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

J Biomol NMR. 2002 Oct;24(2):149-54. doi: 10.1023/a:1020997118364.

Abstract

The chemical shift difference (delta[13C(beta)]-delta[13C(gamma)]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1,033 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acids / chemistry*
  • Carbon Isotopes / chemistry*
  • Computational Biology* / methods
  • Hydrogen Bonding
  • Models, Molecular
  • Nuclear Magnetic Resonance, Biomolecular / methods
  • Peptides / chemistry*
  • Proline / chemistry*
  • Protein Conformation
  • Proteins / chemistry*
  • Software / statistics & numerical data*
  • Stereoisomerism
  • Thermodynamics

Substances

  • Amino Acids
  • Carbon Isotopes
  • Peptides
  • Proteins
  • Proline