Ty. Shen et al., Statistical analysis of the fractal gating motions of the enzyme acetylcholinesterase - art. no. 041902, PHYS REV E, 6304(4), 2001, pp. 1902
The enzyme acetylcholinesterase has an active site that is accessible only
by a "gorge" or main channel from the surface, and perhaps by secondary cha
nnels such as the "back door." Molecular-dynamics simulations show that the
se channels are too narrow most of the time to admit substrate or other sma
ll molecules. Binding of substrates is therefore "gated" by structural fluc
tuations of the enzyme. Here, we analyze the fluctuations of these possible
channels, as observed in the 10.8-ns trajectory of the simulation. The pro
bability density function of the gorge proper radius (defined in the text)
was calculated. A double-peak feature of the function was discovered and th
erefore two states with a threshold were identified. The relaxation (transi
tion probability) functions of these two states were also calculated. The r
esults revealed a power-law decay trend and an oscillation around it, which
show properties of fractal dynamics with a ''complex exponent.'' The cross
correlation of potential energy versus proper radius was also investigated
. We discuss possible physical models behind the fractal protein dynamics:
the dynamic hierarchical model for glassy systems is evaluated in detail.