Activation of apoptosis in vivo by a hydrocarbon-stapled BH3 helix

BCL-2 family proteins constitute a critical control point for the regulation of apoptosis. Protein interaction between BCL-2 members is a prominent mechanism of control and is mediated through the amphipathic alpha-helical BH3 segment, an essential death domain. We used a chemical strategy, termed hydrocarbon stapling, to generate BH3 peptides with improved pharmacologic properties. The stapled peptides, called "stabilized alpha-helix of BCL-2 domains" (SAHBs), proved to be helical, protease-resistant, and cell-permeable molecules that bound with increased affinity to multidomain BCL-2 member pockets. A SAHB of the BH3 domain from the BID protein specifically activated the apoptotic pathway to kill leukemia cells. In addition, SAHB effectively inhibited the growth of human leukemia xenografts in vivo. Hydrocarbon stapling of native peptides may provide a useful strategy for experimental and therapeutic modulation of protein-protein interactions in many signaling pathways.     

The crystal structure of a T cell receptor in complex with peptide and MHC class II

The crystal structure of a complex involving the D10 T cell receptor (TCR), 16-residue foreign peptide antigen, and the I-Ak self major histocompatibility complex (MHC) class II molecule is reported at 3.2 angstrom resolution. The D10 TCR is oriented in an orthogonal mode relative to its peptide-MHC (pMHC) ligand, necessitated by the amino-terminal extension of peptide residues projecting from the MHC class II antigen-binding groove as part of a mini beta sheet. Consequently, the disposition of D10 complementarity-determining region loops is altered relative to that of most pMHCI-specific TCRs; the latter TCRs assume a diagonal orientation, although with substantial variability. Peptide recognition, which involves P-1 to P8 residues, is dominated by the Valpha domain, which also binds to the class II MHC beta1 helix. That docking is limited to one segment of MHC-bound peptide offers an explanation for epitope recognition and altered peptide ligand effects, suggests a structural basis for alloreactivity, and illustrates how bacterial superantigens can span the TCR-pMHCII surface.     

Theoretical studies of the energetics and dynamics of chemical reactions

Computational studies of basic chemical processes not only provide numbers for comparison with experiment or for use in modeling complex chemical phenomena such as combustion, but also provide insight into the fundamental factors that govern molecular structure and change which cannot be obtained from experiment alone. We summarize the results of three case studies, on HCO, OH + H(2), and O + C(2)H(2), which illustrate the range of problems that can be addressed by using modern theoretical techniques. In all cases, the potential energy surfaces were characterized by using ab initio electronic structure methods. Collisions between molecules leading to reaction or energy transer were described with quantum dynamical methods (HCO), classical trajectory techniques (HCO and OH + H(2)), and statistical methods (HCO, OH + H(2), and O + C(2)H(2)). We can anticipate dramatic increases in the scope of this work as new generations of computers are introduced and as new chemistry software is developed to exploit these computers.     

Respiratory function and pulmonary lesions in pigs infected with porcine reproductive and respiratory syndrome virus

Pulmonary dysfunction was evaluated in pigs infected with porcine reproductive and respiratory syndrome virus (PRRSV, isolate VR-2332) and compared to clinical and pathological findings. Infected pigs developed fever, reduced appetite, respiratory distress and dullness at 9 days post-inoculation (dpi). Non-invasive pulmonary function tests using impulse oscillometry and rebreathing of test gases (He, CO) revealed peripheral airway obstruction, reduced lung compliance and reduced lung CO-transfer factor. PRRSV-induced pulmonary dysfunction was most marked at 9–18 dpi and was accompanied by a significantly increased respiratory rate and decreased tidal volume. Expiration was affected more than inspiration. On histopathological examination, multifocal areas of interstitial pneumonia (more severe and extensive at 10 dpi than 21 dpi) were identified as a possible structural basis for reduced lung compliance and gas exchange disturbances.     

Persistence of Gunnison’s prairie dog colonies in Arizona, USA

Although the five species of prairie dogs (Cynomys spp.) are recognized as important components of grassland ecosystems in western North America, they have experienced major population declines due to poisoning, outbreaks of sylvatic plague, recreational shooting, and habitat conversion. From May 2000 to October 2001, we investigated 270 colonies of Gunnison’s prairie dog (Cynomys gunnisoni) in Arizona. Because these colonies were classified as active in previous surveys (1987, 1990-1994, 1998), we were able to examine their persistence. Most (70%) of the colonies became inactive between the initial and recent surveys, with colony extinctions spanning our study area. Colony persistence was positively associated with the persistence of the nearest neighboring colony but was not associated with major vegetation type, distance to nearest neighboring colony, or initial size of the colony. The amount of area occupied by individual colonies varied between surveys, sometimes dramatically. We found little evidence that the reduction in active colonies was due to poisoning, recreational shooting, or habitat conversion. Rather, direct and indirect evidence suggest plague is the primary factor negatively impacting Gunnison’s prairie dog populations in Arizona. Currently, there is no way to control or prevent plague outbreaks in Gunnison’s prairie dog populations. To mitigate the effects of localized plague outbreaks on the overall population of this species, we suggest that Gunnison’s prairie dog be reintroduced to public lands throughout its historical range.     

