D-amino acid residues in peptides and proteins.
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 (-60 degrees, -45 degrees ) 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.
Mitchell
John B O
JB
Unilever Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK. jbom1@cam.ac.uk
Smith
James
J
D000596:Amino Acids / Q000737:chemistry* / Q000145:classification; D016477:Artifacts; D018360:Crystallography, X-Ray; D016572:Cyclosporine / Q000737:chemistry; D003609:Dactinomycin / Q000737:chemistry; D030562:Databases, Protein; D006096:Gramicidin / Q000737:chemistry; D008555:Melitten / Q000737:chemistry; D015394:Molecular Structure; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013237:Stereoisomerism
D000596:Amino Acids; D010455:Peptides; D011506:Proteins; D006096:Gramicidin; D003609:Dactinomycin; D008555:Melitten; D016572:Cyclosporine