A calculation strategy for the structure determination of symmetric demers by 1H NMR

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Abstract
The structure determination of symmetric dimers by NMR is impeded by the ambiguity of inter‐ and intramonomer NOE crosspeaks. In this paper, a calculation strategy is presented that allows the calculation of dimer structures without resolving ther ambuguity by additional experiments (like asymmetric labeling). The strategy employs a molecular dynamic‐based simulated annealing approach to minimize a traget function. The experimental part of the target function contains distance restraints that correctly describe the ambiguity of the NOE peaks, and a novel term that restrains the symmetry of the dimer without requiring the knowledge of the symmetry axis. The use of the method is illustrated by three examples, using experimentally obtained data and model data derived from a known structure. For the purpose of testing the method, it is assumed that every NOE crosspeak is ambiguous in all three cases. It is shown that the structure of a homologous protein is known and in ab intio structure determination. The method can be extended to higher order symmetric multimers.