Trans peptide

High temperature searches of conformational space (see Quenched Dynamics on page 78), can produce unwanted conformational changes, such as cis-trans peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Wilkes BC, Nguyen TM-D, Weltrowska G, Carpenter KA, Lemieux C, Chung NN, Schiller PW. The receptor-bound conformation of H-Tyr-Tic-(Phe-Phe)-OH related -opioid antagonists contains all trans peptide bonds. J Peptide Res 1998 51 386-394. 

The random coil amide I VCD pattern is exacdy the same shape, but smaller in amplitude and shifted in frequency from the pattern characteristic of poly-L-proline II (PLP II) which is a left-handed 3ihelix of trans peptides (Kobrinskaya et al., 1988 Dukor and Keiderling, 1991 Dukor et al., 1991 Dukor and Keiderling, 1996 Keiderling et al., 1999b). This... 

Fig. 1. Conformational energy diagram for the alanine dipeptide (adapted from Ramachandran et al., 1963). Energy contours are drawn at intervals of 1 kcal mol-1. The potential energy minima for p, ofR, and aL are labeled. The dependence of the sequential d (i, i + 1) distance (in A) on the 0 and 0 dihedral angles (Billeter etal., 1982) is shown as a set of contours labeled according to interproton distance at the right of the figure. The da (i, i + 1) distance depends only on 0 for trans peptide bonds (Wright et al., 1988) and is represented as a series of contours parallel to the 0 axis. Reproduced from Dyson and Wright (1991). Ann. Rev. Biophys. Chem. 20, 519-538, with permission from Annual Reviews.

IR spectroscopy permits reliable discrimination between cis and trans-secondary amide bonds and the presence of 1550 cm bands is indicative of trans-peptide bonds (Table 2). 

Vitagliano, L., Berisio, R., Mastrangelo, A., Mazzarella, L., Zagari, A. Preferred proline puckerings in cis and trans peptide groups implications for collagen stability. Protein Sci. 2001, 10, 2627-32. 

Poly(Pro) can assume two very different conformations poly(Pro)I, a right-handed helix of all cw-peptidestl43] and poly(Pro)II, a left-handed helix of all trans-peptides.[144] Poly(Pro)I is found only in the solid state and in solution in solvents of low polarity, e.g. higher alcohols. Poly(Pro)II is the conformation found in water, TFE, and other polar solvents, and the focus will be on it in this section. The CD spectra of both forms are shown in Figure 8. The poly(Pro)II CD spectrum is characterized by a weak positive nm maximum at 226 nm and a... 

While the trans peptide linkage shown in Fig. 2-4 is usual, the following cis peptide linkage, which is 8 kj/mol less stable than the trans linkage, also occurs in proteins quite often. The nitrogen atom is usually but not always from proline.81 84... 

Figure 1 (Left) Model of the receptor-bound conformation of TIP containing all-trans peptide bonds (heavy lines) in spatial overlap with naltrindole (light lines). (Right) Model of the receptor bound conformation of H-Tyr-Tic-NH2 containing a cis peptide bond (heavy lines) in spatial overlap with naltrindole (light lines). In both cases the N-terminal amino group and the Tyr1 and Tic2 aromatic rings of the peptide are superimposed on the corresponding pharmacophoric moieties in the alkaloid structure.

This planar, trans peptide unit poses serious limitations example, are proteins with catalytic properties. Their on the shapes proteins can adopt. Understanding the catalytic function depends on the shape adopted alter the... 

In addition to the order-disorder transition, observed for a helices, helical structures can also be induced to undergo transitions from one ordered form to another. For example, a crystalline form of poly[p-(p-chlorobenzyl)-L-aspartate] can be made to undergo a phase transition from an a-helical to an co-helical form by heating rotational entropy is computed to play a role in this process.68 Another order-order transition is the solvent-induced interconversion between polyproline 1 (with cis peptide bonds) and polyproline 11 (with trans peptide bonds), a process that has also been subjected to conformational energy calculations.85 The transition has been accounted for in terms of differences in the binding of solvent components to the peptide 0=0 groups. 

Cis as well as trans peptide bonds occur in cyclic peptides containii imino add residues... 

Fig. 5. Gs and trans peptide bonds as shown with N-acetyFN-methylalanine dimethylamide...

Cydo-(Pro-Sai>-Gly)2 CDQ3 CD3OD DMSO 1 C2-symmetric conformation two -tums with two Gly-NH intra H-bond all trans peptide bonds 92% in CDQs, 88% in CD3OD, 76% in DMSO 1 asymmetric conformation one CIS and one trots Pro-Sai peptide bonds one intra and one inter Qy-NH H-boid... 

Figure 22-4. The geometry of the peptide backbone, with the trans peptide bond, showing all the atoms between two C atoms of adjacent residues. (Reprinted from reference 31, with permission.)...

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