Structure Determination by NMR: The Modeling of NMR Parameters as Ensemble Averages
High-resolution NMR has become a well established technique for determining three-dimensional structures of small proteins in solution1. Procedures for assigning resonances to individual spins are being automated in various places. There is general agreement how NMR parameters like initial NOE build-up rates and J couplings must be translated into interatomic distances and dihedral angles. However, there is no consensus yet about the way such parameters are best modeled in three-dimensional structures. Most of the established procedures for interpreting a set of interproton distances result in a family of static structures. A structure is accepted as a member of such a family if it is consistent with all the measured NMR parameters simultaneously. This approach denies the fact that such NMR parameters as NOE’s and J couplings are properties of ensembles of molecules. Recently we presented a procedure, based on molecular dynamics simulation techniques, which generates such an ensemble of molecules2,3. While individual members of the ensemble may violate the experimental constraints, the ensemble taken as a whole must reproduce the data. Using this approach, the resulting set of structures roughly resembles the proper Boltzmann distribution over the conformational states that are accessible at the temperature of the NMR experiments, although the always limited simulation time hinders a complete sampling of such states.
KeywordsExperimental Constraint Distance Restraint Optimization Stage Distance Bound Distance Geometry
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