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Fig. 4 | Biotechnology for Biofuels

Fig. 4

From: Cellular automata modeling depicts degradation of cellulosic material by a cellulase system with single-molecule resolution

Fig. 4

CA model of the action of CBH II on a mixed amorphous–crystalline cellulose substrate. The simulated substrate was a flat amorphous matrix in which a nanocrystal of 16 nm width/height and 100 nm length was embedded in plane. CBH II was placed in saturating amount on the cellulose surface (24 nmol/m2). a Effect of the enzyme’s k cat on the time course of cellobiose released from 25 mm2 of cellulose surface. The same amorphous material was used on all simulations. Note that the rate of cellobiose release depends on the k cat, whereas the maximum amount of cellobiose does not. b When degradation of amorphous cellulose by CBH II (light blue) was simulated whereby CBH II was modeled as a perfectly processive exo-cellulase (k off = 0), it was noted that CBH II became gradually trapped at amorphous material (blue circle). Collision between a complexed CBH II molecule and a structural obstacle (nanocrystal or amorphous material) was the origin of the jam, and a thus stuck CBH II presented an obstacle for other CBH molecules acting processively on amorphous cellulose chains nearby (blue circle). The red scale bar shows 5 nm. c Modeled time courses of cellobiose release by CBH II were not consistent with experiment unless the CA model of the enzyme was expanded to include endo-type chain cleavage in amorphous cellulose. Modeled results are shown for a k endo of 0.03 s−1 and are compared with experimental data. The k off of CBH II was set to 0.7 × 10−2·s−1 in the simulation (Table 1)

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