Limits...
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.

Show MeSH
SCRM-derived  after addition of (a) 10° (b) 20° and (c) 30° synthetic structural noise on the 1ubi X-ray structure used as starting structure for alignment tensor calculation. The agreement between the calculated  and those derived using the noise-free structure (black) shows that SCRM is robust against the influence of structural noise. (d) and (e):  order parameter are derived for d) D23M and e) D36M using the original RDC-based model-free analysis and nine different structures of ubiquitin bound in several complexes as starting structure for the analysis. The different structures have a backbone rmsd between 0.3 and 0.6 Å to the free Xray structure 1ubi (Ramage et al. 1994) (black line) and serve as a test case for severe structural noise. (f) and (g):  order parameter are derived for (f) D23M and (g) D36M using the new SCRM method and the same nine different structures of ubiquitin (free X-ray structure 1ubi black line). While the original model-free approach (Lakomek et al. 2005) is affected by structural difference of the input structure used for tensor calculation, the new SCRM method alleviates the effect of structural noise
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2480484&req=5

Fig5: SCRM-derived after addition of (a) 10° (b) 20° and (c) 30° synthetic structural noise on the 1ubi X-ray structure used as starting structure for alignment tensor calculation. The agreement between the calculated and those derived using the noise-free structure (black) shows that SCRM is robust against the influence of structural noise. (d) and (e): order parameter are derived for d) D23M and e) D36M using the original RDC-based model-free analysis and nine different structures of ubiquitin bound in several complexes as starting structure for the analysis. The different structures have a backbone rmsd between 0.3 and 0.6 Å to the free Xray structure 1ubi (Ramage et al. 1994) (black line) and serve as a test case for severe structural noise. (f) and (g): order parameter are derived for (f) D23M and (g) D36M using the new SCRM method and the same nine different structures of ubiquitin (free X-ray structure 1ubi black line). While the original model-free approach (Lakomek et al. 2005) is affected by structural difference of the input structure used for tensor calculation, the new SCRM method alleviates the effect of structural noise

Mentions: For synthetic structural noise added to the starting structure for the SCRM analysis (see M&M scenario A), the resulting order parameters (using D36M) after 4 SCRM cycles are in excellent agreement with those obtained using the noise-free structure 1ubi), both for 10° and 20° Gaussian noise, as seen in Fig. 5(a, b). Even for 30° structural noise the agreement is reasonably good (see Fig. 5c).Fig. 5


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)

SCRM-derived  after addition of (a) 10° (b) 20° and (c) 30° synthetic structural noise on the 1ubi X-ray structure used as starting structure for alignment tensor calculation. The agreement between the calculated  and those derived using the noise-free structure (black) shows that SCRM is robust against the influence of structural noise. (d) and (e):  order parameter are derived for d) D23M and e) D36M using the original RDC-based model-free analysis and nine different structures of ubiquitin bound in several complexes as starting structure for the analysis. The different structures have a backbone rmsd between 0.3 and 0.6 Å to the free Xray structure 1ubi (Ramage et al. 1994) (black line) and serve as a test case for severe structural noise. (f) and (g):  order parameter are derived for (f) D23M and (g) D36M using the new SCRM method and the same nine different structures of ubiquitin (free X-ray structure 1ubi black line). While the original model-free approach (Lakomek et al. 2005) is affected by structural difference of the input structure used for tensor calculation, the new SCRM method alleviates the effect of structural noise
© Copyright Policy
Related In: Results  -  Collection

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

Fig5: SCRM-derived after addition of (a) 10° (b) 20° and (c) 30° synthetic structural noise on the 1ubi X-ray structure used as starting structure for alignment tensor calculation. The agreement between the calculated and those derived using the noise-free structure (black) shows that SCRM is robust against the influence of structural noise. (d) and (e): order parameter are derived for d) D23M and e) D36M using the original RDC-based model-free analysis and nine different structures of ubiquitin bound in several complexes as starting structure for the analysis. The different structures have a backbone rmsd between 0.3 and 0.6 Å to the free Xray structure 1ubi (Ramage et al. 1994) (black line) and serve as a test case for severe structural noise. (f) and (g): order parameter are derived for (f) D23M and (g) D36M using the new SCRM method and the same nine different structures of ubiquitin (free X-ray structure 1ubi black line). While the original model-free approach (Lakomek et al. 2005) is affected by structural difference of the input structure used for tensor calculation, the new SCRM method alleviates the effect of structural noise
Mentions: For synthetic structural noise added to the starting structure for the SCRM analysis (see M&M scenario A), the resulting order parameters (using D36M) after 4 SCRM cycles are in excellent agreement with those obtained using the noise-free structure 1ubi), both for 10° and 20° Gaussian noise, as seen in Fig. 5(a, b). Even for 30° structural noise the agreement is reasonably good (see Fig. 5c).Fig. 5

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