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Journal of Biomolecular NMR

, Volume 24, Issue 2, pp 149–154 | Cite as

A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics

  • Mario Schubert
  • Dirk Labudde
  • Hartmut Oschkinat
  • Peter Schmieder
Article

Abstract

The chemical shift difference (δ[13Cβ] − δ[13Cγ]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.

13C chemical shifts cis peptide bond peptide bond conformation proline protein structure 

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Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Mario Schubert
    • 1
  • Dirk Labudde
    • 1
  • Hartmut Oschkinat
    • 1
    • 2
  • Peter Schmieder
    • 1
  1. 1.Forschungsinstitut für Molekulare PharmakologieBerlinGermany
  2. 2.Freie Universität BerlinBerlinGermany

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