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Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings

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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.

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  1. Department of Chemistry, Purdue University, West Lafayette, IN, 47907, U.S.A.

    Katya Simon, Jun Xu, Chinpal Kim & Nikolai R. Skrynnikov

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  1. Katya Simon
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  2. Jun Xu
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  3. Chinpal Kim
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  4. Nikolai R. Skrynnikov
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Correspondence to Nikolai R. Skrynnikov.

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Simon, K., Xu, J., Kim, C. et al. Estimating the Accuracy of Protein Structures using Residual Dipolar Couplings. J Biomol NMR 33, 83–93 (2005). https://doi.org/10.1007/s10858-005-2601-7

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