Protein dynamics and distance determination by NOE measurements

Present analysis procedures for NMR structure determination of macromolecules presuppose fixed internuclear distances. Improvement of the precision of the requisite NOE information has stimulated the use of more quantitative distance constraints thus necessitating examination as to whether the assumption of a rigid model systematically biases the distance estimates. Analysis using the simple (r-6) dependence of NOE buildup rates seriously underestimates the correct distance for spatially proximal proton pairs having fluctuations comparable to those observed in X-ray temperature factor analysis. However, by calculating the proper generalized order parameter it is shown that for nuclei undergoing rapid isotropic uncorrelated fluctuations the effective distance is identical to the distance between the mean positions of the nuclei. Similar analysis of molecular dynamics simulation data from bovine pancreatic trypsin inhibitor indicates that the distance obtained from the generalized order parameter predicts the distance between the mean positions to within a few percent regardless of the degree of correlation of the pairwise motion for virtually all main chain and dynamically constrained side chain protons.