Analysis of binding properties and specificity through identification of the interface forming residues (IFR) for serine proteases <Emphasis Type="Italic">in silico</Emphasis> docked to different inhibitors

Background  

Enzymes belonging to the same super family of proteins in general operate on variety of substrates and are inhibited by wide selection of inhibitors. In this work our main objective was to expand the scope of studies that consider only the catalytic and binding pocket amino acids while analyzing enzyme specificity and instead, include a wider category which we have named the Interface Forming Residues (IFR). We were motivated to identify those amino acids with decreased accessibility to solvent after docking of different types of inhibitors to sub classes of serine proteases and then create a table (matrix) of all amino acid positions at the interface as well as their respective occupancies. Our goal is to establish a platform for analysis of the relationship between IFR characteristics and binding properties/specificity for bi-molecular complexes.     

Electron ionization mass spectra of reduced and permethylated urinary oligosaccharides from patients with mannosidosis

The electron ionization mass spectra of reduced and permethylated isomeric mixtures of the major urinary tri- to deca-oligosaccharides of patients with mannosidosis are reported. Many of the oligosaccharide isomers can be differentiated in the mixtures on the basis of their distinct fragmentation patterns.     

5-Chloropicolinic acid is produced by specific degradation of 4-chlorobenzoic acid by Sphingomonas paucimobilis BPSI-3

We have previously shown that the bacterium Sphingomonas paucimobilis BPSI-3, isolated from PCB-contaminated soil, can degrade halogenated biphenyls, naphthalenes, catechols and benzoic acids. However, before such an organism can be used in bioremediation, it is important to characterise the degradation products and determine the degradation pathways to ensure that compounds more toxic or mobile than the original contaminants are not produced. In the degradation of 4-chlorobiphenyl, S. paucimobilis BPSI-3 produces a novel chlorinated picolinic acid. In this paper, we show that 4-chlorobenzoate is an intermediate in this degradation and, through ¹⁵N-labelling, that 5-chloropicolinate is the only nitrogenous metabolite isolated under the extraction conditions used. The position of the chlorine indicates that degradation of 4-chlorocatechol occurs exclusively via a 2,3-extradiol cleavage. These data allow us to postulate a more definitive catabolic pathway for the biodegradation of 4-chlorobiphenyl to 5-chloro-2-hydroxymuconic acid semialdehyde via 4-chlorobenzoate in S. paucimobilis BPSI-3. Received 19 April 1999/ Accepted in revised form 23 July 1999     

Temporal Uncoupling between Energy Acquisition and Allocation to Reproduction in a Herbivorous-Detritivorous Fish

Although considerable knowledge has been gathered regarding the role of fish in cycling and translocation of nutrients across ecosystem boundaries, little information is available on how the energy obtained from different ecosystems is temporally allocated in fish bodies. Although in theory, limitations on energy budgets promote the existence of a trade-off between energy allocated to reproduction and somatic growth, this trade-off has rarely been found under natural conditions. Combining information on RNA:DNA ratios and carbon and nitrogen stable-isotope analyses we were able to achieve novel insights into the reproductive allocation of diamond mullet (Liza alata), a catadromous, widely distributed herbivorous-detritivorous fish. Although diamond mullet were in better condition during the wet season, most reproductive allocation occurred during the dry season when resources are limited and fish have poorer body condition. We found a strong trade-off between reproductive and somatic investment. Values of δ¹³C from reproductive and somatic tissues were correlated, probably because δ¹³C in food resources between dry and wet seasons do not differ markedly. On the other hand, data for δ¹⁵N showed that gonads are more correlated to muscle, a slow turnover tissue, suggesting long term synthesis of reproductive tissues. In combination, these lines of evidence suggest that L. alata is a capital breeder which shows temporal uncoupling of resource ingestion, energy storage and later allocation to reproduction.     

