Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation

• Published in: Journal of the American Chemical Society Vol. 138; no. 19; pp. 6240 - 6251
• Main Authors: Abyzov, Anton, Salvi, Nicola, Schneider, Robert, Maurin, Damien, Ruigrok, Rob W.H, Jensen, Malene Ringkjøbing, Blackledge, Martin
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 18.05.2016
• Subjects: Algorithms; Biochemistry, Molecular Biology; Electromagnetic Fields; Intrinsically Disordered Proteins - chemical synthesis; Intrinsically Disordered Proteins - chemistry; Life Sciences; Magnetic Resonance Spectroscopy; Models, Chemical; Models, Molecular; Monte Carlo Method; Nuclear Magnetic Resonance, Biomolecular; Nucleoproteins - chemical synthesis; Nucleoproteins - chemistry; Protein Conformation; Reproducibility of Results; Sendai virus - chemistry; Structural Biology; Temperature
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.6b02424

The dynamic modes and time scales sampled by intrinsically disordered proteins (IDPs) define their function. Nuclear magnetic resonance (NMR) spin relaxation is probably the most powerful tool for investigating these motions delivering site-specific descriptions of conformational fluctuations from throughout the molecule. Despite the abundance of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rates remains poorly understood. Here we measure an extensive range of auto- and cross-correlated spin relaxation rates at multiple magnetic field strengths on the C-terminal domain of the nucleoprotein of Sendai virus, over a large range of temperatures (268–298 K), and combine these data to describe the dynamic behavior of this archetypal IDP. An Arrhenius-type relationship is used to simultaneously analyze up to 61 relaxation rates per amino acid over the entire temperature range, allowing the measurement of local activation energies along the chain, and the assignment of physically distinct dynamic modes. Fast (τ ≤ 50 ps) components report on librational motions, a dominant mode occurs on time scales around 1 ns, apparently reporting on backbone sampling within Ramachandran substates, while a slower component (5–25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. Extending the study to three protein constructs of different lengths (59, 81, and 124 amino acids) substantiates the assignment of these contributions. The analysis is shown to be remarkably robust, accurately predicting a broad range of relaxation data measured at different magnetic field strengths and temperatures. The ability to delineate intrinsic modes and time scales from NMR spin relaxation will improve our understanding of the behavior and function of IDPs, adding a new and essential dimension to the description of this biologically important and ubiquitous class of proteins.