Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases.

Protein structural alignments are generally considered as 'golden standard' for the alignment at the level of amino acid residues. In this study we have compared the quality of pairwise and multiple structural alignments of about 5900 homologous proteins from 718 families of known 3-D structures. We observe shifts in the alignment of regular secondary structural elements (helices and strands) between pairwise and multiple structural alignments. The differences between pairwise and multiple structural alignments within helical and beta-strand regions often correspond to 4 and 2 residue positions respectively. Such shifts correspond approximately to "one turn" of these regular secondary structures. We have performed manual analysis explicitly on the family of protein kinases. We note shifts of one or two turns in helix-helix alignments obtained using pairwise and multiple structural alignments. Investigations on the quality of the equivalent helix-helix, strand-strand pairs in terms of their residue side-chain accessibilities have been made. Our results indicate that the quality of the pairwise alignments is comparable to that of the multiple structural alignments and, in fact, is often better. We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis.

Effect of fly ash inhalation on biochemical and histomorphological changes in rat lungs.

Effect of respirable fly ash particles inhalation on lungs of rats was investigated by exposing them to respirable aerosols of size classified power plant fly ash at average concentrations of up to 14.4 +/- 1.77 mg/m3 for 4 hr/day for 28 consecutive days. A remarkable increase was found in blood eosinophil counts of fly ash exposed animals. Biochemical indicators of pulmonary damage viz. lactate dehydrogenase (cytoplasmic enzyme used as a measure of cell injury), gamma-glutamyl transferase (Clara cell damage) and alkaline phosphatase (potential measure of Type 11 cell secretions) in broncho alveolar lavage fluid (BALF) of fly ash exposed group showed significant elevation. Clumping of fly ash particles in the lungs was observed as evidenced by fly ash ladened macrophage accumulation in the alveolar region. The results suggest a damage, local inflammation and remodelling of lung as indicated by hypertrophy and hyperplasia. These changes reflect the toxic effects of the fly ash inhalation.