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Domain mobility plays an essential role in the biological function of
multidomain systems. The characteristic times of domain motions fall into the
interval from nano- to milliseconds, amenable to NMR studies. Proper analysis of
NMR relaxation data for these systems in solution has to account for interdomain
motions, in addition to the overall tumbling and local intradomain dynamics.
Here we propose a model of interdomain mobility in a multidomain protein, which
considers domain reorientations as exchange/interconversion between two distinct
conformational states of the molecule, combined with fully anisotropic overall
tumbling. Analysis of 15N-relaxation data for Lys48-linked diubiquitin at pH 4.5
and 6.8 showed that this model adequately fits the experimental data and allows
characterization of both structural and motional properties of diubiquitin, thus
providing information about the relative orientation of ubiquitin domains in
both interconverting states. The analysis revealed that the two domains reorient
on a time scale of 9-30 ns, with the amplitudes sufficient for allowing a
protein ligand access to the binding sites sequestered at the interface in the
closed conformation. The analysis of a possible mechanism controlling the
equilibrium between the interconverting states in diubiquitin points toward
protonation of His68, which results in three different charged states of the
molecule, with zero, +e, and +2e net charge. Only two of the three states are
noticeably populated at pH 4.5 or 6.8, which assures applicability of the
two-state model to diubiquitin at these conditions. We also compare our model
with the "extended model-free" approach and discuss possible future developments
of the model.
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