Skip to main content


Log in

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

  • Communication
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript


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.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3


  • Andrews BT, Roy M, Jennings PA (2009) Chromophore packing leads to hysteresis in GFP. J Mol Biol 392:218–227

    Article  Google Scholar 

  • Baldwin RL (2008) The search for folding intermediates and the mechanism of protein folding. Annu Rev Biophys 37:1–21

    Article  MathSciNet  Google Scholar 

  • Cavalli A, Salvatella X, Dobson CM, Vendruscolo M (2007) Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 104:9615–9620

    Article  ADS  Google Scholar 

  • Cornilescu G, Delaglio F, Bax A (1999) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR 13:289–302

    Article  Google Scholar 

  • Day IJ, Maeda K, Paisley HJ, Mok KH, Hore PJ (2009) Refolding of ribonuclease a monitored by real-time photo-CIDNP NMR spectroscopy. J Biomol NMR 44:77–86

    Article  Google Scholar 

  • Dorman DE, Bovey FA (1973) C-13 magnetic resonance spectroscopy––spectrum of proline in oligopeptides. J Org Chem 38:2379–2383

    Article  Google Scholar 

  • Howarth OW, Lilley DMJ (1978) Carbon-13 NMR of peptides and proteins. Prog Nucl Magn Reson Spectrosc 12:1–40

    Article  Google Scholar 

  • Jahn TR, Parker MJ, Homans SW, Radford SE (2006) Amyloid formation under physiological conditions proceeds via a native-like folding intermediate. Nat Struct Mol Biol 13:195–201

    Article  Google Scholar 

  • Kohlhoff KJ, Robustelli P, Cavalli A, Salvatella X, Vendruscolo M (2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic distances. J Am Chem Soc 131:13894–13895

    Article  Google Scholar 

  • Kontaxis G, Delaglio F, Bax A (2005) Molecular fragment replacement approach to protein structure determination by chemical shift and dipolar homology database mining. Meth Enzymol 394:42–78

    Article  Google Scholar 

  • Lindfors HE, de Koning PE, Drijfhout JW, Venezia B, Ubbink M (2008) Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR. J Biomol NMR 41:157–167

    Article  Google Scholar 

  • London RE, Wingad BD, Mueller GA (2008) Dependence of amino acid side chain C-13 shifts on dihedral angle: Application to conformational analysis. J Am Chem Soc 130:11097–11105

    Article  Google Scholar 

  • Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions. J Biomol NMR 40:153–155

    Article  Google Scholar 

  • Neal S, Nip AM, Zhang HY, Wishart DS (2003) Rapid and accurate calculation of protein H-1, C-13 and N-15 chemical shifts. J Biomol NMR 26:215–240

    Article  Google Scholar 

  • Pahlke D, Freund C, Leitner D, Labudde D (2005) Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence. Bmc Struct Biol 5

  • Pascal C, Pate F, Cheynier V, Delsuc MA (2009) Study of the interactions between a proline-rich protein and a Flavan-3-ol by NMR: residual structures in the natively unfolded protein provides anchorage points for the ligands. Biopolymers 91:745–756

    Article  Google Scholar 

  • Robustelli P, Cavalli A, Vendruscolo M (2008) Determination of protein structures in the solid state from NMR chemical shifts. Structure 16:1764–1769

    Article  Google Scholar 

  • Schubert M, Labudde D, Oschkinat H, Schmieder P (2002) A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on C-13 chemical shift statistics. J Biomol NMR 24:149–154

    Article  Google Scholar 

  • Severin A, Joseph RE, Boyken S, Fulton DB, Andreotti AH (2009) Proline isomerization preorganizes the Itk SH2 domain for binding to the Itk SH3 domain. J Mol Biol 387:726–743

    Article  Google Scholar 

  • Shen Y, Bax A (2007) Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology. J Biomol NMR 38:289–302

    Article  Google Scholar 

  • Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu GH, Eletsky A, Wu YB, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A (2008) Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 105:4685–4690

    Article  ADS  Google Scholar 

  • Shen Y, Delaglio F, Cornilescu G, Bax A (2009a) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223

    Article  Google Scholar 

  • Shen Y, Vernon R, Baker D, Bax A (2009b) De novo protein structure generation from incomplete chemical shift assignments. J Biomol NMR 43:63–78

    Article  Google Scholar 

  • Siemion IZ, Wieland T, Pook KH (1975) Influence of distance of proline carbonyl from beta and gamma carbon on C-13 chemical shifts. Angew Chem-Int Edit Engl 14:702–703

    Article  Google Scholar 

  • Torchia DA, Sparks SW, Young PE, Bax A (1989) Proline assignments and identification of the Cis K116/P117 peptide-bond in liganded staphylococcal nuclease using isotope edited 2d NMR-spectroscopy. J Am Chem Soc 111:8315–8317

    Article  Google Scholar 

  • Wedemeyer WJ, Welker E, Scheraga HA (2002) Proline cis-trans isomerization and protein folding. Biochemistry 41:14637–14644

    Article  Google Scholar 

  • Weininger U, Jakob RP, Eckert B, Schweimer K, Schmid FX, Balbach J (2009) A remote prolyl isomerization controls domain assembly via a hydrogen bonding network. Proc Natl Acad Sci USA 106:12335–12340

    Article  ADS  Google Scholar 

  • Weiss MS, Jabs A, Hilgenfeld R (1998) Peptide bonds revisited. Nat Struct Biol 5:676

    Article  Google Scholar 

  • Wishart DS, Arndt D, Berjanskii M, Tang P, Zhou J, Lin G (2008) CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data. Nucleic Acids Res 36:496–502

    Article  Google Scholar 

  • Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York

    Google Scholar 

Download references


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.

Author information

Authors and Affiliations


Corresponding author

Correspondence to Ad Bax.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 196 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Shen, Y., Bax, A. Prediction of Xaa-Pro peptide bond conformation from sequence and chemical shifts. J Biomol NMR 46, 199–204 (2010).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: