Posttranslational modification profiling

1 Posttranslational modification profiling Specific biochemical methods are used to identify the abundance of targets with specific posttranslational modifications (such as phosphorylated proteins) (Zheng and Chan, 2002). Monitoring protein phosphorylations is particularly important in mapping the intracellular signaling network 

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The results for bacterial whole-cell analysis described here establish the utility of MALDI-FTMS for mass spectral analysis of whole-cell bacteria and (potentially) more complex single-celled organisms. The use of MALDI-measured accurate mass values combined with mass defect plots is rapid, accurate, and simpler in sample preparation then conventional liquid chromatographic methods for bacterial lipid analysis. Intact cell MALDI-FTMS bacterial lipid characterization complements the use of proteomics profiling by mass spectrometry because it relies on accurate mass measurements of chemical species that are not subject to posttranslational modification or proteolytic degradation. 

ExPASy Proteomics tools (http //expasy.org/tools/), tools and online programs for protein identification and characterization, similarity searches, pattern and profile searches, posttranslational modification prediction, topology prediction, primary structure analysis, or secondary and tertiary structure prediction. 

Figure 4.3. Fields of proteomic research. Proteomic research can be classified into six general research fields. Proteomic mapping and proteomic profiling constitute the first tier of proteomic analysis based upon identification and quantitation of proteins within a defined space of interest that can range from the entire organism to the protein level. The second tier of proteomic analyses is shown below involving global characterization of structure, function, posttranslational modifications, and association with other proteins (or other biochemical components).

The above example also gives an indication of the relative importance of carbohydrate analysis. Without question, protein glycosylation is the most complex of all posttranslational modifications made in eukaryotic cells, the importance of which cannot be underestimated. For many compounds, glycosylation can readily affect protein solubility (as influenced by folding), protease resistance, immunogenicity, and pharmacokinetic/pharmacodynamic profiles (i.e., clearance and efficacy) [36], Typical analytical methodologies used to assess carbohydrate content are also listed in Table 2. 

Recent comparison of gene expression profiles of von Hippel-lindau-i- versus von Hippel-lindau-ceU lines obtained from the clear cell RCC subtype identified proteins that might serve as candidate molecular markers. Inactivation of VHL is a hallmark in most sporadic clear cell RCC and it occurs early in renal carcinogenesis (Skates and Iliopoulus., 2004 Latifet al, 1993). Furthermore, the profile of secreted proteins could be directly AQ4 determined by analyzing comparatively the genomic and proteomic patterns of these cell lines as well as their conditioned tissue culture supernatants (Ferguson et al, 2004). A combination of cDNA microarray and proteome analyses appears reasonable since not every difference at the transcriptome level will translate into differences at the protein level, whereas posttranscriptional/posttranslational modifications were not detectable by tran-scriptomics. 

Manufacturing changes are more likely to affect the clinical profile of biological compounds than small chemical entities. Small changes in the three-dimensional folding, posttranslational modification or glycosylation of proteins can significantly... 

The overall decision criteria, however, is the pharmacological activity profile of the yielded protein in context with the posttranslational modification pattern followed by rentability. 

Given this perspective that proteomics is not so much a new field as the substantial expansion of an old one, it is germane to briefly consider where this synthesis of old and new technologies has brought us in terms of some of the more active areas of research before discussing some of the future prospects. Table 3 lists four such areas, which not surprisingly correlate quite closely to the definitions described in Table 1. There is necessarily some overlap between these. For example, both the determination of co-/posttranslational modifications and the identification of protein-protein interactions are also major components of expression profiling in addition to... 

Cathine is a known inhibitor of monoamine oxidase and a central stimulant as an indirect sympathomimetic. It is found in anorectic products. Cathine is reported to be a stimulant alkaloid in the natural reproduction ability of sperm and can be used clinically in reducing or enhancing natural fertil-ity 1,105 findings suggest that cathine reduces posttranslational modification of intracellular signal transducers in killer cells and monocytes and results in signaling profiles with B-lymphocytes and natural killer cells. Norephedrine has an identical or similar stimulation activity as cathine. 

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