Paramagnetic NMR Spectroscopy and Lowly Populated States - Recent Developments in Biomolecular NMR - page 133

further reading, more detailed reviews of paramagnetic labelling are

available. 4,28

6.1.3 Ensemble Modelling
NMR spectroscopy signals of dynamic protein structures and protein
complexes generally represent a weighted average of all present conformations;
therefore, using this data to reconstruct the ensemble offers infinite solutions. 37
Various ensemble modelling approaches have been proposed, each with its
own advantages and disadvantages.
First, ensembles of protein-protein or protein-DNA complexes can be
generated using ensemble docking, in which multiple conformations are
docked simultaneously. This procedure generates equilibrium ensembles
consisting of both specific and non-specific complexes, which allows for the
populations of each to be estimated. 38 Alternatively, simulated docking based
on electrostatic interactions, using either Brownian dynamics 39 or Monte
Carlo simulations, 40 can be used to generate an ensemble that can be compared
to the experimental data. Random rotation modelling also generates a
simulated ensemble that can be compared to experimental data by rotating one
protein around the other until the experimental data is fit. 41-43 Finally, the
surface area of one protein sampled by the other in an encounter complex can
be mapped by generating all possible orientations and comparing them to the
experimental data. 24,44
For generating ensembles that represent the internal dynamics of proteins,
ensemble refinement of structures, sometimes in combination with molecular
dynamics calculations, on the basis of the NMR data is performed, yielding an
ensemble of structures that, as a whole, matches the data, such as RDCs, 45-48
relaxation data 49 or PREs. 50 Disordered or unfolded proteins can also be
described using ensemble selection in which an algorithm first generates a large
ensemble of all possible conformers for a given condition. Then an ensemble-
selection algorithm is used, along with the experimental data, to select a small
set of conformers that best describe the data. 51,52
For domain motions, the maximum occurrence method can be used. This
method determines the maximum possible fraction of a given protein
conformer. By repeating this procedure for many conformers, their relative
contribution to the ensemble can be established. The absolute fractions add to
more than 100%, indicating an overestimation of each contribution. 53,54

6.2 Residual Dipolar Couplings and Pseudo-Contact

Shifts

6.2.1 RDC Theory
Within an external magnetic field, paramagnetic centers will induce partial
alignment of the molecules to which they are bound. When this occurs,