| Abstrakt: |
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;50:563571. © 2003 Wiley-Liss, Inc. |
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