Protein Conformation and Dynamics. Effects of Crankshaft Motions on ¹H NMR Cross-Relaxation Effects

In this paper, the slow backbone motions for segments of interleukin 1β and calbindin D_9k are characterized and the effects of these motions on the interproton cross-relaxation effects are investigated. We assume that the flexible loop segments are involved in three motions: fast librational vibrations, slow crankshaft motions, and the overall tumbling motion of the protein. The parameters characterizing the conformers and dynamics (amplitude and time scale) of the flexible segments are estimated by fitting the calculated data to the experimental heteronuclear ¹⁵N relaxation data. NOESY spectra simulated by using the flexible model are in better agreement with the experimental data than those simulated by using the rigid model. Neglecting flexibility may cause biases in the estimated interproton distances derived from cross-relaxation peaks by up to 1 Å.