Simulation of the activation of -chymotrypsin: Analysis of the pathway and role of the propeptide

Supplemental Research Data

Files in this Data Supplement:

• MS Word File (82 B) - Three figures are given as supplementary materials. The first shows three activation TMD trajectories of the bWT species together with the corresponding MD runs. The second shows three activation TMD trajectories and the corresponding MD trajectories for bdeltaA variant. The third figure presents 5 activation TMD trajectories of the rdeltaA species and the MD trajectories belonging to the activation TMD trajectory that is discussed in detail in the text. We omitted the rest of the MD trajectories because we wanted to keep the clarity of the figure and show more than three activation TMD trajectories at the same time.In all the cases for the additional MD simulations (active and inactive) a 1ps long MD run was performed to generate different initial velocity vectors according to the different random number seeds starting from the same initial coordinates. That 1ps MD generated the initial coordinates for each individual MD simulation, which are indicated together with the final structures by individual symbols. Each additional activation TMD run was performed starting from the final structure of the inactive MD simulations and targeting towards the final structure of the active MD simulation.