D‐amino acid residues in peptides and proteins

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Abstract
We have investigated the D‐amino acid residues present in Protein Data Bank (PDB) entries, categorizing them into “real” D‐residues and artifacts. In polypeptide chains of more than 20 residues, only a single instance of a “real” D‐residue, other than those deliberately designed or engineered, was found. This example was the result of a slow chemical epimerization process. Another 12 designed D‐residues were found in these longer polypeptide chains. Smaller peptides of 20 or fewer residues contained 479 “real” D‐residues, the majority in various gramicidin, actinomycin, or cyclosporin structures. We found 148 PDB entries with “real” D‐residues and a further 186, in which all apparent D‐residues are artifacts. Investigating the (ϕ, ψ) preferences of the “real” D‐residues, we found that the region around (−60°, −45°) was almost completely unoccupied, even though it is not formally disallowed. We link the low propensity to occupy this region with the α‐helix destabilizing properties of D‐residues. Proteins 2003;50:563–571.