Can we infer peptide recognition specificity mediated by SH3 domains?

Protein interaction domain families that modulate the formation of macromolecular complexes recognize specific sequence or structural motifs. For instance SH3 and WW domains bind to polyproline peptides while SH2 and FHA domains bind to peptides phosphorylated in Tyr and Thr respectively. Within each family, variations in the chemical characteristics of the domain binding pocket modulate a finer peptide recognition specificity and, as a consequence, determine the selection of functional protein partners in vivo. In the proteomic era there is the need for reliable inference methods to help restricting the sequence space of the putative targets to be confirmed experimentally by more laborious experimental approaches. Here we will review the published data about the peptide recognition specificity of the SH3 domain family and we will propose a classification of SH3 domains into eight classes. Finally, we will discuss whether the available information is sufficient to infer the recognition specificity of any uncharacterized SH3 domain.     

The molluscicidal activity of niclosamide (Bayluscide WP70(R)) on Melanoides tuberculata (Thiaridae), a snail associated with habitats of Biomphalaria glabrata (Planorbidae)

The aim of this study was to determine the toxicity of niclosamide (Bayluscide (R)) on Melanoides tuberculata and Biomphalaria glabrata under laboratory conditions. The latter species is the intermediate host of Schistosoma mansoni (Sambon 1917). M. tuberculata was successfully used as competitor of B. glabrata in biological control programs in French West Indies. Both molluscicide and biological control using M. tuberculata have proved to be successful in reducing the population density of B. glabrata. The associated use of molluscicide in this area would be an effective measure if M. tuberculata were less susceptibility to the molluscicide than B. glabrata. Three hundreds individuals each of B. glabrata and of M. tuberculata, collected in Sumidouro, State of Rio de Janeiro, were used in the experiment. The molluscs were exposed to 14 different concentrations of niclosamide as recommended by the World Health Organization. Probit analysis was used to determine the LC 50 and LC 90. The LC 50 and LC 90 values for B. glabrata were 0.077 mg/l and 0.175 mg/l, respectively and the LC 50 and LC 90 values for M. tuberculata were 0.082 mg/l and 0.221 mg/l respectively. As the lethal concentrations of niclosamide were approximately the same to both species, this could be a disadvantage when controlling B. glabrata with niclosamide in an area of M. tuberculata occurrence. It might therefore be preferable to utilize the latex extracted from the Euphorbia splendens, which presented a much higher efficiency for B. glabrata than to M. tuberculata.     

Characterization of aspartate aminotransferase isoenzymes from leaves of Lupinus albus L. cv Estoril

Two aspartate aminotransferase (EC 2.6.1.1) isoenzymes (AAT-1 and AAT-2) from Lupinus albus L. cv Estoril were separated, purified, and characterized. The molecular weight, pI value, optimum pH, optimum temperature, and thermodynamic parameters for thermal inactivation of both isoenzymes were obtained. Studies of the kinetic mechanism, and the kinetics of product inhibition and high substrate concentration inhibition, were performed. The effect of some divalent ions and irreversible inhibitors on both AAT isoenzymes was also studied. Native PAGE showed a higher molecular weight for AAT-2 compared with AAT-1. AAT-1 appears to be more anionic than AAT- 2, which was suggested by the anion exchange chromatography. SDS-PAGE showed a similar sub-unit molecular weight for both isoenzymes. The optimum pH (between 8.0 and 9.0) and temperature (60-65 degrees C) were similar for both isoenzymes. In the temperature range of 45-65 degrees C, AAT-2 has higher thermostability than AAT-1. Both isoenzymes showed a high affinity for keto-acid substrates, as well as a higher affinity to aspartate than glutamate. Manganese ions induced an increase in both AAT isoenzymes activities, but no cooperative effect was detected. Among the inhibitors tested, hydroxylamine affected both isoenzymes activity by an irreversible inhibition mechanism.     

