Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.
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For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors <S2(rdc)>0.72 +/- 0.02 compared to <S2(LS)> = 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-supra-tau(c) window by about 34%.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 (S2(rdc)(NH) = 0.59 +/- 0.03), while it is inconspicuous (S2(LS)(NH)= 0.82) on the sub-tau(c) as well as on micros-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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Affiliation: Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, Germany.
ABSTRACT
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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-tau(c) (tau(c) < supra-tau(c) < 50 micros). 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 |
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Mentions: As described in the Material and methods section, the SCRM method was designed to iteratively improve the accuracy of the alignment tensor determination and to adjust the average inter-nuclear vector orientations, and as a result, to further reduce the static Q-values and increase the Pearson correlation coefficient . Indeed, after already 4 SCRM-cycles, the static Q-values decreased to less than half of the original value with = 0.062 for both D23M and D36M (Fig. 2a, b). Simultaneously, the correlation coefficients increased to = 0.997 on average (Fig. 2c, d). Convergence was attained in already 4 cycles of SCRM after which the inter-nuclear vector orientations were found to deviated by less than 0.5 between consecutive SCRM cycles (Figure S2a and S2b in the Supporting Information). Thus the iterative procedure rapidly improves the fit of the static structure to the RDCs as compared to the input X-ray structure.Fig. 2 |
View Article: PubMed Central - PubMed
Affiliation: Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, Germany.