File:Conformational-Analysis-of-Clostridium-difficile-Toxin-B-and-Its-Implications-for-Substrate-pone.0041518.s005.ogv

English: Conformational features of the NM-RhoA molecular dynamics simulation. The normal mode motions are again observed in this simulation, but to a lesser degree. Repacking of the NM-RhoA interface is observed, most significantly the folding down of the active site flap. This obscures the catalytic center of TcdB and does not allow close approach of the signaling loop of RhoA. Absence of UDP-Glucose is presumed to be the cause for this occurrence, as during a catalytic event it would occupy the space the side chains of the flap begin to enter. Regardless, it is interesting to note that the restriction of the conformational space indicates that upon protein-protein binding, the conformational space of TcdB is severely restricted, again pointing towards a conformational selection mechanism. A smoothed trajectory was used for visualization as described for Figure 3.