Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling

Here, we present a new approach for protein ligand screening based on the use of limited exoproteolysis coupled to MALDI-TOF mass spectrometry, combined with computational modelling and prediction of binding energies. As a test for this combined approach, we have screened a combinatorial library containing 8000 peptides (organized in 60 peptide samples) based on positional scanning format. This library is attached to a poly-Pro framework, and screened against the Abl-SH3 domain. The results obtained demonstrated the validity of the experimental and theoretical approaches in identifying better ligands and in rationalizing the changes in affinity. Exoproteolysis coupled to MALDI-TOF mass spectrometry could be used to screen complex libraries in a fast and efficient way.     

New species of benthopelagic hydromedusae from the Weddell Sea

Four medusa species were collected by an epibenthic sledge during the "Polarstern" ANT XV/3 cruise carried out from January to March 1998 in the eastern Weddell Sea. The specimens were collected in the benthic boundary layer at depths ranging between 1,583 and 2,034 m; 2 of the species collected are new to science. The narcomedusa Sigiweddellia bathypelagica gen. nov. et sp. nov. is characterised by two types of marginal tentacles and closed marginal statocysts. The trachymedusa Voragonema laciniata sp. nov. (known only from the single holotype) is characterised by the number and irregular shape of the centripetal canals. These findings are the first to report benthopelagic hydromedusae in deep Antarctic waters. Examination of several specimens of Benthocodon pedunculata (Bigelow 1913) leads us to move it to the genus Voragonema Naumov 1971 because of the clear presence of centripetal expansions in the ring canal.     

Dissecting planarian central nervous system regeneration by the expression of neural-specific genes

The planarian central nervous system (CNS) can be used as a model for studying neural regeneration in higher organisms. Despite its simple structure, recent studies have shown that the planarian CNS can be divided into several molecular and functional domains defined by the expression of different neural genes. Remarkably, a whole animal, including the molecularly complex CNS, can regenerate from a small piece of the planarian body. In this study, a collection of neural markers has been used to characterize at the molecular level how the planarian CNS is rebuilt. Planarian CNS is composed of an anterior brain and a pair of ventral nerve cords that are distinct and overlapping structures in the head region. During regeneration, 12 neural markers have been classified as early, mid-regeneration and late expression genes depending on when they are upregulated in the regenerative blastema. Interestingly, the results from this study show that the comparison of the expression patterns of different neural genes supports the view that at day one of regeneration, the new brain appears within the blastema, whereas the pre-existing ventral nerve cords remain in the old tissues. Three stages in planarian CNS regeneration are suggested.     

Characterization of aromatase activity in the sea bass: effects of temperature and different catalytic properties of brain and ovarian homogenates and microsomes

Two aromatase genes have been discovered in the brain and ovary of some teleosts. However, data on native aromatase enzyme kinetics and thus actual catalytic activity are scarce in fish, impeding comparison of aromatase activity (AA) from different organs within and between species. In the present study, the tritiated water assay was optimized and validated to measure AA in the sea bass using 1 beta-[3H]-androstenedione as a substrate in crude homogenates and microsomes. Optimized assay variables included pH, temperature, buffer strength, incubation time, amount of fresh tissue, substrate, and cofactor concentration. Specificity of the assay was verified by using known inhibitors, inappropriate substrates, and heat-inactivation. Subcellular fractionation revealed ten-fold more activity in the microsomal over the cytosolic fraction. The assay was also validated by comparing results from the direct product isolation method. The validated assay described allows measurement of AA to levels as low as < 10 fmol/mg protein/hr. Sex differentiation is temperature-dependent in the sea bass. It was found that in the physiological range of temperatures where the sea bass can live, 10-30 degrees C, AA is highly dependent on temperature in a linear fashion (brain: r2 = 0.92; P < 0.001; ovary: r2 = 0.94; P < 0.001). When AA levels from brain and ovarian homogenates obtained from the same fish during the spawning season were compared, the respective Michaelis-Menten constant (Km) values were 7.3 nM vs. 4.6 nM, with no significant differences detected between the two tissues. Thus, sea bass aromatase has a very high affinity for androstenedione, similar to what has been found in goldfish, but much higher than other piscine or mammalian aromatases (30-435 nM). In contrast, the brain maximum reaction rate (Vmax 7.8 pmol/mg protein/hr) was four-fold higher (P < 0.001) than the ovarian Vmax (2.1 pmol/mg protein/hr). Consistent results were found using purified microsomes. Although this is the first time that the kinetic parameters are reported for a native piscine aromatase in two different tissues within the same fish, it remains to be determined whether this is a reflection of two distinct isoforms in this particular species.     

