File:Conformational-Analysis-of-Clostridium-difficile-Toxin-B-and-Its-Implications-for-Substrate-pone.0041518.s004.ogv

English: Conformational features of the Apo-TcdB molecular dynamics simulation. The general range of conformations observed in the normal mode analysis are apparent over the 300 ns timecourse of the simulation. Additionally, motions near the active site do not result in permanent deformation, but a back-and-forth motion of the active site flap is observed. This wide range of flexibility is likely due to the absence of any substrate or binding partner, and is indicative of a conformational selection mechanism. The trajectory was visually smoothed by selecting frames at regular intervals. These were interpolated with a corkscrew algorithm with a linear interpolation rate over a period of 20 steps. The smoothed simulation is played from start to finish and reversed back to the beginning.