Peptides backbone

It is important to notice that the united-atom simplification cannot be applied to functional hydrogens which are involved in the formation of a hydrogen hond or a salt bridge. This would destroy interactions important for the structural integrity of the protein. Removing the hydrogen at the u-carbon of the peptide backbone is also dangerous, because it prevents racemization of the amino acid. 

Fig. 3. (a) Chemical stmcture of a synthetic cycHc peptide composed of an alternating sequence of D- and L-amino acids. The side chains of the amino acids have been chosen such that the peripheral functional groups of the dat rings are hydrophobic and allow insertion into Hpid bilayers, (b) Proposed stmcture of a self-assembled transmembrane pore comprised of hydrogen bonded cycHc peptides. The channel is stabilized by hydrogen bonds between the peptide backbones of the individual molecules. These synthetic pores have been demonstrated to form ion channels in Hpid bilayers (71). 

Figure 3.13 shows the thermal stability of immobilized ODN and PNA. The signal for the Thy- and Cyt-bases obtained with temperature-programmed (TP) SIMS starts to decrease at approximately 150 °C for ODN and 200 °C for PNA. This variance is caused by the different strengths of binding between the bases and the sugar-phosphate and peptide backbones, respectively. 

Peptide bond resonance has several important consequences. First, it restricts free rotation around the peptide bond and leaves the peptide backbone with only two degrees of freedom per amino acid group rotation around... 

FIGURE 5.4 The coplanar relationship of the atoms in the amide group is highlighted as an imaginary shaded plane lying between two successive u-carbon atoms in the peptide backbone. 

Why should the cores of most globular and membrane proteins consist almost entirely of a-helices and /3-sheets The reason is that the highly polar N—H and C=0 moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein. The extensively H-bonded nature of a-helices and /3-sheets is ideal for this purpose, and these structures effectively stabilize the polar groups of the peptide backbone in the protein core. 

This group is used for peptide backbone protection. The acetoxy group makes it stable to TFA that is used to cleave the BOC group during peptide synthesis. 

R I he secondary structure of a protein describes how segments of the peptide backbone orient into a regular pattern. 

Rituximab is a recombinant mouse/human chimeric monoclonal antibody whose in vitro activity varies with the number of terminal galactose moieties glycosylated to the peptide backbone at residue asparagine 301 [8]. The ability to monitor the levels of each discrete species present would allow the manufacturing process to... 

Table 5.4 Enzymes used for the cleavage of proteins for sequence investigations and the corresponding amino acid residues at which they break the peptide backbone...

The methodology employed for the study of glycoproteins is somewhat different in that it is not just the saccharide sequence that is required but the position at which it is joined to the peptide backbone. 

Alternatively, rigidification of the y-peptide backbone to avoid H-bonds between nearest neighbors can be achieved by the introduction of an a,y9-unsaturation into the backbone of each y-amino acid constituent (vinylogous peptides) ]208, 209]. Recent ab-initio calculations suggested that the a,/9-unsaturated y-peptide backbone might support the formation of helices with large 19- and 22-membered H-bonded pseudocycles ]221]. 

Optimal pre-organization of the y-peptide backbone towards the formation of open-chain turn-like motifs is promoted by unlike-y " -amino acid residues. This design principle can be rationalized by examination of the two conformers free of syn-pentane interaction (f and II", Fig. 2.34). Tetrapeptide 150 built from homo-chiral unlike-y -amino acid building blocks 128e has been shown by NMR experiments in pyridine to adopt a reverse turn-like structure stabilized by a 14-mem-bered H-bond pseudocycle [202] (Fig. 2.37 A). 

Enantiopure N,N -hnked oligoureas were originally described in 1995 by Burgess and coworkers as novel peptide backbone mimetics [271, 272]. Several synthetic approaches have been reported, all of which involve sequential acylation and amine deprotection cycles using appropriately protected carbonyl synthons [83, 271, 272, 274, 286-288]. Although elongation can be performed in solution, most of the synthetic procedures are elaborated on solid supports starting from Rink s... 

The development of the aminoethylglycine polyamide (peptide) backbone oligomer with pendant nucleobases linked to the glycine nitrogen via an acetyl bridge now often referred to by PNA (peptide nucleic acid Fig. 4.1), was inspired... 

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