Surface functional properties of native, acid-treated, and reduced soy glycinin. 2. Emulsifying properties

Emulsifying properties of native and chemically modified soy glycinins were studied. The influence of ionic strength, protein sample composition and concentration, and assay conditions on the flocculation-creaming process and coalescence resistance was analyzed. Differences in these emulsifying properties were exhibited by native glycinins, which have a variable content of 4S, 11S, and 15S forms. Structure and functionality of native glycinin were modified by means of combined treatments: mild acidic treatments without heating or with heating at variable time and with or without disulfide bonds reduction. Modified glycinins presented different degrees of deamidation, surface hydrophobicity, and molecular mass. A slight enhancement of emulsifying stability at moderated deamidation degrees was observed. In different protein samples, a positive relationship between the flocculation-creaming rate constant and equilibrium oil volume fraction of emulsions with surface hydrophobicity was detected. A remarkable difference was observed between reduced and nonreduced samples, mainly with respect to behavior at low or high ionic strength.     

Centimeter-scale variability in the chemistry of convective rains

A standard National Atmospheric Deposition Program (NADP) rain collection bucket was sectioned with 220 test tubes of 1.5 cm diameter. Eleven rains from thunderstorms were collected. Analyses were made for Ca, Na and K concentrations in the test tube liquids. The relative standard deviation (RSD), after correction for the analytical RSD, was 0 to 15% for Ca, 0 to 24% for Na, and 0 to 17% for K. Analytical RSD for Ca, Na and K determined from standards were, respectively, 5.4, 6.6 and 12%. Calculations indicate that the difference of 2 to 3 giant nuclei per test tube of calcite (Ca), sea salt (Na) and clay (K) would account for these different RSDs. Concentration ranges in the rains varied from 0.14 to 2.95 mg L^?1 for Ca, 0.024 to 0.23 mg L^?1 for Na, and 0.014 to 0.064 mg L^?1 for K. The area between the test tubes which was 40% of the total collector area provided a bottom sample which on average agreed within 1.3% of the average value of the test tubes.     

The impact of harvester ants on decomposition, N mineralization, litter quality, and the availability of N to plants in the Mojave Desert

In arid areas of North America, nests of the seed-harvesting ant Pogonomyrmex rugosus tend to be elevated in mineral nitrogen and other soil nutrients relative to other microhabitats. We investigated the roles of decomposition, N mineralization, and plant nutrient uptake in maintaining high standing stocks of nutrients in P. rugosus ant nests. Decomposition rates of standard cellulose substrates placed on the surface of ant nests and other desert microhabitats suggest that conditions found in ant nests and bare areas are conducive to higher rates of decomposition than conditions under shrubs. In laboratory incubations of moist soil, net N mineralization rates were significantly higher in soil from ant nests than from bare areas and under two of three plant species. Net N mineralization rates measured in situ were much lower than those measured in laboratory incubations, but ant nest soil still exhibited higher rates at one of two sites. Litter collected from ant mounds, composed chiefly of seed chaff, was similar in N content to litter collected from underneath the dominant plant species, but had a significantly higher mean δ¹⁵N. Using this distinctive isotope signature as a tracer, we found no evidence that large perennial shrubs tap ant nests as a source of N. An invasive, annual grass species was significantly enriched in ¹⁵N, had higher leaf %N, and produced more seeds when growing on the mound than when growing several meters away; however P. rugosus nest surfaces are typically free of such annuals. We conclude that both high rates of nutrient cycling relative to other Mojave Desert microhabitats and low N utilization by the surrounding vegetation contribute to high standing stocks of mineral N in P. rugosus nests.     

Surface functional properties of native, acid-treated, and reduced soy glycinin. 1. Foaming properties

Foaming properties of native and chemically modified glycinin were evaluated. Effects of ionic strength and glycinin composition and concentration on foam formation and stabilization were studied. Glycinin was modified by means of combined treatments: cold or hot acidic treatments, with or without later disulfide bridges reduction. Modified proteins obtained from glycinin present different degrees of dissociation, deamidation, and as consequence, varied surface hydrophobicity and molecular size. Parameters of forming and stabilizing of foam were correlated with both deamidation and dissociation degrees of modified and native glycinin samples. A positive relationship was observed between surface behavior and foaming properties of different protein species. Results show that dissociation, deamidation, and reduction have produced structural changes on glycinin (increased surface hydrophobicity, increased net charge, decreased molecular size) which enhance the adsorption and anchorage of proteins at the air-water interface and, consequently, improve the foam forming and stabilizing capacities.