Native peptide

The amino acids proline and hydroxyproline exert a stabilizing influence on the triple helix as described in detail in Sect. 4.5. By examining the CB peptides of collagen, a structural stability which is directly proportional to the itnino acid content may thus be found. It has, however, not been possible to synthesize model peptides displaying structural stability comparable to that of the native peptides having corresponding amino acid contents. 

Figure 17.24 The traceless Staudinger reaction can be used to form larger peptides from smaller peptides, if one contains an azido group at the N-terminal and the other one contains a phosphine ester at its C-terminal. The reaction gives a native peptide (amide) bond with loss of the phosphine group.

Fig. 9. Peptidomimetic design principle of SH2 antagonists derived from a fragmentation of the native peptide ligand. The lead finding efforts discussed in Sect. 3 are classified according to the modules given above the peptide lead sequence...

Shogren-Knaak, M.A., Fry, C.J. and Peterson, C.L. (2003) A native peptide ligation strategy for deciphering nudeosomal histone modifications. The Journal of Biological Chemistry, 278, 15744-15748. 

In view of the large diversity of structures listed in Tables 1 and 2, only the synthetic methods developed for the most common and biologically most important peptide derivatives will be discussed in the following sections. Additional attention will be paid to the often-ingenious design of artificial modifications capable of mimicking the native peptide transformations in an efficient and biologically competent manner. 

As exemplarily shown in the case of charybdotoxin, a 37-residue peptide with three intramolecular disulfide bonds,[70] operating in redox buffer was crucial for efficient formation of the correct disulfide bonds.[71] When the reduced peptide was oxidized in 0.1 M NHtOAc buffer (pH 8.0) at 0.11 mM concentration in the presence of redox reagents (peptide/GSH/GSSG ratio of 1 60 6), the main product was the native peptide contaminated... 

Fifth run Inject 2-4 tg of the native peptide dissolved in 0.5 mL of collected eluent from run 1, diluted with water (1 1) to 1 mL total volume, and run the same gradient as above. Collect the eluent containing the desired peptide (ca. 250 pL). 

In this manner, all injections are of the same volume and of the same composition (within a factor of 2) the same amount of peptide are injected in runs 3 and 5 and absorbances of synthetic and native peptides should be about the same. Coelution run 6 will contain twice as much material as runs 3 and 5 and absorbance should be twice as intense as that seen in these runs. Such an experiment is illustrated in Figure 2. 

Examples of native peptide hormones, neurotransmitters, and releasing factors... 

However, it was immediately recognized by peptide chemists that, even in the cases where a direct (backbone)peptide -protein(backbone) interaction is not operative, the backbone conformation may dramatically influence the biological response. It is evident that the introduction of new, promising peptidomimetics is based primarily on the combined knowledge of the complementary conformational, topochemical, and electronic properties of the native peptide and of its address (in other words, of the receptor or the active site of the enzyme with which it interacts). Then, the design of peptidomimetics as potential bioactive compounds must take into particular account two structural factors (i) a favorable fit (tertiary structure) with respect to the corresponding complementary spatial situation at the active site (ii) the placement of structural elements (e.g., functional groups, polar and... 

Recently, much attention has been directed toward the synthesis of peptidomimetics. These compounds can replace native peptides in the interaction with receptors. They showed increased metabolic stability, better bioavailability, and longer duration of action than native peptides, thus displaying favorable pharmacological properties [52-54]. In this sense, the design and synthesis of conformationally restricted peptidomimetics is an important approach toward improving the potency, selectivity, and metabolic stability of peptide based chugs. 

In contrast, ProteinChip technology allows the detailed analysis of A(3 fragments and their modifications (22). Peptides are captured on arrays coated with anti-Ap Ab, washed to remove nonspecifically bound fragments, and finally detected by SELDI-TOF MS. The resolution of the technique allows the discrimination of peptides of similar mass and modified products, e.g., oxidized peptides versus native peptides, which differ by only 16 Da. ProteinChip technology has been used extensively to detect Af> fragments in various samples, including cell culture supernatants, serum, plasma, and cerebrospinal fluid (CSF) (21-23). 

Figure 5. FAB-MS chynotryptic peptide nap of glycosylated lysozyae. Glycosylated peptides containing one (+G) or two (+2G) Amadori adducts are found at 162 or 324 nass unit increnents above the corresponding native peptide.

Fig. 3. Two-dimensional analysis of PDZ proteins interacting with the 5-HT2A and the 5-HT2C receptors C-termini. (A) Proteins from mice brain that bind to the C-terminus of the last 14 residues of the receptors were separated on 2D gels and stained with silver. Proteins that interact specifically (directly or indirectly) with the PDZ ligand of the receptor (arrows) were detected comparing protein patterns obtained with the native peptides (see Fig. 1) and mutant peptides in which the last residue was replaced by alanine. The position of one protein retained in a PDZ-independent manner by the 5-HT2A receptor C-terminus is also indicated (arrowhead). (B) Molecular determinants in the C-terminus of 5-HT2A receptor involved in its preferential interaction with CIPP.

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