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Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.

Lakomek NA, Walter KF, Farès C, Lange OF, de Groot BL, Grubmüller H, Brüschweiler R, Munk A, Becker S, Meiler J, Griesinger C - J. Biomol. NMR (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, Germany.

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-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 0.72 +/- 0.02 compared to = 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%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(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 (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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(a) and (b): The average difference  of RDC-based  order parameter between subsequent SCRM cycles for (a) D23M and (b) D36M is shown: . RDC-based order parameters  have converged after 4 cycles of SCRM with less than 0.01 difference  between subsequent SCRM cycles. (c) and (d): Residue-specific RDC-rmsd values  are shown for (c) D23M and (d) D36M after 4 SCRM cycles. For D23M, the average RDC-rmsd is  = 0.28 Hz and 0.52 Hz for D36M. (e) and (f): Dynamic Q-values  for the different alignment conditions are back-calculated, for D23M the average dynamic Q-value is  = 0.027 and for D36M  = 0.037
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Fig3: (a) and (b): The average difference of RDC-based order parameter between subsequent SCRM cycles for (a) D23M and (b) D36M is shown: . RDC-based order parameters have converged after 4 cycles of SCRM with less than 0.01 difference between subsequent SCRM cycles. (c) and (d): Residue-specific RDC-rmsd values are shown for (c) D23M and (d) D36M after 4 SCRM cycles. For D23M, the average RDC-rmsd is = 0.28 Hz and 0.52 Hz for D36M. (e) and (f): Dynamic Q-values for the different alignment conditions are back-calculated, for D23M the average dynamic Q-value is = 0.027 and for D36M = 0.037

Mentions: In parallel with the improvement of the static Q-values and correlation coefficients , the RDC-based order parameters also converged after 4 cycles of SCRM (Fig. 3a, b).Fig. 3


Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.

Lakomek NA, Walter KF, Farès C, Lange OF, de Groot BL, Grubmüller H, Brüschweiler R, Munk A, Becker S, Meiler J, Griesinger C - J. Biomol. NMR (2008)

(a) and (b): The average difference  of RDC-based  order parameter between subsequent SCRM cycles for (a) D23M and (b) D36M is shown: . RDC-based order parameters  have converged after 4 cycles of SCRM with less than 0.01 difference  between subsequent SCRM cycles. (c) and (d): Residue-specific RDC-rmsd values  are shown for (c) D23M and (d) D36M after 4 SCRM cycles. For D23M, the average RDC-rmsd is  = 0.28 Hz and 0.52 Hz for D36M. (e) and (f): Dynamic Q-values  for the different alignment conditions are back-calculated, for D23M the average dynamic Q-value is  = 0.027 and for D36M  = 0.037
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2480484&req=5

Fig3: (a) and (b): The average difference of RDC-based order parameter between subsequent SCRM cycles for (a) D23M and (b) D36M is shown: . RDC-based order parameters have converged after 4 cycles of SCRM with less than 0.01 difference between subsequent SCRM cycles. (c) and (d): Residue-specific RDC-rmsd values are shown for (c) D23M and (d) D36M after 4 SCRM cycles. For D23M, the average RDC-rmsd is = 0.28 Hz and 0.52 Hz for D36M. (e) and (f): Dynamic Q-values for the different alignment conditions are back-calculated, for D23M the average dynamic Q-value is = 0.027 and for D36M = 0.037
Mentions: In parallel with the improvement of the static Q-values and correlation coefficients , the RDC-based order parameters also converged after 4 cycles of SCRM (Fig. 3a, b).Fig. 3

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department for NMR-based Structural Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, Goettingen, Germany.

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-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 0.72 +/- 0.02 compared to = 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%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(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 (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.

Show MeSH
Related in: MedlinePlus