Peptide bond, configuration

In this case, we point to the fact that a fast (r < 5 s) and a slow phase have been observed in temperature-jump experiments also with the peptide Col 1-3. The slow phase - as already mentioned - has been associated with the cis-trans isomerism of peptide bonds in the direct neighborhood of the helical part. Only peptide bonds to which proline or hydroxyproline contribute their secondary nitrogen are able to assume a cry-configuration at equilibrium (cis to trans ratios of 1 40 to 1 l)l45). Therefore, the fast... 

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

All X-Pro peptide bonds—where X represents any residue—are synthesized in the trans configuration. However, of the X-Pro bonds of mature proteins, approximately 6% are cis. The cis configuration is particularly common in P-turns. Isomerization from trans to cis is catalyzed by the enzyme proline-CM,tr(2 r-iso-merase (Figure 5-9). 

Figure 5-9. Isomerization of the N-a, prolyl peptide bond from a cis to a trans configuration relative to the backbone of the polypeptide.

Stereospecific enzymes catalyse reactions with one type of optical isomer but may also react with a series of related compounds of the same configuration. Many proteolytic enzymes hydrolyse only peptide bonds linking laevorotatory (L-) amino acids. 

Enzyme specificity is often explained in terms of the geometric configuration of the active site of the enzyme. The active site includes the side chains and peptide bonds that either come into direct contact with the substrate or perform some direct function during catalysis. Each site is polyfunctional in that certain parts of it may hold the substrate in a position where the other parts cause changes in the chemical bonding of... 

Fig. 17.11 Region from a 13C-edited NOESY spectrum of an HIV peptide 13C,15N- labeled at positions Glyl2, Prol3 and Gly 14. The characteristic NOEs for a cis configuration of the Gly-Pro peptide bond are indicated (left). Similarly, the ex-...

Fig. 3.6. Stereoelectronic control of the cleavage of the tetrahedral intermediate during hydrolysis of a peptide bond by a serine hydrolase. The thin lines represent the reactive groups of the enzyme (serine, imidazole ring of histidine) the thick lines represent the tetrahedral intermediate of the transition state. The full circles are O-atoms open circles are N-atoms. The dotted lines represent H-bonds the thick double arrow indicates an unfavorable dipole-dipole interaction [21]. A (R)-configured N-center B (S)-configured N-center.

Substitution of the l-amino acids with their D-amino acid configurational analogue, will enhance resistance to enzymatic cleavage of peptide bonds. The ll isomer of cyclo(Leu-Leu) hydrolyzes 3.5 times faster than the DL isomer in the presence of 0.5 moll HCl. This difference was explained by both steric shielding ui-trans isomer) and steric strain (ll- j isomer). ... 

Even though the atoms within a peptide bond are coplanar, they can exist in two possible configurations, cis and trans ... 

The nature of the covalent bonds in the polypeptide backbone places constraints on structure. The peptide bond has a partial doublebond character that keeps the entire six-atom peptide group in a rigid planar configuration. The N—C and Ca—C bonds can rotate to assume bond angles of (p and ip, respectively. 

---