Chemical models of peptide formation in translation

Ribosomal incorporations of N-alkyl amino acids including proline are slower than incorporations of non-N-alkyl l-amino acids. The chemical reactivity hypothesis proposes that these results and the exclusion of nonproline N-alkyl amino acids from the genetic code are explained by intrinsic chemical reactivities of the amino acid nucleophiles. However, there is little data on the reactivities relevant to physiological conditions. Here, we use nonenzymatic, aqueous-based, buffered reactions with formylmethionine-N-hydroxysuccinimide ester to model 11 amino acid nucleophiles in dipeptide formation. The relative rates in the nonenzymatic and translation systems correlate well, supporting the chemical reactivity hypothesis and arguing that peptide bond formation, not accommodation, is rate limiting for natural Pro-tRNA(Pro) isoacceptors. The effects of N-substitution sterics, side chain sterics, induction, and pK(a) were evaluated in the chemical model. The dominant factor affecting relative rates was found to be N-substitution sterics.