Protein dynamics at the local level

RDC methods used to probe the structural dynamics between relatively large molecular fragments such as domains in multi-domain proteins can be 

The analysis of side-chain RDCs is potentially complicated due to the possibility of extensive internal motions coupled with concomitant uncertainties of overall molecular alignment. Thus an attractive target for RDC-based 

Mittermaier and Kay have carried out a detailed RDC-based study of Xi rotamer distributions for the B1 domain of peptostreptococcal protein 

133 Using two sets of backbone RDC data, collected in bacteriophage Pfl and bicelle media, they obtained order tensor parameters using a set of crystallographic coordinates for the structural model. This allowed the refinement of C -C bond orientations, which then provided the basis for their quantitative interpretation of C -H RDCs for 38 out of a possible 49 residues in the context of three different models. The three models were (A) a static xi rotameric state (B) gaussian fluctuations about a mean xi torsion and (C) the population of multiple rotameric states. They found that nearly 75% of xi torsions examined could be adequately accounted for by a static model. By contrast, the data for 11 residues were much better fit when jumps between rotamers were permitted (model C). The authors note that relatively small harmonic fluctuations (model B) about the mean rotameric state produces only small effects on measured RDCs. This is supported by their observation that, except for one case, the static model reproduced the data as well as the gaussian fluctuation model. 

The success of these new multi-alignment approaches for the extraction of generalized order parameters from RDCs relies on a couple of fundamental assumptions. The first of these, as described in Section 2, is that the molecule is structured enough that the internal dynamics remain uncorrelated with the overall alignment. This corresponds to the assumption that the separation of averaging in Eq. (21) remains valid. If this does not hold, then overall alignment and internal motion will be convoluted in some nonlinear manner. The second assumption is that the structure and dynamics of the molecule is not influenced by change of medium. Provided that both of these assumptions are permissible, the acquisition of sufficient 

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