Most peptides found in nature possess homochirality, that is, they contain almost exclusively L-amino acids. Nonetheless, D-amino acids have been discovered in peptides from various organisms. This study investigated the modes of post-translational D-amino acid incorporation in the ribosomal peptides, dermorphin and contryphan-R, through molecular modeling and molecular docking simulation techniques. The structures and interactions of the propeptides with appropriate isomerizing enzymes (racemases) were explored. Depending on the position and interaction with the bound prodermorphin, the dimeric alanine racemase adopted either a closed or an open conformation. On the other hand, regardless of the position of the procontryphan-R, a tryptophan-targeting racemase with broad substrate specificity assumed only the closed conformation. Analysis of the total energies from the different interaction types involved in the enzyme-substrate models revealed that the total energy present in the dimeric configuration of the racemase was reduced in the presence of the propeptide. A complex combination of these interactions occurred at specific racemase conformations, which suggest possible energy tradeoffs associated with the association of the racemase and the propeptide. These conformational changes may represent different mechanisms through which different racemases may act on specific substrates. Analysis of the structural bases for the D-amino acid incorporation provides insights into the rare occurrence of these non-proteinogenic amino acids in peptides. The post-translational L- to D-amino acid isomerization process may be further explored for the functional benefits that it offers, including its application for the development of novel peptide-based therapies.
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