Protein and lipid trafficking induced in erythrocytes infected by malaria parasites

The human malaria parasite Plasmodium falciparum develops in a parasitophorous vacuolar membrane (PVM) within the mature red cell and extensively modifies structural and antigenic properties of this host cell. Recent studies shed significant new, mechanistic perspective on the underlying processes. There is finally, definitive evidence that despite the absence of endocytosis, transmembrane proteins in the host red cell membrane are imported in to the PVM. These are not major erythrocyte proteins but components that reside in detergent resistant membrane (DRM) rafts in red cell membrane and are detected in rafts in the PVM. Disruption of either erythrocyte or vacuolar rafts is detrimental to infection suggesting that raft proteins and lipids are essential for the parasitization of the red cell. On secretory export of parasite proteins: an ER secretory signal (SS) sequence is required for protein secretion to the PV. Proteins carrying an additional plastid targeting sequence (PTS) are also detected in the PV but subsequently delivered to the plastid organelle within the parasite, suggesting that the PTS may have a second function as an endocytic sorting signal. A distinct but yet undefined peptidic motif underlies protein transport across the PVM to the red cell (although all of the published data does not yet fit this model). Further multiple exported proteins transit through secretory 'cleft' structures, suggesting that clefts may be sorting compartments assembled by the parasite in the red cell.     

Influence of 50 Hz electromagnetic fields on recurrent embryogenesis and germination of cork oak somatic embryos

Plant tissue culture techniques are carried out under environmentally controlled conditions in phytotrons. However, electric components of phytotrons generate electromagnetic fields that may act as a environmental factor influencing plant growth and morphogenesis. Isolated somatic embryos of Quercus suber, picked from embryogenic lines, were chronically exposed to a 50 Hz and 15 μT electromagnetic field generated in a Helmholtz-coil system for 8 weeks, in order to examine if the extremely low frequency (ELF) magnetic field (MF) affected the morphogenic behaviour of embryogenic cultures during recurrent embryogenesis. Germination of somatic embryos from genotype G7.1 was carried out under the same electromagnetic field, and also under conditions in which the local geomagnetic field was suppressed. The ELF MF did not influence the growth of embryogenic clumps of the assayed genotypes, but reduced the number of detachable embryos produced by genotype G3.27. The ELF MF did not modify the percentages of germination or plant formation of somatic embryos. However, somatic embryos had better germination when cultured under the suppressed geomagnetic field condition. This revised version was published online in June 2006 with corrections to the Cover Date.     

The Streptomyces peucetius dpsY and dnrX Genes Govern Early and Late Steps of Daunorubicin and Doxorubicin Biosynthesis

The Streptomyces peucetius dpsY and dnrX genes govern early and late steps in the biosynthesis of the clinically valuable antitumor drugs daunorubicin (DNR) and doxorubicin (DXR). Although their deduced products resemble those of genes thought to be involved in antibiotic production in several other bacteria, this information could not be used to identify the functions of dpsY and dnrX. Replacement of dpsY with a mutant form disrupted by insertion of the aphII neomycin-kanamycin resistance gene resulted in the accumulation of UWM5, the C-19 ethyl homolog of SEK43, a known shunt product of iterative polyketide synthases involved in the biosynthesis of aromatic polyketides. Hence, DpsY must act along with the other components of the DNR-DXR polyketide synthase to form 12-deoxyaklanonic acid, the earliest known intermediate of the DXR pathway. Mutation of dnrX in the same way resulted in a threefold increase in DXR production and the disappearance of two acid-sensitive, unknown compounds from culture extracts. These results suggest that dnrX, analogous to the role of the S. peucetius dnrH gene (C. Scotti and C. R. Hutchinson, J. Bacteriol. 178:7316–7321, 1996), may be involved in the metabolism of DNR and/or DXR to acid-sensitive compounds, possibly related to the baumycins found in many DNR-producing bacteria.     

