Structural and Dynamic Analysis of Residual Dipolar Coupling Data for Proteins

TLDR

Residual dipolar couplings measured in weakly aligned proteins can uniquely inform on their solution‑state structure and dynamics, but extracting this information is challenging because the signals convolve structural and dynamic effects. The study introduces a formalism that enables first‑order separation of structural and motional contributions in RDC data, allowing simultaneous determination of both parameters. The authors define a generalized degree of order to quantify motion effects and demonstrate the method on extensive 15N,13C‑labeled ubiquitin RDC measurements in a dilute bicelle solution. The analysis confirms that ubiquitin’s solution structure aligns with the 1UBQ X‑ray model while also revealing a dynamic model with variable amplitudes and anisotropy, indicating RDCs can characterize both structure and anisotropic internal motions. Published in Biol.

Abstract

The measurement of residual dipolar couplings in weakly aligned proteins can potentially provide unique information on their structure and dynamics in the solution state. The challenge is to extract the information of interest from the measurements, which normally reflect a convolution of the structural and dynamic properties. We discuss here a formalism which allows a first order separation of their effects, and thus, a simultaneous extraction of structural and motional parameters from residual dipolar coupling data. We introduce some terminology, namely a generalized degree of order, which is necessary for a meaningful discussion of the effects of motion on residual dipolar coupling measurements. We also illustrate this new methodology using an extensive set of residual dipolar coupling measurements made on 15N,13C-labeled human ubiquitin solvated in a dilute bicelle solution. Our results support a solution structure of ubiquitin which on average agrees well with the 1UBQ X-ray structure (Vijay-Kumar, et al., J. Mol. Biol. 1987, 194, 531−544) for the protein core. However, the data are also consistent with a dynamic model of ubiquitin, exhibiting variable amplitudes, and anisotropy, of internal motions. This work suggests the possibility of primary use of residual dipolar couplings in characterizing both structure and anisotropic internal motions of proteins in the solution state.