In recent years, there has been a rapid and steady increase in the number of nucleic acid binding proteins (NABPs) and the list is continually increasing. However, a significant percentage of NABPs, the so-called hypothetical or predicted proteins has only been presumed based upon nucleic acid sequences and therefore remain to be shown to exist at the protein level. In general, neither the expression pattern analysis nor a protein hunting strategy to validate these proteins has been reported. In the present article, we summarize our studies on the application of a proteomics approach to document the identification and expression patterns of several of these proteins in a series of individual cell lines. The power of the two dimensional gel electrophoresis with subsequent in-gel digestion of protein spots followed by mass spectrometry based identification was used for the concomitant demonstration and verification of a series of NABPs in bronchial epithelial, amnion, mesothelial, lymphocyte, and kidney cell lines. Several heterogeneous nuclear ribonucleoproteins (e.g. A/B, R), Non-POU-containing octamer-binding protein, similar to paraspeckle protein, Alf-C1, similar to NS-1 associated protein 1, proteins with septin domains, GTP-binding proteins, components of the splicing, transcription and translation machinery as well as NABPs with still unknown function were unambiguously identified and these contribute to the many pathways and cascades of NABPs in a cell specific pattern.
Keywords: hypothetical proteins, 2 d-Gel electrophoresis, maldi, nucleic acid binding, proteins, proteome, human cell lines, protein hunting, protein map
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