A Thorough Dynamic Interpretation of Residual Dipolar Couplings in Ubiquitin

Abstract

The presence of slow motions with large amplitudes, as detected by measurements based on residual dipolar couplings [Peti, W., Meiler, J., Brueschweiler, R. and Griesinger, C. (2002) J. Am. Chem. Soc., 124, 5822-5833], has stirred up much discussion in recent years. Based on ubiquitin NH residual dipolar couplings (rdcs) measured in 31 different alignment conditions, a model-free analysis of structure and dynamics [Meiler, J., Peti, W., Prompers, J., Griesinger, C. and Brueschweiler, R. (2001) J. Am. Chem. Soc., 123, 6098-6107] is presented. Starting from this broad experimental basis, rdc-based order parameters with so far unattained accuracy were determined. These rdc-based order parameters underpin the presence of new modes of motion slower than the inverse overall tumbling correlation time. Amplitudes and anisotropies of the motion were derived. The effect of structural noise on the results was proven to be negligible.

Side‐Chain Orientation and Hydrogen‐Bonding Imprint Supra‐τc Motion on the Protein Backbone of Ubiquitin

“…A model free analysis on backbone NH rdcs has been performed on ubiquitin by Lakomek et al [7] The analysis of order parameters has been performed with Origin 6.1 and hydrogen bonds have been reported in the literature (see Supporting Information). [11,12] Figures 2 and 3 have been Table 1: Average order parameters for core and exposed residues and for residues involved in 0,1, or 2 hydrogen bonds.…”

“…[6] Residual dipolar couplings (rdcs) were recognized early on as an ideal tool to widen the time window of dynamics that can be characterized by NMR spectroscopy, since they are sensitive to motional averaging occurring over the sub-and supra-t c time scales (ps to ms). [4] We recently analyzed NH rdcs of ubiquitin measured in 31 different alignment conditions and derived the order parameters 7] To differentiate between the sub-and supra-t c time scale, these order parameters were compared to Lipari-Szabo order parameters S 2 LS that are derived from conventional relaxation time measurements and that are only sensitive to the sub-t c time scale. [8,9] Interestingly, a periodic variation of the S 2 rdc value can be observed with a periodicity of two residues in the b strands of ubiquitin (amino acids 2-6, 12-16, 41-45, 66-71), while it is largely absent from the S 2 LS and exchange-rate data.…”

Multi‐Timescale Conformational Dynamics of the SH3 Domain of CD2‐Associated Protein using NMR Spectroscopy and Accelerated Molecular Dynamics

“…[7][8][9][10] It has been demonstrated that the measurement of a sufficient number of RDCs in differently aligning media allows the accurate determination of the motional properties of the protein backbone. Two generic approaches to the interpretation of the experimental data can be distinguished-either direct analysis of the RDCs to extract averaged spherical harmonic terms describing the angular averaging of the internuclear bonds, [11][12][13][14] or exploiting MD simulation (with or without restraints) to reproduce the motional amplitudes and modes in terms of an explicit conformational ensemble. [15][16][17][18][19][20][21] Such RDC-based studies allowed the identification of nano-to millisecond motions that were localized predominantly in the molecular recognition sites of the small proteins ubiquitin (Ub) and GB3.…”

Combining experimental and simulation data of molecular processes via augmented Markov models

“…S1). The AMMs used observables from NMR spectroscopy as experimental restraints: N H− α H 3 J couplings (46) and an extensive set of H-N residual dipolar couplings (RDCs) from 36 different alignment conditions (47)(48)(49)(50).…”