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The war of tools: how can NMR spectroscopists detect errors in their structures?

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Abstract

Protein structure determination by NMR methods has started in the mid-eighties and has been growing steadily since then. Ca. 14% of the protein structures deposited in the PDB have been solved by NMR. The evaluation of the quality of NMR structures however is still lacking a well-established practice. In this work, we examined various tools for the assessment of structural quality to ascertain the extent to which these tools could be applied to detect flaws in NMR structures. In particular, we investigated the variation in the scores assigned by these programs as a function of the deviation of the structures induced by errors in assignments or in the upper distance limits used. These perturbations did not distort radically the protein fold, but resulted in backbone RMS deviations up to 3 Å, which is in line with errors highlighted in the available literature. We found that it is quite difficult to discriminate the structures perturbed because of misassignments from the original ones, also because the spread in score over the conformers of the original bundle is relatively large. ϕ–ψ distributions and normality scores related to the backbone conformation and to the distribution of side-chain dihedral angles are the most sensitive indicators of flaws.

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Abbreviations

NMR:

Nuclear magnetic resonance

NOE:

Nuclear Overhauser effect

RMSD:

Root mean standard deviation

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Acknowledgements

This work was stimulated by the activities of the Coordination Action “NMR-Life” (funded by the European Commission, project no. 18758). We thank Prof. Ivano Bertini for many useful discussions. We thank the Ente Cassa di Risparmio di Firenze, the EC (project no. 213010), and MIUR (project PRIN 2005) for financial support. E.S. is the recipient of a fellowship from the FiorGen Foundation.

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Authors and Affiliations

  1. Magnetic Resonance Center, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy

    Edoardo Saccenti & Antonio Rosato

  2. FiorGen Foundation, Via Sacconi 6, 50019, Sesto Fiorentino, Italy

    Edoardo Saccenti

  3. Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy

    Antonio Rosato

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  1. Edoardo Saccenti
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Correspondence to Antonio Rosato.

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Saccenti, E., Rosato, A. The war of tools: how can NMR spectroscopists detect errors in their structures?. J Biomol NMR 40, 251–261 (2008). https://doi.org/10.1007/s10858-008-9228-4

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