50ps_double_system_MD

A supplementary material is represented with a video file (50ps_double_system_MD.avi), which
contains a double membrane system with two copies of Nav1.5 protein inserted in the membranes. The
slice of a molecular dynamics simulation was derived after 55 ns of a CompEl handled molecular
dynamics, which followed a relaxation period of 80 ns. It was cut after the entire equilibration of the
system and the beginning of the ion swapping. The combination of 50 ps repeats and change of camera
views demonstrates the trend of the motion and allows to address the details of the process, when 2
Na+ ions are moving across the membrane. It confirms some conclusions suggested within the paper,
for example, in the absence of the Bupivacaine molecule the ion flow can be observed through the
opened sieve of “DEKA” residues, while in the presence of the LA the ion is getting stuck in the plane of
the “DEKA” ring. The file can be opened in a Pymol or VMD visualizers.