Protein dynamics by NMR has been reviewed extensively in recent years. These surveys show decisively that information on structure should be complemented by information on motion both to properly characterize the protein, and to understand its function. The time scale accessible by NMR extends from picoseconds to days, with different methods accessing different parts of this time axis. Here we focus on heteronuclear NMR spin relaxation used to study ps to ns protein dynamics. The slow limit of this time regime is determined by the global tumbling of the protein, with the rates for internal motion of the probe being typically faster.
Based on experience gained over nearly a decade we came to the conclusion that the traditional method of NMR spin relaxation analysis in proteins and nucleic acids, called “model-free” (MF), does not extract adequately and fully the information inherent in the experimental data largely because it is oversimplified. We have developed an approach that overcomes many of the MF deficiencies. This method, called the slowly relaxing local structure (SRLS) may be regarded as a generalization of MF. SRLS predates the MF approach, and even provided derivations of the exact equivalents of the MF equations .
The issues brought up above will be addressed in detail in this review. It will be shown that analogous, but physically distinct, SRLS and MF analyses often yield substantially different results, indicating that the oversimplifications inherent in MF have unfavorable practical implications. Within a broader perspective, we illustrate the disadvantages of applying parameterization instead of setting forth models, using mathematical instead of physical parameter definitions, and not abiding by the assumptions underlying the various equations used. We offer the concepts that underlie SRLS as an alternative to the model-free point-of-view, and we describe and illustrate how SRLS can be implemented in a practical fashion. We also indicate how improvements to the current SRLS approach can be introduced