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Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

Fig. 4

Interactions between the lipids and CL binding site 1.

A. Histograms of binding event durations (defined as the time for which CL binding site 1 was continuously occupied by a lipid; see Methods for details). B. Interactions of UraA R299 residue with the POPG and CL molecules as a function of the simulation time for one of the CG simulations with the wild type UraA (10 μs simulation; UraA-CG in Table 1). An occupancy index of 1 is used when the lipids are in contact with the protein and 0 when the lipids are not in contact. See S2 Fig. for the same analysis for all residues of UraA. C. The 10 longest stretches of continuous interactions between the different lipid types and CL binding sites 1. The same analysis for the other CL binding sites is shown in S3 Fig.

Fig. 4