Figure 5
From: Alanine substitution in cellobiohydrolase provides new insights into substrate threading
Substrate threading in MD simulations of WT and the N62A mutant. (a) Schematic diagram of the initial cellulose position (reducing end at subsite −5) and the distance between each subsite (−5 to −2) and catalytic residue E234. (b) Time evolution of distance between the C1 atom of the reducing end glucose and Cα atom of catalytic base E234 in the MD simulation of WT (first run in black, second run in grey), and (c) the same time evolution in the MD simulation of N62A (similar colours). The distances for each subsite (−5 to −2) in (a) are plotted with a line to scale the position of the cellulose substrate. Several stages are indicated by blue (WT) or red (N62A) circles. (d) Snapshots of substrate threading in the MD simulations of WT depicted at 1.0, 11.5, 15.0, and 124.8 ns from the first run correspond to initial (1.0 ns), pre-procession (11.5 ns), procession (15.0 ns), and recession (124.8 ns) stages, respectively. The threading cellulose chain is represented by its constituent carbon/oxygen ring chain (thick orange stick). In the leading glucosyl unit, the hydroxyl group at C6 is also drawn. To indicate the position of each subsite, the cellulose strand from the homology model (Fig. 1a) is superimposed (thin yellow stick of carbon ring). N62 and W63 sidechains are shown as thick sticks (CPK colouring and purple, respectively). (e) Substrate in the N62A mutant depicted at 5.0, 32.0, and 109.0 ns from the first run and 99.5 ns from the second run, corresponding to initial (1st, 5.0 ns), pre-procession (1st, 32.0 ns), and procession (1st, 109.0; 2nd, 99.5 ns) stages, respectively.
