SPIN TRAPPING OF FREE RADICALS PRODUCED FROM NITROSOAMINE CARCINOGENS

Abstract— Using the spin trap 5,5-dimethylpyrroline-1-oxide we have demonstrated that the nitrosoamine carcinogen, 1-nitrosopiperidine, upon incubation with rat liver microsomes and nuclei produces two trapped free radical species. One trapped species is the hydroxyl free radical whereas the other is a free radical of unknown structure of the carcinogen itself. Three other nitrosoamine carcinogens tested, including diethylnitrosoamine, dimethylnitrosoamine and 1-nitrosopyrroline yielded similar results with the exception that the trapped carcinogen radical differs dependent upon the compound used. Oxygen was required to produce the hydroxyl free radical but its presence decreased the yield of the carcinogen radical. Both cyanide and α-tocopherol acetate caused a decrease in the yield of the carcinogen free radical. Some heat-labile inhibitor(s) of radical production was/were present in the cytosol. The amount of radical produced was not proportional to the P₄₅₀ content.     

A new palladium-mediated approach to 4-N-arylamino-1-butanols from peroxidic tetrahydrofuran and primary aromatic amines

Reaction of primary aromatic amines with peroxidic tetrahydrofuran (THF) in the presence of hydrogen and 10% palladium on carbon catalyst results in THF ring opening to give 4-N-arylamino-1-butanols in a good yield. The reaction mechanism is believed to involve a free-radical sequence resulting in an imino alcohol subsequently reduced to product.     

Configuration-specific kinetic theory applied to the elastic collisions of hard spherical molecules

Classical trajectory simulations can be used to glean a wealth of information on the geometric details of gas-phase molecular collision events for which the standard theoretical treatment lacks the ability to predict. For instance, the standard treatment gives no information on configuration-specific collision parameters. A configuration-specific parameter is defined here as the average value for a collision parameter that is exclusive to either an ensemble of front-end or an ensemble of rear-end molecular collisions. This paper presents statistical results of simulation "measurements" on several configuration-specific parameters, including the configuration-specific collision frequencies. The simulations use single-component systems of hard spherical molecules confined within a spherical boundary. To complement the simulation effort, a systematic mathematical analysis for the configuration-specific parameters is presented. This analysis uses the Maxwell-Boltzmann distribution of molecular speeds as usual, but exploits the distinction between front-end and rear-end collision space, and uses the line-of-centers speed rather than the relative speed. The configuration-specific expressions derived from this analysis are in very good agreement with the simulation measurements for every molecular collision parameter studied in this work.     

Direct and high resolution characterization of cytochrome c equilibrium folding

Protein folding has emerged as a central problem in biophysics, and the equilibrium folding mechanism of cytochrome c (cyt c) has served as a model system. Unfortunately, the detailed characterization of both the folding process and of any intermediate that might be populated has been limited by the low structural and/or temporal resolution of the available techniques. Here, we report the use of a recently developed technique to study folding that is based on the site-selective incorporation of carbon-deuterium (C-D) bonds and their characterization by IR spectroscopy. Specifically, we synthesize and characterize the protein with deuterated residues spread throughout four structural motifs: (d3)Leu68 in the 60's helix, (d8)Lys72 and (d8)Lys73 in the 70's helix, (d8)Lys79, (d3)Met80, and (d3)Ala83 in the D-loop, and (d3)Leu94, (d3)Leu98, and (d3)Ala101 in the C-terminal helix. The data reveal correlated behavior of the residues within each structural motif, as well as between the residues of the 60's and C-terminal helices and between residues of the 70's helix and D-loop. Residues of the 70's helix and the D-loop are more stable than those within the 60's and C-terminal helices, although the former are more sensitive to added denaturant. The data also suggest that the hydrophobicity of the heme cofactor plays a central role in folding. These results contrast with those from previous H/D exchange studies and suggest that the low denaturant fluctuations observed in the H/D exchange experiments are not similar to those through which the protein actually unfolds. The inherently fast time scale of IR also allows us to characterize the folding intermediate, long thought to be present, but which has proven difficult to characterize by other techniques.     

