A Monte Carlo simulation study of the influence of internal motions on the molecular conformation deduced from two‐dimensional nmr experiments

Abstract

Monte Carlo methods have been used to simulate internal motions of aromatic protons of an oligonucleotide at the nanosecond time scale. Each proton is allowed to fluctuate about its equilibrium position. The longitudinal cross-relaxation rates of such a system of spins have been determined by computing the appropriate correlation functions. Then the interproton distances have been deduced according to the procedure generally used in two-dimensional nmr techniques (nuclear Overhauser effect spectroscopy—NOESY) and compared to the true values. The influence of the amplitude A and of the internal rotational diffusion constant D_int characterizing the dynamics of the system has been checked for in-phase and for uncorrelated motions. It is shown that for the investigated models the distances deduced from NOESY experiments may be under or overestimated, depending strongly on the values of A and D_int. Furthermore, the cross-relaxation rate of a couple of protons is very sensitive to the correlation level of the motions of both protons.