Validation of the first step of the heuristic refinement method for the derivation of solution structures of proteins from NMR data

A new method for the analysis of NMR data in terms of the solution structure of proteins has been developed. The method consists of two steps: first a systematic search of the conformational space to define the region allowed by the initial set of experimental constraints, and second, the narrowing of this region by the introduction of additional constraints and optional refinement procedures. The search of the conformational space is guided by heuristics to make it computationally feasible. The method is therefore called the heuristic refinement method and is coded in an expert system called PROTEAN. The paper describes the validation of the first step of the method using an artificial NMR data set generated from the known crystal structure of sperm whale carbon monoxymyoglobin. It is shown that the initial search procedure yields a low-resolution structure of the myoglobin molecule, accurately reproducing its main topological features, and that the precision of the structure depends on the quality of the initial data set.     

Demonstration of a COOH-terminal extension on equine lutropin by means of a common acid-labile bond in equine lutropin and equine chorionic gonadotropin

The beta subunits of equine lutropin and equine chorionic gonadotropin were incubated in 0.013 N HCl for 30 min at 110 degrees C and separated into two fragments by reverse-phase high performance liquid chromatography. The amino acid and carbohydrate compositions of both fragments from each subunit were analyzed. The results demonstrated that equine lutropin-beta has a glycosylated COOH-terminal extension that differs only in carbohydrate composition from the COOH-terminal portion of equine chorionic gonadotropin-beta. This is the first demonstration of a glycosylated COOH-terminal extension in a pituitary glycoprotein hormone.     

Depicting the Spatial Distribution of Proteins in Human Tumor Tissue Combining SELDI and MALDI Imaging and Immunohistochemistry

Carcinoma tissue consists of not only tumor cells but also fibroblasts, endothelial cells or vascular structures, and inflammatory cells forming the supportive tumor stroma. Therefore, the spatial distribution of proteins that promote growth and proliferation in these complex functional units is of high interest. Matrix-assisted laser desorption/ionization imaging mass spectrometry is a newly developed technique that generates spatially resolved profiles of protein signals directly from thin tissue sections. Surface-enhanced laser desorption/ionization mass spectrometry (MS)combined with tissue microdissection allows analysis of defined parts of the tissue with a higher sensitivity and a broader mass range. Nevertheless, both MS-based techniques have a limited spatial resolution. IHC is a technique that allows a resolution down to the subcellular level. However, the detection and measurement of a specific protein expression level is possible only by semiquantitative methods. Moreover, prior knowledge about the identity of the proteins of interest is necessary. In this study, we combined all three techniques to gain highest spatial resolution, sensitivity, and quantitative information. We used frozen tissue from head and neck tumors and chose two exemplary proteins (HNP1–3 and S100A8) to highlight the advantages and disadvantages of each technique. It could be shown that the combination of these three techniques results in congruent but also synergetic data. (J Histochem Cytochem 58:929–937, 2010)     

Solute contents in roots and root calli of NaCl-tolerant and NaCl-sensitive tissues ofLycopersicon

Biomass, relative growth rate (RGR), organic and inorganic solute contents in control and NaCl (50–100 mM) affected roots or calli of the wild tomato genotypeLycopersicon pennellii and theLycopersicon esculentum wilty mutantflacca were compared. Under NaCl-stress, the RGR of calli fromL. pennellii was higher than that of the mutantflacca, while the root biomass of the former was lower than that of the latter. Constant water contents were found in calli and roots, irrespective of the genotypes and NaCl concentrations. Taking into account the solute contents of the apoplasm, Na⁺ accumulation was similar in the sensitive tissues (calli fromL. flacca, roots ofL. pennellii) and the tolerant ones (calli fromL. pennellii, flacca roots). Decreased K⁺ and Mg²⁺ and increased proline contents were found in both sensitive tissues. In comparison with sensitiveL. pennellii roots, salt sensitiveflacca calli showed increased total organic acid and amino acid contents.     

Conserved exon-intron organization in two different caerulein precursor genes of Xenopus laevis. Additional detection of an exon potentially coding for a new peptide

From a genomic library of Xenopus laevis, two genes coding for different preprocaeruleins have been isolated and sequenced. These correspond to the type I and type III precursors analyzed previously at the cDNA level [Richter, K., Egger, R. and Kreil, G. (1986) J. Biol. Chem. 261, 3676-3680]. The type III gene comprises eight exons; the type I apparently contains eight exons as well, of which six have been sequenced. The genetic information for the dekapeptide caerulein is present on small exons of 45 base pairs. The two genes are highly homologous in their 5'-flanking region, the exon/intron boundaries, and long stretches of intron sequences. A possible scheme for the evolution of this small family of genes through exon and gene duplications is presented. In the type I gene, in place of one of the caerulein exons, a potential exon with conserved splice sites was discovered. If expressed in some frog cells, this exon would code for a new peptide 60% homologous to caerulein.     

Surface markers of a purified peritoneal eosinophil population from Mesocestoides corti-infected BALB/c male mice

Eosinophils of approximately 95% purity were prepared from the peritoneal cavities of BALB/c male mice infected with larval cestode, Mesocestoides corti. The alloantigenic surface marker phenotype of this cell population was shown to be H-2+Ly4+Ly5+Lyt-1-,2-,3-Ly-6-,7-Ia-Thy-1-TL-. Two of four anti-Lyt-2 sera were positive when tested on purified eosinophils by using the Staphylococcus aureus protein A sheep erythrocyte rosetting method, but absorption studies indicated that this reaction was not due to anti-Lyt-2 antibodies. Eosinophils are therefore Lyt-2-, although some Lyt-2 sera contain additional eosinophil reactive antibodies. A proportion (20 to 40%) of the population of eosinophils was positive for the Fc receptor, but all were negative for the C3 receptor and for surface immunoglobulin.     

Formation of Basal Bodies in Ciliary Epithelium of Molluscs Buccinum undatum L. and Lymnaea stagnalis L.

Electron microscopic studies of the leg ciliary epithelium was carried out in two mollusks. In the epithelium of the leg of adult animals, the centrioles were mostly formed de novo with participation of deuterosomes during the formation of basal bodies. Transformation of the centriolar cylinder in a mature basal body is accompanied by the cylinder elongation and appearance of pericentriolar structures, such as rootlet system, basal legs, and basal plate. Centriolegenesis proceeds in both ciliate and nonciliate (with microvilli) cells of the epithelium. It has been proposed that the cell with microvilli represent a transitional stage in differentiation of the ciliary cells.