Expansion properties for finite subdivision rules I

Among Thurston maps (orientation-preserving, postcritically finite branched coverings of the 2-sphere to itself), those that arise as subdivision maps of a finite subdivision rule form a special family. For such maps, we investigate relationships between various notions of expansion—combinatorial, dynamical, algebraic, and coarse-geometric.     

Activation state-dependent binding of small molecule kinase inhibitors: structural insights from biochemistry

Interactions between kinases and small molecule inhibitors can be activation state dependent. A detailed understanding of inhibitor binding therefore requires characterizing interactions across multiple activation states. We have systematically explored the effects of ABL1 activation loop phosphorylation and PDGFR family autoinhibitory juxtamembrane domain docking on inhibitor binding affinity. For a diverse compound set, the affinity patterns correctly classify inhibitors as having type I or type II binding modes, and we show that juxtamembrane domain docking can have dramatic negative effects on inhibitor affinity. The results have allowed us to associate ligand-induced conformational changes observed in cocrystal structures with specific energetic costs. The approach we describe enables investigation of the complex relationship between kinase activation state and compound binding affinity and should facilitate strategic inhibitor design.     

Determinants of unnatural nucleobase stability and polymerase recognition

Six new unnatural nucleobases have been synthesized and characterized in terms of stability and selectivity of self-pairing in duplex DNA and efficiency and fidelity of self-pairing during polymerase-mediated replication. Each nucleobase has a conserved ring structure but differs from the others in its specific pattern of substitution with oxygen and sulfur atoms. Heteroatom derivatization within the conserved scaffold is shown to have only moderate effects on unnatural self-pair synthesis by the polymerase; larger effects were observed on the thermal stability and polymerase-mediated extension of the self-pairs. The largest effects of heteroatom substitution were on the stability and synthesis of mispairs between the unnatural and natural bases. Certain heteroatom substitutions were found to have a general effect while others were found to have effects that were specific for a particular unnatural or natural base. The data are useful for designing stable and replicable third base pairs and for understanding the contributions of nucleobase shape, polarity, and polarizability to the stability and replication of DNA.     

Hydroformylation of high polymers

A new class of polymeric materials has been prepared and subjected to preliminary evaluation. These materials were obtained by hydroformylation of diene-based polymers. The olefinic bonds were saturated and aldehyde groups attached. The extent of reaction may be varied at will up to 100% double bond conversion. The properties of these polymers are dominated by the active aldehyde groups. One of the chief characteristics of simple aldehydes is their ability to polymerize forming mainly aldehyde trimers and tetramers. This same phenomenon has been shown to occur with polymeric aldehydes with consequent gel formation. The gelling tendency has been closely related to the aldehyde content per unit volume which may be conveniently varied by (1) the concentration of the initial polymer, (2) the degree of unsaturation in the polymer, and (3) the extent of double bond conversion. Any combination which gives a free aldehyde concentration in excess of 1 × 10^?4 mole/ml. is very prone to gel. The loose gels can be readily reversed by conditions which depolymerize aldehydes. The propensity of the aldehyde polymers to crosslink upon evaporation of the solvent was used to form films. These films were not discolored by ultraviolet light but under such treatment became quite brittle. The products may be stabilized by conversion of the aldehyde groups to more stable derivative, in particular the acetal. The extent of acetal formation has been shown to be controlled by steric factors. Complete polyacetal formation was possible only when the aldehyde groups were well dispersed along the polymer chain. Certain aldehyde derivatives (acetals, oximes) are thermoplastic. They soften at lower temperature than commercial plastics.     

Ion beam analyses of carbon nanotubes

The utility of ion beam analysis (IBA) techniques to quantitatively determine impurities in carbon nanotubes (CNTs) over a wide range of atomic numbers is demonstrated. Such techniques have not previously been used to monitor impurities and their effects in this unique material. Despite the difficulty in mounting the samples (which generally are formed into a powdery aggregate rather in a thin film), it is shown that reliable and accurate measurements of impurity concentrations can be achieved. Particle-induced X-ray emission (PIXE) and elastic recoil detection (ERD) analyses were used to characterize both metallic and very light (e.g., hydrogen) impurities in CNTs. This paper reports the first direct measurement of hydrogen in CNTs using an IBA technique. This is significant because CNTs are being actively investigated for hydrogen storage technology for energy applications.