Communication

Journal of Biomolecular NMR

, Volume 46, Issue 3, pp 199-204

Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts

  • Yang ShenAffiliated withLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health
  • , Ad BaxAffiliated withLaboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health Email author 

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Abstract

We present a program, named Promega, to predict the Xaa-Pro peptide bond conformation on the basis of backbone chemical shifts and the amino acid sequence. Using a chemical shift database of proteins of known structure together with the PDB-extracted amino acid preference of cis Xaa-Pro peptide bonds, a cis/trans probability score is calculated from the backbone and 13Cβ chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-13Cγ, Promega calculates the statistical probability that a Xaa-Pro peptide bond is cis. Besides its potential as a validation tool, Promega is particularly useful for studies of larger proteins where Pro-13Cγ assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and 13Cβ chemical shifts.

Keywords

Backbone chemical shifts CS-Rosetta NMR Omega angle Proline Structure prediction