Risks, Causality, and the Precautionary Principle

Abstract

The model-free approach (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546-4559; 4559-4570) is the standard method for the analysis of NMR relaxation data from proteins. The method assigns to each interaction vector a generalized order parameter S(2), which is a measure of the spatial restriction that the vector experiences in a molecular reference frame. A variety of techniques for the interpretation of S(2) values and their underlying assumptions are tested here for a dynamic alpha-helix represented by an ensemble of peptide structures that satisfies a set of predefined constraints. A self-consistent picture is developed that characterizes the influence of major determinants, including backbone dihedral angle fluctuations and their correlations, separability of internal and overall motion, the preservation of hydrogen bonds, restricted end-to-end distance fluctuations, locally anisotropic dynamics, and local contacts between interaction vector atoms and their environment. Many of the features parallel experimental NMR and computational observations of helices in proteins. The understanding gained from this model system is expected to contribute toward the ever more detailed interpretation of experimental order parameter profiles.