INFLUENCE OF MOLECULAR-MOTION ON THE ACCURACY OF NMR-DERIVED DISTANCES - A MOLECULAR-DYNAMICS STUDY OF 2 SOLVATED MODEL PEPTIDES

The law that relates the quotient of two NOE enhancements to the quotient of the corresponding internuclear distances raised to the negative sixth powers is the result of several assumptions concerning molecular motion: elongation and rotation of internuclear distance vectors are assumed to be uncorrelated, and the reorientational motion of all internuclear distance vectors of a given system are described by the same motional model (e.g. rotational diffusion) with the same parameters; that is, there is no allowance for individual rotational correlation times for each pair of nuclei. In order to check the validity of these rather restrictive assumptions, we calculated the dipolar correlation functions for a set of internuclear distances in the linear type II beta-turn-forming pentapeptide Tyr-Pro-Gly-Asp-Val and the cyclic peptide N-triglycin[Lys(8)]vasopressin by molecular dynamics simulations (simulation time: more than 2 ns). The structures of these peptides have been determined by combination of H-1-H-1-NOE data and molecular dynamics calculations using time-averaged distance constraints. Calculation of the correlation functions has been carried out by simulation in water (long-range interactions have been treated with the method of Ewald summation). We calculated the total dipolar correlation functions as well as the angular part and the distance part of the correlation functions and determined correlation times and generalized order parameters. For the studied set of H-H pairs the assumption of uncorrelated elongation and rotation has turned out to be a suitable approximation, while rotational correlation times are quantities specific for each spin pair of the studied peptides. The relative contribution of reorientation and distance fluctuation to the spectral density is quantitatively analyzed. On the basis of these findings a modified calibration formula is suggested.