Abstract
We present here the computer program AUREMOL-RFAC-3D that is a generalization of the previously published program RFAC for the fully automated estimation of residual indices (R-factors) from 2D NOESY spectra. It is part of the larger AUREMOL software package (www.auremol.de). RFAC-3D calculates R-factors directly from two-dimensional homonuclear NOESY spectra as well as from three-dimensional 15N or 13C edited NOESY-HSQC spectra and thus extends the application range to larger proteins. The fully automated method includes automated peak picking and integration, a Bayesian noise and artifact recognition and the use of the complete relaxation matrix formalism. To enhance the reliability of the calculated R-factors the method is also generalized to calculate combined R-factors from a set of 2D and 3D-spectra. For an optimal combination of the information derived from different sources a plausible formalism had to be derived. In addition, we present a novel direct R-factors based measure that correlates an R-factors as defined in this paper to the root mean square deviation of the actual structure from the optimal structure. The new program has been successfully tested on the histidine containing phosphocarrier protein (HPr) from Staphylococcus carnosus and on the Ras-binding domain (RBD) of the Ral guanine-nucleotide dissociation stimulation factor (RalGDS).
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Abbreviations
- HPr:
-
histidine containing phosphocarrier protein
- RalGDS-RBD:
-
Ral guanine-nucleotide dissociation stimulation factor
- RBD:
-
Ras-binding domain
- HSQC:
-
heteronuclear single quantum coherence
- NOE:
-
nuclear Overhauser effect
- NOESY:
-
nuclear Overhauser effect spectroscopy
- rmsd:
-
root mean square deviation.
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Acknowledgements
We thank W. Hengstenberg, C. Hermann and A.␣Wittinghofer for providing HPr from S. carnosus and RalGDS-RBD, respectively. This work is supported by the Deutsche Forschungsgemeinschaft, the Fonds der Chemischen Industrie and the European Commission (SPINE-consortium).
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Gronwald, W., Brunner, K., Kirchhöfer, R. et al. AUREMOL-RFAC-3D, combination of R-factors and their use for automated quality assessment of protein solution structures. J Biomol NMR 37, 15–30 (2007). https://doi.org/10.1007/s10858-006-9096-8
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DOI: https://doi.org/10.1007/s10858-006-9096-8