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

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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.

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Acknowledgments

This work was funded by the Intramural Research Program of the NIDDK, NIH, and by the Intramural AIDS-Targeted Antiviral Program of the Office of the Director, NIH. CS-Rosetta calculations were carried out on the NIH CIT Biowulf cluster.

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Correspondence to Ad Bax.

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Shen, Y., Bax, A. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts. J Biomol NMR 46, 199–204 (2010). https://doi.org/10.1007/s10858-009-9395-y

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