Properties of Prolyl Peptide Bonds

The peptide bond shows considerable double bond character, and the distance between the carbonyl carbon and the nitrogen is 0.15 A (15 pm) 

JTo facilitate reading I use the terms cis and trans proline for proline residues preceded by a cis or a trans peptide bond in the folded protein nativelike and incorrect, nonnative denote whether or not a particular prolyl peptide bond in an unfolded state shows the same conformation as in the native state. Further, I use the expression isomerization of Xaa for the isomerization of the peptide bond preceding Xaa. Peptide bonds preceding proline are referred to as prolyl bonds, and those preceding residues other than proline are termed as nonprolyl bonds. The folding reactions that involve Xaa—Pro isomerizations as rate-limiting steps are called proline-limited reactions. 

The peptide bonds that precede proline (prolyl bonds) (Fig. 1) are much more often found in the cis conformation because here the cis and trans conformations differ only slightly in energy. In short unstructured peptides cis contents of 10-30% are frequently observed (Cheng and Bovey, 1977 Grathwohl and Wuthrich, 1981 Reimer et al., 1998). The actual cis/trans ratio depends on the size and chemical nature of the flanking amino acids. 

In folded proteins the conformational state of a prolyl bond is usually well defined, because in most cases only one of the two conformations (cis or trans) can be accommodated in the folded structure. Of 1435 nonredundant protein structures in the Brookhaven protein database, 43% contain at least one cis peptidyl-prolyl bond (Reimer et al., 1998), and 7% of all prolyl peptide bonds in folded proteins are cis (Stewart et al., 1990 Macarthur and Thornton, 1991). 

Prolyl cis trans isomerizations are slow reactions with time constants between 10 and 100 s (at 25°C) because they involve the rotation around a partial double bond. The barrier to isomerization (80-100 kj/mol) is enthalpic in nature the activation entropy is almost zero. This suggests that the aqueous solvent is not reorganized in the activated state of isomerization. 

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