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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., de Groot, B. L., Grubmüller, H., et al. (2008). Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics. Journal of Biomolecular NMR, 41(3), 139-155. doi:10.1007/s10858-008-9244-4.

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 Creators:
Lakomek, Nils-Alexander1, Author
Walter, Korvin F. A.1, Author
Farès, Christophe1, Author           
Lange, Oliver F.2, Author
de Groot, Bert L.2, Author
Grubmüller, Helmut2, Author
Brüschweiler, Rafael3, Author
Munk, Axel4, Author
Becker, Stefan1, Author
Meiler, Jens5, Author
Griesinger, Christian1, Author
Affiliations:
1Department of NMR Based Structural Biology, MPI for Biophysical Chemistry, Max Planck Society, ou_578567              
2Department for Theoretical and Computational Biophysics, Max-Planck Institute for Biophysical Chemistry, Goettingen, Germany, ou_persistent22              
3NHFML, Florida State University, Tallahassee, FL, USA, ou_persistent22              
4Institut for Mathematical Stochastics, University of Goettingen, Goettingen, Germany, ou_persistent22              
5Department of Chemistry, Center of Structural Biology, Vanderbilt University, Nashville, TN, USA, ou_persistent22              

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Free keywords: Dynamics; Proteins; RDCs; Structural noise; Ubiquitin
 Abstract: 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-τcc < supra-τc < 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 ⟨S2rdc⟩=0.72±0.02 compared to ⟨S2LS⟩ = 0.778 ± 0.003 for the Lipari–Szabo order parameters, indicating that the inclusion of the supra-τc window increases the averaged amplitude of mobility observed in the sub-τc window by about 34%. For the β-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2rdc(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-τc time scale (S2rdc(NH) = 0.59 ± 0.03), while it is inconspicuous (S2LS(NH) = 0.82) on the sub-τc 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.

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Language(s): eng - English
 Dates: 2008-03-032008-04-222008-06-042008-06-04
 Publication Status: Published in print
 Pages: 17
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1007/s10858-008-9244-4
 Degree: -

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Title: Journal of Biomolecular NMR
  Abbreviation : J. Biomol. NMR
Source Genre: Journal
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Publ. Info: Dordrecht, The Netherlands : Springer Science+Business Media
Pages: - Volume / Issue: 41 (3) Sequence Number: - Start / End Page: 139 - 155 Identifier: ISSN: 0925-2738
CoNE: https://pure.mpg.de/cone/journals/resource/954925566734