Peptide classification

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... 

Their value as building blocks to make proteins stems from the fact that amino acids can join together into long chains by Forming amide bonds between the -NH2 of one amino acid and the -C02H of another. For classification purposes, chains with fewer than 50 amino acids are often called peptides, while the term protein is used for larger chains. 

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

Woolfson and Mahmoud have classified the routes to preparation of decorated self-assembling peptide materials [53] as (1) co-assembly, where the functional part is already attached to a self-assembling component prior to assembly, and (2) postassembly, where a non-functionahsed self-assembled structure is modified by covalent or non-covalent means. This discussion adheres to this classification. A third route, beyond the scope of this review, is the use of structured peptides as templates for inorganic materials. Section 4.1 discusses functionalised self-assemblies formed from co-assembly-type approaches, while post-assembly modifications of self-assembled structures are considered in Sect. 4.2. 

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... 

The Osborne classification, which dates from 1907, was updated at a symposium on gluten in 1996. Gianibelli el al. point out that at least 1300 peptides can be obtained from wheat endosperm proteins after disulfide bond rupture using two-dimensional fractionation.6... 

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.

Note that this classification does not cover all the theoretical possibilities. For example, a cleavable signal peptide cannot direct the creation of a topology opposite to a type I (according to the loop model). Why other types are not observed must be explained from their insertion mechanisms. This classification can be naturally expanded into multi-spanning proteins (polytopic proteins) based on the location of their N terminus (therefore, type IV cannot be defined). 

Enzymes that act on peptide bonds (i.e., peptidases and proteases) hydrolyze peptide bonds in peptides and proteins. We examine first their classification before outlining their localizations and some physiological roles. 

The classification adopted by the Nomenclature Committee (NC) of the International Union of Biochemistry and Molecular Biology (IUBMB) divides peptidases into classes and subclasses according to the positional specificity in the cleavage of the peptide link of the substrate. The last publication of the complete printed version of the Enzyme Nomenclature was in 1992 [1][2], but a constantly updated version with supplements is available on the World Wide Web at http //www.chem.qmul.ac.uk/iubmb/enzyme/. Similarly, all available Protein Data Bank (PDB) entries classified as recommended by the NC-IUBMB can be found on the WWW at http //www.bio-chem.ucl.ac.uk/bsm/enzymes/. 

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

An alternative classification scheme was introduced in 2002 and this divides lantibiotics into two subgroups, class I and class II. This scheme primarily classifies lantibiotics according to their biosynthetic enzymes and sequence homology of their leader peptides. Similar to most biosynthetic pathways in bacteria, the genes for lantibiotic biosynthesis are clustered. They have been designated the generic locus symbol Ian, with a more... 

Amino acids are classified as acidic or basic according to their R groups because in proteins, these are the only groups that can dissociate. The a-amino and a-carboxyl groups are in peptide bonds and lose their acid-base character. This system of classification can be confusing since the words add and base are used in a way slightly different than discussed in the section above. 

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