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Amplitudes of Protein Backbone Dynamics and Correlated Motions in a Small α/β Protein: Correspondence of Dipolar Coupling and Heteronuclear Relaxation Measurements†
journal contribution
posted on 2004-08-24, 00:00 authored by G. Marius Clore, Charles D. SchwietersBackbone residual dipolar coupling (N−H, Cα−Hα, N−C‘, and Cα-C‘) data collected in five
different media on the B3 IgG binding domain of streptococcal protein G (GB3) have been analyzed by
simultaneous refinement of the coordinates and optimization of the magnitudes and orientations of the
alignment tensors using single and multiple structure representations. We show, using appropriate error
analysis, that agreement between observed and calculated dipolar couplings at the level of experimental
uncertainty is obtained with a two-structure (Ne = 2) ensemble representation which represents the simplest
equilibrium description of anisotropic motions. The data permit one to determine the magnitude of the
anisotropic motions along the four different backbone bond vectors in terms of 〈S2(jump)〉 order parameters.
The order parameters, 〈
(jump)〉, for the N−H bond vectors are in qualitative agreement with the
generalized order parameters,
(relaxation), derived from 15N relaxation measurements, with a
correlation coefficient of 0.84.
(relaxation) can be regarded as the product of an anisotropic order
parameter, corresponding to 〈
(jump)〉 derived from the residual dipolar couplings, and an axially
symmetric order parameter,
(axial), corresponding to bond librations which are expected to be
essentially uniform along the polypeptide chain. The current data indicate that the average value of
(axial) is ∼0.9. The close correspondence of 〈
(jump)〉 and
(relaxation) indicates that any
large-scale displacements from the mean coordinate positions on time scales longer than the rotational
correlation time are rare and hence do not perturb the observed dipolar couplings. Analysis of a set of
100 Ne = 2 ensembles reveals the presence of some long-range correlated motions of N−H and Cα−Hα
vectors involving residues far apart in the sequence but close together in space. In addition, direct evidence
is obtained for ubiquitous crankshaft motions along the entire length of the polypeptide backbone manifested
by the anticorrelation of the backbone torsion angles φi and ψi-1.