Journal of Biomolecular NMR

, Volume 33, Issue 2, pp 83–93

Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings

  • Katya Simon
  • Jun Xu
  • Chinpal Kim
  • Nikolai R. Skrynnikov
Article
  • 72 Downloads

Abstract

It has been commonly recognized that residual dipolar coupling data provide a measure of quality for protein structures. To quantify this observation, a database of 100 single-domain proteins has been compiled where each protein was represented by two independently solved structures. Backbone 1H–15N dipolar couplings were simulated for the target structures and then fitted to the model structures. The fits were characterized by an R-factor which was corrected for the effects of non-uniform distribution of dipolar vectors on a unit sphere. The analyses show that favorable values \(\tilde{R}\) virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable \(\tilde{R}\) values do not necessarily suggest low accuracy. Based on the simulated data, a simple empirical formula is proposed to estimate the accuracy of protein structures. The method is illustrated with a number of examples, including PDZ2 domain of human phosphatase hPTP1E.

Keywords

NMR PALES software PDZ2 domain from human phosphatase hPTP1E precision and accuracy of protein structures residual dipolar couplings X-ray crystallography 

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Copyright information

© Springer 2005

Authors and Affiliations

  • Katya Simon
    • 1
  • Jun Xu
    • 1
  • Chinpal Kim
    • 1
  • Nikolai R. Skrynnikov
    • 1
  1. 1.Department of ChemistryPurdue UniversityWest LafayetteU.S.A.

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