Fig. 2: The accessibility of CQ to the PfCRT cavity. | Nature Communications

Fig. 2: The accessibility of CQ to the PfCRT cavity.

From: Molecular basis of the functional conflict between chloroquine and peptide transport in the Malaria parasite chloroquine resistance transporter PfCRT

Fig. 2

The free energy surfaces of CQ across the A 3D7-PfCRT, B Dd2-PfCRT, and C Dd2-76K-PfCRT systems. The surfaces are displayed across the X and Z dimensions of the simulation systems (Å), and averaged across a slice of the Y dimension that spans the width of the cavity. The system is oriented such that the vacuolar side of the protein is on the upper side of the graph, and the cytosolic on the lower. The color indicates the free energy of an atom of CQ at that position within the simulation system, with red indicating regions where the ΔG > 0 and blue regions where ΔG < 0. The free energy is relative to the average of a slice in bulk solution. The solid line represents the position of the PfCRT protein in that simulation system, and the interior dotted line, the region of Lys76’s motion. For Dd2-PfCRT, the range of Lys76 is from the corresponding 3D7-PfCRT simulation. D The average number of simulation frames for which there is a CQ molecule in the PfCRT cavity, as a percentage of the number of frames in that replicate. Error bars represent the std. error. n = 20 simulation replicates, T-test (two-sided): p = 1.0 × 10−6, p = 0.97.

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