D-amino acid residues in peptides and proteins

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48 Citations (Scopus)

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 (phi, psi) preferences of the "real" D-residues, we found that the region around (-60degrees, -45degrees) was almost completely unoccupied, even though it is not formally disallowed. We link the low propensity to occupy this region with the alpha-helix destabilizing properties of D-residues. (C) 2003 Wiley-Liss, Inc.

Original languageEnglish
Pages (from-to)563-571
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume50
Issue number4
DOIs
Publication statusPublished - 1 Mar 2003

Keywords

  • protein data bank
  • epimers
  • chirality
  • stereoisomerism
  • D-configurations
  • secondary structure
  • ANGSTROM RESOLUTION
  • CITRATE SYNTHASE
  • ALPHA-HELIX
  • D-MONELLIN
  • COMPLEX
  • DESIGN
  • INHIBITOR
  • CONFORMATIONS
  • ISOMERIZATION
  • POLYPEPTIDE

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