Krzysztof Pawłowski

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RATIONALE The molecular mechanisms involved in airway oxidative stress responses reported in healthy smokers and in those with chronic obstructive pulmonary disease (COPD) are poorly understood. OBJECTIVES To assess the expression of genes involved in oxidative stress responses in the bronchial epithelium of smokers with or without COPD and in relation to(More)
Advanced protein structure prediction methods combined with structure modeling show that the mammalian proteins, described until now as calcium-activated chloride channels (CLCAs), appear in fact to be membrane anchored metal-dependent hydrolases, possibly proteases. A metallohydrolase structural domain was predicted, unexpectedly, in the CLCA sequences.(More)
Many 'omics' studies, gene expression microarray experiments in particular, aim at charting the molecular mechanisms of physiology, disease and drug response. This short review discusses the bias present in many such studies whereas the focus is set on the well understood and established molecular scenarios. The under-reporting rate of 'hypothetical' or(More)
Protein function assignments based on postulated homology as recognized by high sequence similarity are used routinely in genome analysis. Improvements in sensitivity of sequence comparison algorithms got to the point, that proteins with previously undetectable sequence similarity, such as for instance 10-15% of identical residues, sometimes can be(More)
Sequence alignments for distantly homologous proteins are often ambiguous, which creates a weak link in structure prediction by homology. We address this problem by using several plausible alignments in a modeling procedure, obtaining many models of the target. All are subsequently evaluated by a threading algorithm. It is shown that this approach can(More)
Peroxide turnover and signalling are involved in many biological phenomena relevant to human diseases. Yet, all the players and mechanisms involved in peroxide perception are not known. Elucidating very remote evolutionary relationships between proteins is an approach that allows the discovery of novel protein functions. Here, we start with three human(More)
A database of functional sites for proteins with known structures, SITE, is constructed and used in conjunction with a simple pattern matching program SiteMatch to evaluate possible function conservation in a recently constructed database of fold predictions for Escherichia coli proteins (Rychlewski L et al., 1999, Protein Sci 8:614-624). In this and other(More)
The small, obscure group of selenoprotein oxidoreductases and the huge clan of kinases, the workhorses of cellular signalling, are rarely discussed together. Focusing on selenoproteins of unknown structures, we predict a thioredoxin-like fold for the Selenoprotein N (SelN) family and use the structure to rationalise effects of the muscular myopathy-linked(More)