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Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics
Ist Teil von
Journal of biomolecular NMR, 2008-07, Vol.41 (3), p.139-155
Ort / Verlag
Dordrecht: Dordrecht : Springer Netherlands
Erscheinungsjahr
2008
Quelle
MEDLINE
Beschreibungen/Notizen
Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra- [graphic removed] ( [graphic removed] < supra- [graphic removed] < 50 μs). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters--independent of the details of the structure used for alignment tensor calculation--as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors [graphic removed] compared to [graphic removed] = 0.778 ± 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra- [graphic removed] window increases the averaged amplitude of mobility observed in the sub- [graphic removed] window by about 34%. For the β-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter [graphic removed] = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra- [graphic removed] time scale ( [graphic removed] = 0.59 ± 0.03), while it is inconspicuous ( [graphic removed] = 0.82) on the sub- [graphic removed] as well as on μs-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data.