the fishy odor, a headspace trap gas chromatography with mass spectrometry method was developed and validated. Six volatile compounds formed during the degradation of rapeseed oil were quantified: 1‐penten‐3‐one, (Z)‐4‐heptenal, hexanal, nonanal, (E,E)‐heptadienal, and (E)‐2‐heptenal. Validation using accuracy profiles allowed us to determine the valid ranges of concentrations for each compound, with acceptance limits of 40% and tolerance limits of 80%. This method was then successfully applied to real samples of degraded oils.     

Using ANOVA-PCA for discriminant analysis: application to the study of mid-infrared spectra of carrageenan gels as a function of concentration and temperature

In this work the ANOVA-PCA method is applied to a MIR spectroscopy dataset of carrageenan in order to evaluate which of the factors within its fixed effects experimental design are significant in relation to the residual error. The factors defined in the experimental design are concentration (1% and 2%), temperature (30, 40, 45, 50, and 60 degrees C), day (1 and 2) and sample (20 samples, 3 repetitions). The two factors, concentration and temperature, were considered as significant and the main features related with its physico-chemical properties were identified. It is also of interest to acquire a better understanding of the interaction between concentration and temperature and its effect on the adhesion of gels onto the surface of contact. In fact, no significant interaction was found between the two factors, but it was shown that the factor temperature behaves in a non-linear way. As classification using the ANOVA-PCA procedure has not been developed until now, a new method is proposed for the classification of new samples in respect to the levels of each significant factor.