Fig. 4.

MD simulation of YfkE shows Ca²⁺-mediated conformational changes within the TM5-6 loop. (A) Superimposition of YfkE snapshots at time t = 0 (red) and t = 99 ns (blue); (B) Conformation of the TM5-6 loop (t = 99 ns) showing one Ca²⁺ (green sphere) coordinated by the residues from the acidic motif (red sticks). The XIP region is highlighted using dashed lines and its interactions in the intracellular cavitiy are demonstrated in the inner panel (black square). The XIP (blue sticks) is stabilized in the intracellular cavity by H-bond interactions (yellow dashed lines) between Arg¹⁸² and other residues (red sticks) and is interacted with TMs 1 and 2a (gold). (C) Superimposition of TMs 2 and 7 for snapshots from the trajectory taken at t = 0 (red), 50 (white), and 99 ns (blue); the region of the transport Ca²⁺ site is highlighted using dashed lines and is further demonstrated in detail in D. (D) superimposition of residues Glu⁷² and Glu²⁵⁵ in MD snapshots colored from red (0 ns) through blue (99 ns).