Rel domain

One important application of RDC measurements is the structural refinement of biomolecules that consist of several domains that are connected by more or less flexible linkers. Because of the flexibility of the linker and the distance between domains, J-couplings and NOE restraints will frequently not be sufficient for correct determination of the relative domain orientation. The addition of RDC restraints in structure calculation not only refines the biomolecular structure but also allows the relationship between structure and function to be studied. Interactions with other biomolecules and ligand binding may induce an intramolecular rearrangement of the relative orientation of domains that is detectable through RDC measurements (21, 22). 

Orientational restraints, which are derived by paramagnetic labeling of a single domain of a protein, are especially important for the analysis of domain-domain interactions (141). The paramagnetic tag induces anisotropic alignment, which is scaled for the two domains of the protein according to their relative domain mobility. 

A graphical approach was also used by Millet and Pons to analyse anisotropy of rotational diffusion in proteins. The values of Z)j and DJD compatible with R IRi ratios are presented as a contour plot. The intersection of the contour plots for different residues provides the values of anisotropy parameters compatible with experimental data. The obtained parameters can be used as starting values for further optimisation. The method is apphcable to axially symmetric rotation. A combination of approximate and exact methods was used by Ghose et al. to reduce the computational time of the determination of rotational diffusion tensor from NMR relaxation data. The initial values of the tensor components and its orientation are evaluated from the approximate solution, which substantially reduces the search space during the exact calculations. The method was applied for the estimation of relative domain orientation of a dual domain protein. 

TROSY spectra. Relative domain orientation could then be modelled in MODULE, prior to refinement of the entire structure in XPLOR-NIH under RDC, ambiguous NOE and radius of gyration restraints. In the model, domains 2, 4 and 6 pack together into a core flanked by propeller blades of 1,3 and 5, explaining the increased rotational tumbling measured from amide backbone dynamics in these domains. Mitogen-activated... 

In their review on NMR of high-molecular-weight proteins Tugarinov et al. have discussed Dhn residual dipolar couplings as a tool for determination of domain orientation. Lipsitz and Tjandra have reviewed the use of residual dipolar couplings in the study of conformational fold, relative domain orientation and in structure refinement of DNA and proteins. 

NF-kB (nuclear factor-kappa B) is a transcription factor so named because its first identified binding site is located within an enhancer in the Ig k light chain gene in mature B cells. The functional NF-kB is a homo- or heterodimer of homologous proteins that share a common structure motif called the Rel domain. The Rel family in the vertebrate includes five cellular proteins p50 (NF-kB 1), p52 (NF-kB2), p65 (RelA), RelB, and c-Rel. The most common NF-kB consists of a p65 p50 heterodimer, but there exists a variety of homodimers and heterdimers, each of which activates its own characteristic set of genes. 

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