Isolation of chromatin fragments rich in non-histone protein after endonuclease digestion of rat liver nuclei

Detergent-washed rat liver nuclei, prepared in the presence of a protease inhibitor, were incubated for up to 60 min at 37 °C. The action of endonucleases produced chromatin fragments which could be removed from the nuclei by extraction with 8 M urea 50 mM phosphate, pH 7.6, 15% of the total nuclear DNA being extracted. No DNA could be detected in this extract after incubation of nuclei at 4 °C. The chromatin fragments were sedimented by centrifugation at 90000 g or by chromatography on Sepharose 4B. The DNA fragment sizes were similar to those found in nucleosome particles but the protein/DNA ratio was approx. 5.3:1. The nuclei were prelabelled with [³H]tryptophan and 60% of the label present in the 8 M urea extract was found to sediment with the chromatin fraction. SDS polyacrylamide gel electrophoresis of the latter showed the presence, in addition to histones, of at least 25 polypeptide species of tightly bound non-histone proteins with molecular weights in excess of 30000.     

Traits explain sorting of C4 grasses along a global precipitation gradient

1. Species distributions are closely associated with moisture availability, but the underlying mechanisms remain unresolved. Drought relations are especially important for plants such as C₄ grasses that dominate seasonally dry ecosystems. Here, we test the hypothesis that C₄ grass species sampled across global precipitation gradients show variation in survival under drought that can be explained by their traits.
2. Our experiment subjected 18 C₄ grass species to a lethal drought under controlled environmental conditions. The number of days until death was measured, along with root traits, senescence, and aspects of hydraulic function.
3. We identified two strategies: Drought‐avoiding species that stayed green as the water potential declined and drought‐tolerating species that senesced more quickly but could extend survival via drought‐tolerant meristems.
4. Plants that stay‐green for longer occupied drier habitats and had the longest survival under drought, facilitated by narrow root diameter and isohydric stomatal behavior. Plants that senesced quickly had thicker roots, an anisohydric strategy, and occupied wetter habitats.
5. Global distributions of C₄ grasses can be predicted by variation in rates of senescence, meristem survival, root traits, and stomatal strategy, showing the value of these traits for understanding plant distributions in relation to climate.

     

Modified Methodology to Improve Flow Cytometric Dna Histograms from Paraffin-Embedded Material

Flow Cytometric (FCM) DNA content analysis of paraffin-embedded tissues has become a widely accepted procedure in assessing the biologic course in some tumors from archival material. Difficulty in interpreting histograms is frequently due to high levels of debris, and wide coefficients of variation (CV). These may lead to underestimating near-diploid abnormality. Although the clinical significance of low-degree aneuploidy has yet to be established, the procedure reported here improved our endeavor to detect DNA Indices (DI) of at least 1.1%. Experience has shown that careful technique can result in overall improvement of DNA histograms by lowering levels of debris and % CV, dramatically so in some cases. Archival histograms can be generated that rival in quality fresh tissue results. Archival material is currently employed for diagnostic and research purposes.     

EDC3 phosphorylation regulates growth and invasion through controlling P‐body formation and dynamics

Regulation of mRNA stability and translation plays a critical role in determining protein abundance within cells. Processing bodies (P‐bodies) are critical regulators of these processes. Here, we report that the Pim1 and 3 protein kinases bind to the P‐body protein enhancer of mRNA decapping 3 (EDC3) and phosphorylate EDC3 on serine (S)161, thereby modifying P‐body assembly. EDC3 phosphorylation is highly elevated in many tumor types, is reduced upon treatment of cells with kinase inhibitors, and blocks the localization of EDC3 to P‐bodies. Prostate cancer cells harboring an EDC3 S161A mutation show markedly decreased growth, migration, and invasion in tissue culture and in xenograft models. Consistent with these phenotypic changes, the expression of integrin β1 and α6 mRNA and protein is reduced in these mutated cells. These results demonstrate that EDC3 phosphorylation regulates multiple cancer‐relevant functions and suggest that modulation of P‐body activity may represent a new paradigm for cancer treatment.