Anatomy of a trans-cis peptide transition during least-squares refinement of rubrerythrin.
A detailed view is presented of the effects of one round of 20 cycles of restrained least-squares refinement of rubreythrin in which a trans peptide between Gly78 and Ile79 converts to a cis conformation automatically. While the omega angle for the peptide changes by nearly 180 degrees , the maximum shift in any atomic position is 1.32 Angstroms. The peptide converts by passing through a non-ideal structure containing a nearly linear C-N-C(alpha) bond angle. The overall motion is not possible for real or virtual molecular models with ideal bond lengths, angles and torsion angles. Strengthening the stereochemical bond length and bond angle restraints halts the structural change.
Stenkamp
Ronald E
RE
Department of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, 98195, USA. stenkamp@u.washington.edu
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D005288:Ferredoxins / Q000737:chemistry*; D005998:Glycine / Q000737:chemistry; D006422:Hemerythrin; D007532:Isoleucine / Q000737:chemistry; D016018:Least-Squares Analysis; D011487:Protein Conformation; D012416:Rubredoxins
D001426:Bacterial Proteins; D005288:Ferredoxins; D006422:Hemerythrin; D012416:Rubredoxins; C055857:rubrerythrins; D007532:Isoleucine; D005998:Glycine