Novel base triples in RNA structures revealed by graph theoretical searching methods

Background: Highly hydrogen bonded base interactions play a major part in stabilizing the tertiary structures of complex RNA molecules, such as transfer-RNAs, ribozymes and ribosomal RNAs. Results: We describe the graph theoretical identification and searching of highly hydrogen bonded base triples, where each base is involved in at least two hydrogen bonds with the other bases. Our approach correlates theoretically predicted base triples with literature-based compilations and other actual occurrences in crystal structures. The use of 'fuzzy' search tolerances has enabled us to discover a number of triple interaction types that have not been previously recorded nor predicted theoretically. Conclusions: Comparative analyses of different ribosomal RNA structures reveal several conserved base triple motifs in 50S rRNA structures, indicating an important role in structural stabilization and ultimately RNA function

A predicted structure of the cytochrome c oxidase from Burkholderia pseudomallei

Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily. A recombinant plasmid carrying a 2.0 kb insert from a Burkholderia pseudomallei genomic library was subjected to automated DNA sequencing utilizing a primer walking strategy. Analysis of the 2002 bp insert revealed a 1536 bp open reading frame predicted to encode a putative cytochrome c oxidase. Further analysis using sequence alignments and tertiary structure analysis tools demonstrated that the hypothetical B. pseudomallei cytochrome c oxidase is similar to cytochrome c oxidases from other organisms such as Thermus thermophilus (36% protein sequence identity), Paracoccus denitrificans and bovine heart mitochondrial, the latter two which crystal structures available. The deduced 512 residue protein sequence includes the six canonical histidine residues involved in binding the low spin heme B and the binuclear center CuB/hemeA. The predicted tertiary structure of the hypothetical protein is consistent with previous models of electron transfer for cytochrome c oxidase

Molecular characterisation of Eimeria tenella porin, a potential anticoccidial drug target

Eimeria tenella is an apicomplexan parasite that causes the economically important disease coccidiosis in chickens. An estimated loss over $3 billion USD per annum has been reported. Control of coccidiosis relies on chemotherapy and vaccination but drug resistance is common and live vaccines are relatively expensive. Therefore, there is an urgent need to develop new drugs to control Eimeria infections. Recent studies have shown that the pore forming structures of porin play important roles in many eukaryotic organisms. In this study, we have generated and characterised a putative porin cDNA sequence from E. tenella that we have named Etporin. Sequence alignments showed that Etporin is 47 % similar to the putative porin sequence of Toxoplasma gondii, while a search against the Conserved Domain Database (CDD) shows that Etporin contains the Porin3 superfamily domain. Multiple sequence alignment with porin sequences from various eukaryotic organisms showed that the conserved VKXKX and GLK/STK motifs are present in Etporin. Analysis of the predicted Etporin 3D structure showed a classic beta barrel structure consisting of 19 beta-strands. Taken together, these results suggested Etporin has the potential to be developed into an anticoccidial drug target

Rafflesia tuanku-halimii (Rafflesiaceae), a new species from Peninsular Malaysia

Rafflesia tuanku-halimii, a new species from Peninsular Malaysia, is herewith described and illustrated. It is related to R. azlanii and R. sharifah-hapsahiae by coalesced warts on it lobes. Rafflesia tuanku-halimii is different from them in having window covered by almost united rings and these rings almost wholly covering the window