computer modeling in molecular biology.pdf

120 E. WesthoJ C. Rubin-Carrez, and K Fritsch-51 9 8 I I I 1 I 1 I I JIIIIIIII,,/,,.I,,,,,l,,l , , , / , , ,0 5 10 15 20IO~/T (~-1)Figure 5-9. Plot of In T versus 1/T for the mean lifetimes of the three-center hydrogen bonds(0) and for the mean lifetimes of the adenine sugar in the C2’-endo pseudorotational domain(0) during a simulation of poly(dA)-poly(dT) with E,,,. The theoretical curves, given by theequation5 (ps) = v -’ exp (AG*/RT)with v -1 = 0.16 ps, correspond to AG* equal to 0.2, 0.5, and 1 kcal/mol. (From Fritsch andWesthof [34]).each potential hydrogen bond was recorded as a series of 1 (if present) and 0 (if absent)defining the quantity S (t) [41]. The autocorrelation function is then given bywhere to = 5, 6t is the time at which the measurement begins along the simulationrun (with 6t = 0.05 ps and tmin = tmin6t = 5 ps). With such a definition, bonds notunformed at time to are ignored, and more importantly, bonds present at time t,whatever the number of intervening “breakage and re-formation” events, are included.Two examples are shown in Figure 5-10. With E (r) = 4r, the autocorrelationcurves depend strongly on the geometrical criteria used for defining the three-centerhydrogen bonds. This is much less the case with the sigmoidal dielectric function,indicating again its superiority. In all curves, there is a very rapid drop of autocorrelationfollowed by a smooth transition to a plateau value of 0.5, reached after