Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics
2008 | journal article; research paper. A publication with affiliation to the University of Göttingen.
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Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics
Lakomek, N.-A. ; Walter, K. F. A.; Farès, C.; Lange, O. F.; Groot, B. L. de ; Grubmüller, H. & Brueschweiler, R. et al. (2008)
Journal of Biomolecular NMR, 41(3) pp. 139-155. DOI: https://doi.org/10.1007/s10858-008-9244-4
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- Authors
- Lakomek, Nils-Alexander ; Walter, Korvin F. A.; Farès, Christophe; Lange, Oliver F.; Groot, Bert L. de ; Grubmüller, Helmut ; Brueschweiler, Rafael; Munk, Axel ; Becker, Stefan ; Meiler, Jens; Griesinger, Christian
- Abstract
- Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of internuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 mu s). 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 < S-rdc(2)> = 0: 72 +/- 0: 02 compared to < S-LS(2)> = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S-rdc(2) (NH) = (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-tau(c) time scale (S-rdc(2) (NH) = 0.59 +/- 0.03), while it is inconspicuous (S-LS(2) (NH) = 0.82) on the sub-tau(c) as well as on mu s-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.
- Issue Date
- 2008
- Journal
- Journal of Biomolecular NMR
- ISSN
- 0925-2738
- Language
- English