Details

Autor(en) / Beteiligte

• Lakomek, Nils-Alexander
• Walter, Korvin F. A
• Farès, Christophe
• Lange, Oliver F
• de Groot, Bert L
• Grubmüller, Helmut
• Brüschweiler, Rafael
• Munk, Axel
• Becker, Stefan
• Meiler, Jens
• Griesinger, Christian

Titel

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.