Estimating the accuracy of protein structures using residual dipolar couplings

J Biomol NMR. 2005 Oct;33(2):83-93. doi: 10.1007/s10858-005-2601-7.

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 R values virtually guarantee high accuracy of the model structure (where accuracy is defined as the backbone coordinate rms deviation). On the other hand, unfavorable 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.

MeSH terms

  • Computer Simulation
  • Databases, Protein
  • Humans
  • Models, Molecular
  • Nitrogen Isotopes
  • Nuclear Magnetic Resonance, Biomolecular
  • Protein Conformation*
  • Protein Structure, Tertiary
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13
  • Protein Tyrosine Phosphatases / chemistry
  • Protons
  • Software

Substances

  • Nitrogen Isotopes
  • Protons
  • PTPN13 protein, human
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13
  • Protein Tyrosine Phosphatases