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

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 C-13(beta) chemical shifts of the proline and its neighboring residues. For an arbitrary number of input chemical shifts, which may include Pro-C-13(gamma), 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-C-13(gamma) assignments can be challenging, and for on-going efforts to determine protein structures exclusively on the basis of backbone and C-13(beta) chemical shifts.