Characterization of local motions in proteins detected by nuclear magnetic resonance relaxation studies.

Abstract

The study of protein structure and function is incomplete without an understanding of protein dynamics. We use nuclear magnetic resonance (NMR) relaxation studies to probe pico and nano second dynamics in E. coli flavodoxin, measuring both $\sp{15}$N and $\rm\sp{13}C\sp\prime$ relaxation. Observing poor correlation between the generalized order parameters, $S\sp2,$ for the N-NH and C$\sp\prime$-C$\sb{\alpha}$ vectors in this nearly spherical molecule, we conclude that local or semi-local anisotropic motions are present. A new experiment is introduced from which the cross correlation, R$\rm\sb{cc},$ between the carbonyl chemical shift anisotropy relaxation and the C$\sp\prime$-C$\sb{\alpha}$ dipole-dipole relaxation is obtained. Theoretical modeling of the behavior of $S\sp2\sb{\rm N-NH},\ S\sp2\sb{C\sp\prime-C\sb{\alpha}},$ and R$\rm\sb{cc}$ under specific anisotropic motions allows the construction of motional restriction maps. Analyzing our experimental data in terms of these motional maps allows for the identification of local motions which might otherwise have gone undetected and, more importantly, allows for the nature of the motions to be characterized. This is demonstrated for several helices of flavodoxin which appear to be executing concerted limited rotations about their helical axes.