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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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RDC-based  order parameters (red and blue) scaled according to the method described in the supplement are compared to the Lipari–Szabo  (black) for (a) D23M and (b) D36M. Both error bars for  = 0.3 Hz and  are indicated as horizontal lines. While for some residues  and  have almost equal values, for others, mainly in loop regions but also in secondary structure elements,  values are significantly lower. The average RDC-based order parameter is  = 0.72  0.02 for D23M and = 0.72 0.02 for D36M compared to  = 0.778 ± 0.003 for the Lipari–Szabo order parameter. (c) RDC-based order parameters  derived from D23M (red) and D36M (blue) are compared. Both data sets D36M and D23M give  that are identical within the error, with a very few exceptions for Gly35, Lys63 and Leu71. The correlation coefficient is  = 0.945. (d) and (e): comparison of (d)  and (e)  order parameter distributions, The 25th percentile of the  distribution is P25 = 0.68, the 75th percentile is P75 = 0.80 for D23M, giving and interquantile range (P25 to P75) of IQR = 0.12. (Identical values are obtained for D36M.) In contrast, the distribution of Lipari–Szabo order parameters  is 2.4 times narrower with P25 = 0.78, P75 = 0.83 and an interquantile range of IQR = 0.05. For the RDC-based order parameter  the IQR is more than double than that for the Lipari–Szabo  showing that the RDC-based order parameters detect a much wider range of mobility
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Fig4: RDC-based order parameters (red and blue) scaled according to the method described in the supplement are compared to the Lipari–Szabo (black) for (a) D23M and (b) D36M. Both error bars for = 0.3 Hz and are indicated as horizontal lines. While for some residues and have almost equal values, for others, mainly in loop regions but also in secondary structure elements, values are significantly lower. The average RDC-based order parameter is  = 0.72  0.02 for D23M and = 0.72 0.02 for D36M compared to = 0.778 ± 0.003 for the Lipari–Szabo order parameter. (c) RDC-based order parameters derived from D23M (red) and D36M (blue) are compared. Both data sets D36M and D23M give that are identical within the error, with a very few exceptions for Gly35, Lys63 and Leu71. The correlation coefficient is = 0.945. (d) and (e): comparison of (d) and (e) order parameter distributions, The 25th percentile of the distribution is P25 = 0.68, the 75th percentile is P75 = 0.80 for D23M, giving and interquantile range (P25 to P75) of IQR = 0.12. (Identical values are obtained for D36M.) In contrast, the distribution of Lipari–Szabo order parameters is 2.4 times narrower with P25 = 0.78, P75 = 0.83 and an interquantile range of IQR = 0.05. For the RDC-based order parameter the IQR is more than double than that for the Lipari–Szabo showing that the RDC-based order parameters detect a much wider range of mobility

Mentions: For both D23M and D36M the resulting RDC-based order parameters are identical within the error, with very few exceptions for Gly35, Lys63 and Leu71 (Fig. 4c). The correlation coefficient between the derived from both data sets D23M and D36M is = 0.945. The inter-nuclear angle enclosed between the dynamic average vectors derived from D23M and derived from D36M agree very well with an average value of 1.4° (compare Supporting Information Figure S2e). A higher deviation is observed for Gly35 and Asp52 which also shows a higher discrepancy of the .Fig. 4


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)

RDC-based  order parameters (red and blue) scaled according to the method described in the supplement are compared to the Lipari–Szabo  (black) for (a) D23M and (b) D36M. Both error bars for  = 0.3 Hz and  are indicated as horizontal lines. While for some residues  and  have almost equal values, for others, mainly in loop regions but also in secondary structure elements,  values are significantly lower. The average RDC-based order parameter is  = 0.72  0.02 for D23M and = 0.72 0.02 for D36M compared to  = 0.778 ± 0.003 for the Lipari–Szabo order parameter. (c) RDC-based order parameters  derived from D23M (red) and D36M (blue) are compared. Both data sets D36M and D23M give  that are identical within the error, with a very few exceptions for Gly35, Lys63 and Leu71. The correlation coefficient is  = 0.945. (d) and (e): comparison of (d)  and (e)  order parameter distributions, The 25th percentile of the  distribution is P25 = 0.68, the 75th percentile is P75 = 0.80 for D23M, giving and interquantile range (P25 to P75) of IQR = 0.12. (Identical values are obtained for D36M.) In contrast, the distribution of Lipari–Szabo order parameters  is 2.4 times narrower with P25 = 0.78, P75 = 0.83 and an interquantile range of IQR = 0.05. For the RDC-based order parameter  the IQR is more than double than that for the Lipari–Szabo  showing that the RDC-based order parameters detect a much wider range of mobility
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2480484&req=5

Fig4: RDC-based order parameters (red and blue) scaled according to the method described in the supplement are compared to the Lipari–Szabo (black) for (a) D23M and (b) D36M. Both error bars for = 0.3 Hz and are indicated as horizontal lines. While for some residues and have almost equal values, for others, mainly in loop regions but also in secondary structure elements, values are significantly lower. The average RDC-based order parameter is  = 0.72  0.02 for D23M and = 0.72 0.02 for D36M compared to = 0.778 ± 0.003 for the Lipari–Szabo order parameter. (c) RDC-based order parameters derived from D23M (red) and D36M (blue) are compared. Both data sets D36M and D23M give that are identical within the error, with a very few exceptions for Gly35, Lys63 and Leu71. The correlation coefficient is = 0.945. (d) and (e): comparison of (d) and (e) order parameter distributions, The 25th percentile of the distribution is P25 = 0.68, the 75th percentile is P75 = 0.80 for D23M, giving and interquantile range (P25 to P75) of IQR = 0.12. (Identical values are obtained for D36M.) In contrast, the distribution of Lipari–Szabo order parameters is 2.4 times narrower with P25 = 0.78, P75 = 0.83 and an interquantile range of IQR = 0.05. For the RDC-based order parameter the IQR is more than double than that for the Lipari–Szabo showing that the RDC-based order parameters detect a much wider range of mobility
Mentions: For both D23M and D36M the resulting RDC-based order parameters are identical within the error, with very few exceptions for Gly35, Lys63 and Leu71 (Fig. 4c). The correlation coefficient between the derived from both data sets D23M and D36M is = 0.945. The inter-nuclear angle enclosed between the dynamic average vectors derived from D23M and derived from D36M agree very well with an average value of 1.4° (compare Supporting Information Figure S2e). A higher deviation is observed for Gly35 and Asp52 which also shows a higher discrepancy of the .Fig. 4

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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