Time Scales of Slow Motions in Ubiquitin Explored by Heteronuclear Double Resonance

Understanding how proteins function at the atomic level relies in part on a detailed characterization of their dynamics. Ubiquitin, a small single-domain protein, displays rich dynamic properties over a wide range of time scales. In particular, several regions of ubiquitin show the signature of chemical exchange, including the hydrophobic patch and the beta 4-alpha 2 loop, which are both involved in many interactions. Here, we use multiple-quantum relaxation techniques to identify the extent of chemical exchange in ubiquitin. We employ our recently developed heteronuclear double resonance method to determine the time scales of motions that give rise to chemical exchange. Dispersion profiles are obtained for the backbone NHN pairs of several residues in the hydrophobic patch and the beta 4-alpha 2 loop, as well as the C-terminus of helix alpha 1. We show that a single time scale (ca. 50 mu s) can be used to fit the data for most residues. Potential mechanisms for the propagation of motions and the possible extent of correlation of these motions are discussed.