Protein conformation and dynamics. Effects of crankshaft motions on H-1 NMR cross-relaxation effects

In this paper, the slow backbone motions for segments of interleukin 1 beta and calbindin D-9k are characterized and the effects of these motions on t he interproton cross-relaxation effects are investigated. We assume that th e flexible loop segments are involved in three motions: fast librational vi brations, slow crankshaft motions, and the overall tumbling motion of the p rotein. The parameters characterizing the conformers and dynamics (amplitud e and time scale) of the flexible segments are estimated by fitting the cal culated data to the experimental heteronuclear N-15 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. Neglec ting flexibility may cause biases in the estimated interproton distances de rived from cross-relaxation peaks by up to 1 Angstrom.