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Estimating the accuracy of protein structures using residual dipolar couplings
Katya Simon1, Jun Xu, Chinpal Kim
1Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
Journal of Biomolecular NMR
|November 1, 2005
Summary
Residual dipolar coupling data can assess protein structure quality. Favorable R-factor values indicate high accuracy, but unfavorable values do not always mean low accuracy.
Area of Science:
- Biophysics
- Structural Biology
- Biochemistry
Background:
- Residual dipolar couplings (RDCs) are recognized as valuable indicators of protein structure quality.
- Quantifying the relationship between RDCs and structural accuracy is crucial for reliable structure determination.
Purpose of the Study:
- To systematically evaluate the correlation between RDC data and protein model accuracy.
- To develop a method for estimating protein structure accuracy using RDC analysis.
Main Methods:
- A database of 100 single-domain proteins with two independently solved structures was created.
- Backbone 1H-15N dipolar couplings were simulated for target structures and fitted to model structures.
- An R-factor, corrected for vector distribution, was used to characterize the fits.
Main Results:
- Favorable R-factor values strongly correlate with high protein model accuracy (backbone coordinate RMSD).
- Unfavorable R-factor values do not definitively indicate low structural accuracy.
- A simple empirical formula was proposed to estimate protein structure accuracy from simulated RDC data.
Conclusions:
- RDC analysis provides a reliable measure for assessing protein structure quality.
- The proposed empirical formula offers a practical approach to estimate structural accuracy.
- This method aids in validating and refining protein structural models, as demonstrated with the PDZ2 domain example.
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