Applications in Peptide and Protein Structure Investigations

The application of NMR chemical shift constraints in the structure refinement of soluble proteins is now a standard procedure, since the ll, N and C chemical shifts have to be assigned to produce NOE constraints. The empirical C and CP shift surfaces from Kuszewski et and the proton chemical shift formulae were included into X-PLOR and thus belong to the standard procedures in protein structure analysis. 

An interesting approach of structure refinement is based on the use of NOEs plus chemical shifts that are caused by intermolecular interactions. Iwadate et performed calculations on the geometry of a melittin tetramer at dilferent temperatures. The structural models rely on a relatively small number of intermolecular chemical shifts caused by the interaction of special groups such as tryptophan rings with protons. There are even a number of examples where aggregation chemical shifts are used to build and refine molecular models.For example, van Rossum et used the shift 

Chemical shift target functions proved their power especially in the refinement of smaller peptides as for example a vasopressin derivative.Using only traditional constraints, this cyclic peptide switched in MD simulations between two conformations. h chemical shift constraints forced the structure into a single conformation that not only fits the chemical shift constraints well but also satisfies the NOE constraints better than in their absence. Despite the fact that the accuracy of this type of chemical shift calculation for protons is still relatively low (about 0.25 ppm), chemical shift constraints can significantly reduce the conformational space allowed for the structures. 

The energetically most stable structure is illustrated in Fig. 10(a). The NH2-group position of the N-alkyl chain is important since it is the most obvious structural difference between the first two conformations. Complex 6(a) possesses two additional hydrogen bonds as compared to conformation (b), thus stabilizing (a). In contrast to (a) and (b), structure (c) shows two trans-cis alterations and an imidazole ring flip. 

These calculations demonstrate that it is possible to obtain highly refined structures using chemical shift pseudo-forces. The resulting differences between measured and calculated BPT chemical shifts are in the range of the experimental error. BPT pseudo-forces are in the same range as electrostatic interactions, and they act on all atoms that contribute to the chemical shift of a site. 

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