Can a Place of Origin of the Main Cystic Fibrosis Mutations Be Identified?

The genetic background of the mutations that most often cause cystic fibrosis (CF) is different from that of non-CF chromosomes in populations of European origin. It is not known whether these haplotype backgrounds could be found at high frequencies in populations in which CF is, at present, not common; such populations would be candidates for the place of origin of CF mutations. An analysis of haplotypes of CF transmembrane conductance regulator, together with their variation in specific CF chromosomes, in a worldwide survey of normal chromosomes shows (1) a very low frequency or absence of the most common CF haplotypes in all populations analyzed and (2) a strong genetic variability and divergence, among various populations, of the chromosomes that carry disease-causing mutations. The depth of the gene genealogy associated with disease-causing mutations may be greater than that of the evolutionary process that gave rise to present-day human populations. The concept of "population of origin" lacks either spatial or temporal meaning for mutations that are likely to have been present in Europeans before the ethnogenesis of present populations; subsequent population processes may have erased the traces of their geographic origin.     

TranScout: prediction of gene expression regulatory proteins from their sequences

MOTIVATION: The advent of genomics yields thousands of reading frames in search of function. Identification of conserved functional motifs in protein sequences can be helpful for function prediction. RESULTS: A database and a classification of reported DNA-binding protein motifs has been designed. A program ('TranScout') has been developed for the detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function. The efficiency of the program is shown in a benchmark against a database obtained from SWISS-PROT without the protein sequences used to train the program. All motifs were detected with a mean average sensitivity of 0.98 and a mean average specificity of 0.92. AVAILABILITY: The program is freely available for use on the internet at http://luz.uab.es/transcout/. The user can find additional information at this site.     

Statistical Analysis of the Loop-Geometry on a Non-Redundant Database of Proteins

The conformations of protein loops from a non-redundant set of 347 proteins with less than 25% sequence homology have been studied in order to clarify the topological variation of protein loops. Loops have been classified in five types (α-α, α-β, β-α, β-links and β-hairpins) depending on the secondary structures that they embrace. Four variables have been used to describe the loop geometry (3 angles and the end-to-end distance between the secondary structures embracing the loop). Loops with well defined geometry are identified by means of the internal dependency between the geometrical variables by application of information-entropy theory. From this it has been deduced that loops formed by less than 10 residues show an intrinsic dependency on the geometric variables that defines the motif shape. In this interval the most stable loops are found for short connections owing to the entropic energy analysed.     

In vitro antiprotozoal activity of alkaloids from Phaedranassa dubia (Amaryllidaceae)

The bulbs of Phaedranassa dubia (Amaryllidaceae) were found to contain the novel compound phaedranamine, together with seven known alkaloids. The structure and stereochemistry of the alkaloids were determined by physical and spectroscopic methods. An in vitro screening against four different parasitic protozoa was carried out using the isolated compounds. The alkaloids ungeremine, pseudolycorine and haemanthamine showed good activity in in vitro assays against Trypanosoma brucei rhodesiense, T. cruzi and Plasmodium falciparum with IC₅₀ values in the range of 3.66 μM or lower.