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 th e 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 fu nctions related to the C-13-NMR relaxation parameters of the C1'-H1' b onds of the sugar rings. The calculated effective correlation times ta u(e)(similar to 13 ps) and the order parameter S-2 (similar to 0.82) o f the Lipari and Szabo formalism (Lipari and Szabo 1982a, b) are in sa tisfactory agreement with those determined previously by NMR (Gaudin e t al. 1995, 1996). H-1-H-1 NOE buildups have also been measured experi mentally and agree with those computed from the simulation. These resu lts validate the simulation, and a more detailed analysis of the inter nal dynamics of the dodecamer was undertaken. Analysis of the distribu tions and of the autocorrelation functions of the glycosidic angle flu ctuations chi shows that the rotational motion of the sugar rings abou t 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 agree ment 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.