Accueil > Publications > Recherche par années > Années 1990 > 1997

Gaudin, F ; Genest, D ; Lancelot, G

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

European Biophysics Journal 26 (3) 239-245

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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 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.