Internal dynamics of d(CGCAAATTTGCG)(2): a comparison of NMR relaxation measurements with a molecular dynamics simulation

We report the analysis of a 250 ps molecular dynamics simulation of the dodecamer d(CGCAAATTT-GCG)(2) immersed in a rectangular box of 3469 water molecules with 22 Na+ counterions. The internal dynamics of the molecule were investigated by studying the relevant autocorrelation functions related to the C-13-NMR relaxation parameters of the C1'-H1' bonds of the sugar rings. The calculated effective correlation times tau(e)(similar to 13 ps) and the order parameter S-2 (similar to 0.82) of the Lipari and Szabo formalism (Lipari and Szabo 1982a, b) are in satisfactory agreement with those determined previously by NMR (Gaudin et al. 1995, 1996). H-1-H-1 NOE buildups have also been measured experimentally and agree with those computed from the simulation. These results validate the simulation, and a more detailed analysis of the internal dynamics of the dodecamer was undertaken. Analysis of the distributions and of the autocorrelation functions of the glycosidic angle fluctuations chi shows that the rotational motion of the sugar rings about their glycosidic bond conforms to a restricted diffusion mechanism. The amplitude of the motions and the diffusion constant are 20 degrees and 17.10(9) rad(2)s(-1) respectively. These values are in good agreement with C-13 NMR data. Furthermore the simulation allows us to rule out another model also consistent with the experiment, consisting of a two-state jump between a syn and an anti conformation.