Fig. 3: LPC-18:1 binds stably within the central region of MFSD2A.
From: Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A
Time-evolution of a the distance along the vertical z-axis between the phosphorus (P) atom of the penetrating LPC-18:1 and the Cα of F399 (dz), b the distance between the carboxyl carbon atom of E312 and the P of the penetrating LPC-18:1, and c the distance between the carboxyl carbon atom of E312 and the closest Na+ in two separate MD trajectories (Traj-1 and Traj-2). d Representative snapshots from Traj-1 (left) and Traj-2 (right) showing LPC-18:1 insertion. LPC-18:1 is shown in stick representation and the protein is represented as in previous figures. e, f Detailed view of the protein central region from the snapshots shown in panel d, highlighting the modes of LPC-18:1 binding in Traj-1 and Traj-2. g Conformations of E312 and F399 from the trajectory frames of Traj-1 superimposed on the initial structure of the protein. The sidechain positions are coloured according to time, with red representing the starting frames, white – the middle, and blue – the last third of the trajectory.
