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Provides information on a study which analyzes the metals of the cytochrome c oxidase structures of the bovine heart mitochondrion and the soil bacterium Paracoccus denitrificans which include a dicopper center, magnesium, two proximal hemes, a copper atom and a calcium. Methods, data and terminology; Results and discussion; Summary.

Presents information on a study which measures residue densities in protein structures centering on the atom density about different amino acid types. Methodology of the study; Results and discussion on the study.

Identifies commonalities and disparities of the extended environment of mononuclear metal sites centering on copper, iron, manganese and zinc, in proteins. Layers of an extended environment on a metal site within a protein; Purposes of metals in proteins; Facets emphasized by metal environment of the protein structure; Identification of statistically significant three-dimensional residue clusters.

Examines the extended metal environment, particularly zinc, in protein structures. Details on the second shell of mononuclear zinc centers; Similarities and dissimilarities of the extended metal environment of zinc metal sites; Roles served by zinc in biological systems; What the principal ligands coordinating zinc ions comprises of; Details on the study.

Investigates the identification of statistically significant charge clusters in tertiary protein structures from a large representative collection of protein structures. Coordination of negative charge clusters with calcium, magnesium or zinc ions; Localization of mixed-charge clusters at interchain contacts; Role of charge clusters in protein-protein interaction and substrate binding.

Presents new method for the identification and statistical analysis of three-dimensional protein structures residue clusters. Analysis of surface residues or those outside the threshold level of side solvent accessibility; Detection of the extent of residue conservation in protein families; Catalytic and structural roles of metals; Aid in identification of distinctive sites.

To maximise the assignment of function of the proteins encoded by a genome and to aid the search for novel drug targets, there is an emerging need for sensitive methods of predicting protein function on a genome-wide basis. GeneAtlas™ is an automated, high-throughput pipeline for the prediction of protein structure and function using sequence similarity detection, homology modelling and fold recognition methods. GeneAtlas is described in detail here. To test GeneAtlas, a 'virtual' genome was used, a subset of PDB structures from the SCOP database, in which the functional relationships are known. GeneAtlas detects additional relationships by building 3D models in comparison with the sequence searching method PSI-BLAST. Functionally related proteins with sequence identity below the twilight zone can be recognised correctly. [ABSTRACT FROM AUTHOR]

Summary To address the need for new approaches to antibiotic drug development, we have identified a large number of essential genes for the bacterial pathogen, Staphylococcus aureus , using a rapid shotgun antisense RNA method. Staphylococcus aureus chromosomal DNA fragments were cloned into a xylose-inducible expression plasmid and transformed into S. aureus . Homology comparisons between 658 S. aureus genes identified in this particular antisense screen and the Mycoplasma genitalium genome, which contains 517 genes in total, yielded 168 conserved genes, many of which appear to be essential in M. genitalium and other bacteria. Examples are presented in which expression of an antisense RNA specifically reduces its cognate mRNA. A cell-based, drug-screening assay is also described, wherein expression of an antisense RNA confers specific sensitivity to compounds targeting that gene product. This approach enables facile assay development for high throughput screening for any essential gene, independent of its biochemical function, thereby greatly facilitating the search for new antibiotics. [ABSTRACT FROM AUTHOR]