Principles of Protein Structure - H. Schultz 1982

The structural role of the peptide bond
Cis- and trans-configurations

One of the alternatives must be universal. Up to this point, we have assumed that all peptide bonds adopt a trans rather than a cis configuration (Fig. 2.1, b). Obviously, ribosomal Peptide Synthesis is stereospecific and must therefore yield exclusively either cis or trans bonds. In either case, one of the alternatives has to be universal; otherwise, the synthesis mechanism and Genetic Code would become unnecessarily complex, which is disadvantageous from an organizational standpoint. Post-translational isomerization is likewise unfavorable, as it would require a multitude of specialized Enzymes. Spontaneous isomerization during polypeptide chain folding is also out of the question, given that the energy barrier between the trans and cis configurations is roughly ~20 kcal/mol. This barrier is lower only for Pro residues, where geometric alterations of the pyrrolidine ring reduce it to 13 kcal/mol. During folding, Pro residues can undergo spontaneous isomerization (Sec. 8.2). The energy difference between the cis and trans isomers is about ~2 kcal/mol in favor of the trans isomer; this difference is smallest for Pro, because transitioning from the trans to the cis isomer merely replaces the contact between the C^a_i and C^a_i+1 atoms with an analogous contact between the C^a_i and C^δ_i+1 atoms (Fig. 1.1).

Several cis-Peptides have been identified in Globular Proteins. Cis bonds occur frequently in numerous cyclic peptides, particularly on the N-terminal side preceding Pro residues [37, 38]. Within globular protein structures, however, only a handful of cis bonds have been discovered—for instance, preceding Pro-93 and Pro-114 in Ribonuclease S [39], preceding Pro-168 in subtilisin [40], preceding Pro-116 in staphylococcal nuclease [E. Hazen, personal communication], preceding Pro-8 and Pro-95 in the variable chain of a Bence-Jones protein [42], and between Ser-197 and Tyr-198 in Carboxypeptidase A [43]. Molecules of synthetic poly-L-Pro I contain exclusively cis bonds. Thus, among all standard amino acid types, Pro has the highest propensity for forming cis bonds, which agrees well with energetic calculations. As a general rule, however, cis bonds are exceedingly rare.

If a strictly all-cis protein were to form, its conformational freedom would be overly restricted. Given the necessity for a single universal isomer, why was trans chosen over cis? A compelling argument in favor of the trans isomer is the severe restriction of the allowed conformational space in an all-cis polypeptide chain. For an isolated C_a atom, the steric hindrance does not differ between cis and trans isomers. Yet in a hypothetical all-cis polypeptide chain, repulsive interactions between neighboring side chains increase dramatically. This is illustrated in Fig. 2.6 for poly-L-cis-Ala. Under these conditions, the chain forms sharp bends, bringing adjacent C_a atoms into close proximity.

Ramachandran and Sasisekharan [29] attempted to map the allowed Conformations for such a chain. Applying a hard-sphere model with standard contact radii, they found only a very small allowed region at (—155°, +105°). Even when using a hard-sphere model with lower-limit radii, the allowed region remained extremely restricted, as seen in Fig. 2.3, b. In contrast to chains composed entirely of cis peptide groups, the trans configuration provides sufficient conformational flexibility to support The formation of numerous globular proteins. On the other hand, chains consisting solely of trans peptide groups possess moderate rigidity, meaning that spontaneous folding does not require substantial Energy Expenditure to pull disparate Regions of the protein together (Sec. 3.5). It is worth noting in this context that the 2 kcal/mol energetic preference of the trans isomer over the cis isomer is not necessarily critical, since a chain with cis peptide groups would be inherently stiffer and therefore might not require as large a binding energy to achieve a unique protein conformation as a chain with trans peptide groups.

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Fig. 2.6. Poly-L-cis-Alanine. The (—, ψ) angles are marked with an x in Fig. 2.3, b. The conformation is allowed assuming a hard-sphere model with lower-limit contact radii (Table 2.1).