Activated oxygen‐mediated metabolic functions of leaf peroxisomes

Peroxisomes are subcellular organelles with an essentially oxidative type of metabolism. The presence in these organelles of superoxide dismutases and the generation of superoxide radicals (O₂^??) was first demonstrated in plant tissues and in recent years different experimental evidence has suggested the existence of cellular functions related to activated oxygen species. Some of these functions are analyzed in this work. In purified intact peroxisomes from pea (Pisum sativum L.) leaves, xanthine oxidase and urate oxidase were found to be present. The occurrence and the level of the metabolites xanthine, hypoxanthine, uric acid, and allantoin were studied in extracts of pea leaf peroxisomes by HPLC. Xanthine, uric acid, and allantoin were detected in peroxisomes. These results suggest a cellular role for leaf peroxisomes in the catabolism of purines. In peroxisomal membranes, 3 polypeptides (PMPs) with molecular masses of 18, 29 and 32 kDa, respectively, have been shown to generate superoxide radicals. These PMPs were purified from pea leaf peroxisomal membranes and characterized. While the 18- and 32-kDa PMPs use NADH as electron donor for O₂^?? production, the 29-kDa PMP was clearly dependent on NADPH. Very recently, the occurrence in pea leaf peroxisomes of all the enzymes of the ascorbate-glutathione cycle has been demonstrated. NADPH is required for the glutathione reductase activity of the cycle and this implies the reduction of NADP⁺ to NADPH. This recycling function could be carried out by the NADP-dependent glucose-6-phosphate dehydrogenase (G6PDH), 6-phosphogluconate dehydrogenase (6PGDH), and isocitrate dehydrogenase (ICDH). These 3 dehydrogenases have been demonstrated to be present in the matrix of pea leaf peroxisomes. The catabolism of purines, the superoxide-generating PMPs, the ascorbate-glutathione cycle, and the dehydrogenase-mediated recycling of NADPH, are activated oxygen roles of leaf peroxisomes that add to other functions previously known for peroxisomes from eukaryotic cells.     

Synthesis and characterization of gold(III) complexes of 1,4-benzodiazepin-2-ones. Crystal structure of trichloro-[7-chloro-1-(cyclopropylmethyl)-1,3-dihydro-5-phenyl-2H-1,4-benzodiazepin-2-one]gold(III)

The reaction of gold(III) chloride with several 1,4-benzodiazepin-2-ones, L, gives 1:1 adducts, (L)AuCl₃*, which were characterized by IR, Raman and ¹H NMR spectroscopy. In the title compound the coordination of the ligand, ascertained through a X-ray structure determination, was shown to occur through the 4-nitrogen atom.     

Growth factors that stimulate human granulocyte—macrophage colony formation produced by the cell line CM-S

CM-S is an autonomous cell line of human hemopoietic precursor cells inducible to monocyte-macrophage differentiation in response to appropriate inducing agents. CM-S cells produce factors that stimulate their own growth and proliferation, and are also capable of stimulating clonal proliferation of human, but not mouse, monocytic and granulocytic bone marrow progenitor cells in viscous medium. Preliminary purification steps have demonstrated at least two species, one of which (MW 30,000–50,000) retains both these activities, while the other (MW ≤ 10,000) apparently retains only the autostimulatory activity. CM-S cells could thus be a useful source for the purification of human colony stimulating factors (CSFs). CM-S cells also respond to factors present in human placenta conditioned medium, known to contain human CSF. This suggests that CM-S cells could provide a homogeneous target cell population for testing CSFs from other human sources.     

LIFE CYCLE,SIZE REDUCTION PATTERNS,AND ULTRASTRUCTURE OF THE PENNATE PLANKTONIC DIATOM PSEUDO‐NITZSCHIA DELICATISSIMA (BACILLARIOPHYCEAE)1

Pseudo‐nitzschia delicatissima (Cleve) Heiden is a very common pennate planktonic diatom found in temperate marine waters, where it is often responsible for blooms. Recently, three distinct internal transcribed spacer types have been recorded during a P. delicatissima bloom in the Gulf of Naples (Mediterranean Sea, Italy), which suggests the existence of cryptic diversity. We carried out mating experiments with clonal strains belonging to the most abundant internal transcribed spacer type. Pseudo‐nitzschia delicatissima is heterothallic and produces two functional anisogametes per gametangium. The elongated auxospore possesses a transverse and a longitudinal perizonium. The sexual phase was observed to occur over a wide size spectrum, spanning 19–80 μm and corresponding to almost the whole range of cell length observed for P. delicatissima. We also investigated cell morphology, valve ultrastructure and morphometry of parental, F1‐generation strains, and the progeny of crosses between parental and F1 strains. Although ultrastructural features match those described for P. delicatissima, variability in cell shape was recorded in the largest cells of the F1 generation as well as in valves with an abnormal arrangement of poroids. As many other diatoms, P. delicatissima undergoes size reduction over its life cycle, and cells of different size showed differences in growth rates and the amount of size reduction per cell cycle. Cells between 60 and 30 μm in length showed the fastest growth and the slowest rates of size reduction per generation. In culture, P. delicatissima cells can decrease to 8 μm in length; however, such small cells (≤30 μm) are not recorded in the sea, and this raises interesting questions about the factors that control their survival in the natural environment.