Fig. 5
From: Direct protein-lipid interactions shape the conformational landscape of secondary transporters
Closing of the intracellular side of XylE in PC:PG:CL bilayers. MD simulations predict different conformational changes of XylE in PC vs. PE bilayers. a Representative snapshots at the beginning (t = 0 ns) and end of the simulation (t = 500 ns) show a closing of the intracellular side in PC nanodisc (left) compared to PE nanodisc (right). b Time trace showing the intracellular gate distance over simulation time. PC simulation sets are coloured orange and red, while the PE simulation sets are coloured green and blue. The inset on the right depicts the normalized distribution of the intracellular gate distance for the last 200 ns of the trajectory. c Snapshot describing the definition of the intracellular gates in XylE. The intracellular gating distance is defined as the center of mass (COM) distance between the two groups of Ca-Ca residues: group1 residues (75–80, 149–154, 160–16) and group2 residues (332–337, 391–397, 404–410)
