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Fig. 4 | BMC Structural Biology

Fig. 4

From: Structure and dynamics of a human myelin protein P2 portal region mutant indicate opening of the β barrel in fatty acid binding proteins

Fig. 4

MD simulations of P2-F57A. a Fluctuation of the distance between Phe57 and helix α2 shows flipping of the Phe57 side chain in wt-P2 during the simulation. The simulation was run with (magenta) and without (black) the fatty acid ligand. b The two conformations of Phe57 (cyan). Left: Phe57 points inwards and interacts with the fatty acid (magenta). Right: Phe57 points outwards. Bovine P2 crystal structure is shown superposed in yellow, with the same conformation. c The structure shows the distance measured when studying barrel opening. d Distance between the tips of the β3-β4 and β5-β6 loops during the simulation. Black: wt-P2; red: F57A; green: P38G. Left: simulations without ligand. Right: simulations with bound palmitate. The red and green arrows indicate the positions of the snapshopt in the next panel. e Structural snapshots from the simulations. Left: Closed starting structure for F57A; middle: open F57A structure at 1.5 μs; right: open P38G structure with ligand at 2.2 μs, identified from our earlier trajectories [25]. f RMSF of wt-P2 (black) and F57A (red) in the simulations. Thick lines indicate unliganded simulations and thin lines those with bound fatty acid

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