Classification, of peptides

Fig. 2.3 Classification of peptide pool components exhibiting different types of activity...

One additional important concept to consider is that of peptide classification. If each sequence in peptide space is considered an individual species, then our clusters of green boxes are representative of a higher order of classification, the genus. With this concept in mind, Table 1 is an attempt to produce a generic classification of peptides. The number of individual species in each genus is, of course, variable and no doubt the future will see the evolution of new genera... 

Proteases are grossly subdivided into two major groups, such as exopeptidases and endopeptidases, depending on their site of action. Based on the functional group present at the active site, proteases are further classified into four prominent groups, such as serine, aspartic, cysteine, and metal-loproteases (Hartley, 1996). There are a few miscellaneous proteases that do not precisely fit into the standard classification and one of them is ATP-dependent proteases (Menon et al., 1987). The flow sheet for classification of peptide hydrolases is given in Figure 9.3. 

FIGURE 9.3 Flow sheet for classification of peptide hydrolases (International Union of... 

During the classification of peptides we have already designated proteins as high molecular weight substances. The actual size of protein molecules, however, was measured first with the ultracentrifuge developed by T. Svedberg (1925-1930). 

Fig. 2.33 Classification of y-peptides according to their substitution patterns (Seebach s nomenclature) and folding propensity...

Silica-based restricted access materials (RAM) have been developed for cleanup in bioanalysis, first for low molecular weight compounds in biofluids (Rbeida et al., 2005) and subsequently for biopolymers such as peptides (Wagner et al., 2002). A classification of different types of RAM has been given by Boos and Rudolphi (1997). Novel RAMs with strong cation-exchange functionality have been synthesized and implemented in the sample cleanup of biofluids. Racaityte et al. (2000) have shown that this type of RAM is highly suitable for the online extraction and analysis of... 

In one study by Hood et al., 282 of 1153 identified proteins were identified by at least 2 unique tryptic peptides from FFPE prostate cancer (PCa) tissue.9 According to the gene ontology classification of the proteins identified, -65% of proteins were predicted to be intracellular proteins, while -50% of the total human proteome is predicted to be located in the intracellular compartment. Additionally, 20% of the proteins identified in the PCa tissue were classified as membrane proteins, which is significantly less than the predicted 40% for the human proteome. This relative disparity is not unexpected, considering the Liquid Tissue sample preparation kit lacks specific protocols for membrane protein extraction. The Liquid Tissue method has also been used for proteomics studies of a variety of FFPE tissue samples, including pancreatic tumors,28 squamous cell carcinoma,4 and oral human papillomavirus lesions.27... 

Fig. 3. Classification of single-spanning membrane proteins based on topology, (a) The loop model for explaining the biogenesis of type I topology in the translocon. The stop-transfer signal stops the integration, (b) Type I protein and a cleaved signal peptide, (c) Type II (NcytCexo) is made by a type II signal-anchor, (d) Type III (Nexo-Ccyto often called type I) is made by a type I signal-anchor, (e) Type IV (C-tail) is made independently from the translocon.

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