ISSN:
1432-1017
Keywords:
Key words Molecular dynamics
;
DNA
;
NMR relaxation
;
Correlation times
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
,
Physics
Notes:
Abstract 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 13C-NMR relaxation parameters of the C1′-H1′ bonds of the sugar rings. The calculated effective correlation times τ e (∼13 ps) and the order parameter S2 (∼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). 1H-1H 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 flucuations χ 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° and 17.109 rad2s–1 respectively. These values are in good agreement with 13C 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.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/s002490050076
