The design, synthesis, and crystallization of an alpha-helical peptide

Twelve- and sixteen-residue peptides have been designed to form tetrameric alpha-helical bundles. Both peptides are capable of folding into amphiphilic alpha-helices, with leucyl residues along one face and glutamyl and lysyl residues along the opposite face. Four such amphiphilic alpha-helices are capable of forming a noncovalently bonded tetramer. Neighboring helices run in antiparallel directions in the design, so that the complex has 222 symmetry. In the designed tetramer, the leucyl side chains interdigitate in the center in a hydrophobic interaction, and charged side chains are exposed to the solvent. The designed 12-mer (ALPHA-1) has been synthesized, and it forms helical aggregates in aqueous solution as judged by circular dichroic spectroscopy. It has also been crystallized and characterized by x-ray diffraction. The crystal symmetry is compatible with (but does not prove) the design. The design can be extended to a four-alpha-helical bundle formed from a single polypeptide by adding three peptide linkers.     

Improved Detection of Remote Homologues Using Cascade PSI-BLAST: Influence of Neighbouring Protein Families on Sequence Coverage

Background

Development of sensitive sequence search procedures for the detection of distant relationships between proteins at superfamily/fold level is still a big challenge. The intermediate sequence search approach is the most frequently employed manner of identifying remote homologues effectively. In this study, examination of serine proteases of prolyl oligopeptidase, rhomboid and subtilisin protein families were carried out using plant serine proteases as queries from two genomes including A. thaliana and O. sativa and 13 other families of unrelated folds to identify the distant homologues which could not be obtained using PSI-BLAST.

Methodology/Principal Findings

We have proposed to start with multiple queries of classical serine protease members to identify remote homologues in families, using a rigorous approach like Cascade PSI-BLAST. We found that classical sequence based approaches, like PSI-BLAST, showed very low sequence coverage in identifying plant serine proteases. The algorithm was applied on enriched sequence database of homologous domains and we obtained overall average coverage of 88% at family, 77% at superfamily or fold level along with specificity of ∼100% and Mathew’s correlation coefficient of 0.91. Similar approach was also implemented on 13 other protein families representing every structural class in SCOP database. Further investigation with statistical tests, like jackknifing, helped us to better understand the influence of neighbouring protein families.

Conclusions/Significance

Our study suggests that employment of multiple queries of a family for the Cascade PSI-BLAST searches is useful for predicting distant relationships effectively even at superfamily level. We have proposed a generalized strategy to cover all the distant members of a particular family using multiple query sequences. Our findings reveal that prior selection of sequences as query and the presence of neighbouring families can be important for covering the search space effectively in minimal computational time. This study also provides an understanding of the ‘bridging’ role of related families.     

Follicular epithelial cell apoptosis of atretic follicles within developing ovaries of the mosquito Culex pipiens pallens

Follicular atresia, the degeneration of developing follicles, is always incident to normal oogenesis in both oviparous and viviparous animals. Photo- and electron-microscopic observation of degenerating follicles within developing ovaries taken from blood-fed Culex pipiens pallens mosquitoes showed gradual degradation of the internal structures including yolk granules in the oocyte. The epithelial cells, which sometimes incorporated yolk granules from the oocyte along with the shrinkage of the follicle, gradually lost their uniform columnar shape, while their integrity as a covering layer remained. In situ active caspase analysis detected active enzymes in these epithelial regions. In the latest stages of atresia where either the nurse cells or oocyte were lost, the follicle was mainly comprised of irregularly shaped epithelial cells, and some of these cells' nuclei contained condensed chromatin peripherally, one of the characteristics of apoptotic cells. Also terminaldeoxynucleotidyl transferase-mediated dUTP-biotin nick-end labeling treatment indicated that DNA fragmentation occurred in these follicles. It seems likely that in atretic follicles the epithelial cells survive to play key roles in the event, and then finally undergo their own apoptotic cell death so as to give the developmental site to the next follicle in the same ovariole.     

Structural characterization of an immunoenhancing cytotoxic heteroglycan isolated from an edible mushroom Calocybe indica var. APK2

A water-soluble polysaccharide of an edible mushroom Calocybe indica var. APK2 showed immunoenhancing (macrophage, splenocyte, thymocyte, and bone marrow activation) and cytotoxic activity toward HeLa cell lines and found to consist of d-glucose, d-galactose, and l-fucose in a molar ratio of nearly 3:1:1. On the basis of acid hydrolysis, methylation analysis, and NMR studies (¹H, ¹³C, DEPT-135, TOCSY, DQF–COSY, NOESY, ROESY, HMQC, and HMBC), the structure of the repeating unit of the fuco-galacto-glucan was established as:     

Structural characterization and study of immunoenhancing and antioxidant property of a novel polysaccharide isolated from the aqueous extract of a somatic hybrid mushroom of Pleurotus florida and Calocybe indica variety APK2

A water-soluble polysaccharide was isolated from the aqueous extract of the fruit bodies of somatic hybrid PCH9FB, obtained through intergeneric protoplast fusion between the strains Pleurotus florida and Calocybe indica var. On the basis of total acid hydrolysis, the polysaccharide was found to contain galactose, fucose, and glucose in a molar ratio of nearly 2:1:2. Methylation analysis and NMR experiments ((1)H, (13)C, DEPT-135, DQF-COSY, TOCSY, NOESY, ROESY, HMQC, and HMBC) showed that the structure of the repeating unit present in the polysaccharide was This molecule showed macrophage, splenocyte, thymocyte activation as well as antioxidant property.     

Effects of blood and virus-infected blood on protein expression in the midgut of the dengue vector Aedes albopictus

Although the mosquito midgut is the primary site of bloodmeal storage and the first line of defence against pathogenic infection, little is known about its proteic composition at a time when an increasing number of proteins are reported to impair viral infection. Aedes albopictus Skuse (Diptera: Culicidae) is an important vector of the dengue virus. We compared 2-dimensional protein profiles of the adult midgut in this species, taking into account bloodmeal status. The comparison of profiles from sugar-fed and blood-fed females showed that a considerable number of proteins were present in both midguts. In addition, one set of proteins was present only after sugar intake and another set only after blood intake. The comparison of profiles of blood-fed midguts and dengue virus-2 infected blood-fed midguts revealed that at least six proteins were present only in the infected midguts. These results are discussed in the context of the identification of midgut proteins involved in the dengue virus infection process.