Experimental Characterization of Models for Backbone Picosecond Dynamics in Proteins. Quantification of NMR Auto- and Cross-correlation Relaxation Mechanisms Involving Different Nuclei of the Peptide Plane

Abstract

NMR relaxation parameters were measured for the peptide-plane carbonyl and nitrogen nuclei for the protein Escherichia coli flavodoxin. A poor correlation between the general order parameters of the C‘−Cα vector (Zeng, L.; Fischer, M. W. F.; Zuiderweg, E. R. P. J. Biomol. NMR 1996, 7, 157−162) and the N−NH vector was observed. We interpret this lack of correlation in this nearly spherical protein as evidence of local or semilocal anisotropic motion. A new experiment is introduced from which the cross-correlation between the carbonyl chemical shift anisotropy relaxation and carbonyl-Cα dipole−dipole relaxation is obtained. We show theoretically that the three relaxation measurements, reporting on the dynamics of the C‘−Cα vector, N−NH vector, and CSA tensor components behave differently under anisotropic motion. The cross-correlation order parameter formalism for dipolar cross-correlation spectral densities, as introduced by Daragan and Mayo (Daragan, V. A.; Mayo, K. H. J. Magn. Reson. B 1995, 107, 274−278), has been extended to include cross-correlations between nonaxial chemical shift anisotropy and dipole−dipole relaxation. By analyzing our experimental data with the theoretical models for anisotropic local motion, dynamic models were obtained for the peptide planes of 32 residues of E. coli flavodoxin.

Modélisation de la dynamique de la chaîne peptidique des protéines en solution par RMN à travers les couplages dipolaires

“…Brüschweiler et sonéquipe ont montré que le mouvement d'un peptide (supposé plan et rigide) pouvait etre décrit par un mouvement FAG tridimensionnel défini par trois rotations aléatoires et indépendantes autour de trois axes orthogonaux, l'axe principalétant le long de l'axe C i−1 -C i [30][31][32][33][34]. Une simplification du modèle FAG-3D peutêtre raisonnablement faite en ne prenant en compte que cette composante et en négligeant les autres.…”

An Iterative Fitting Procedure for the Determination of Longitudinal NMR Cross-Correlation Rates

“…The values of Y 2 0 (⍀Ј) in Eq. [3] were assumed to be 1 in the calculation. The spectral density function J() was assumed to be 2 c /(5(1 ϩ 2 c 2 )).…”

“…For instance, the 15 ϩ H Z coherence is recalled in detail in Refs. (3) and (9)). In other words, R 1 cross correlations do not fully isolate a restricted set of relaxation mechanisms and cannot be measured in straightforward manner in spin-dense systems such as proteins.…”

“…In fact, such R 2 cross correlations "isolate" a restricted set of relaxation mechanisms out of a complex relaxation matrix. These properties thus allow detailed insight into the structure and dynamics of labeled proteins, and recent years have seen a flurry of such measurements, many of which measure R 2 interference effects of CSA and dipolar interactions (2)(3)(4)(5)(6)(7)(8)(9).…”

Characterizing semilocal motions in proteins by NMR relaxation studies

“…Moreover, these methods may be used to determine the nature or character of the local motion by deriving likely motional models that are consistent with the observed anisotropic relaxation behavior. The characterization becomes better when the reorientational dynamics of more internuclear vectors and the cross-correlations between relaxation pathways (29) are measured. Recently, order parameters have been correlated with entropy (30,31).…”