Figure 7. Computational model of the CCR5-LukE complex extracted from molecular dynamics (MD) simulations.

(A) Superimposed MD snapshots extracted from the last 300ns of simulation (3 snapshots taken at 100 ns interval). The receptor and toxin are shown in cartoon representation and colored in light gray and magenta, respectively. CCR5 sTyr residues are shown as spheres. (B–E). Close ups of the interactions observed in the proposed model at the sulfotyrosine binding site 2 (B), sulfotyrosine binding site 1 (C), orthosteric pocket (D) and CCR5 eCL2/LukE loop3 region (E). The MD model of CCR5-LukE corresponds to the middle structure of the largest cluster in the MD trajectory. Interacting residues are displayed as sticks. The color code is the same as in (A).

Figure 7—figure supplement 1. Analysis of CCR5-LukE molecular dynamics (MD) simulations.

(A) Starting model and end model snapshots for each of the three independent CCR5-LukE MD trajectories. (B–G) Time-dependent properties of the system extracted from MD simulations for trajectories 1, 2, and 3 (black, red, and green lines, respectively): RMSD of the interface residues relative to the starting model (B), buried surface area in the complex (C), number of interchain hydrogen bonds (D), sTyr10 - Arg263 minimum distance (E), sTyr14 - Tyr269 minimum distance (F), and sTyr15 - Tyr269 minimum distance (G). Interface residues for interface root mean square deviations (iRMSD) calculation were defined based on the starting structure using a 1 nm cutoff, and calculation was performed on Cα atoms.

Figure 7—figure supplement 2. Accelerated weight histogram (AWH) molecular dynamics (MD) simulation of the CCR5-LukE model.

(A) sTyr 10 – Arg263 (site 1 – black line) and sTyr10 – Tyr269 (site 2 – red line) center of mass (COM) distance as a function of simulation time, highlighting the extensive sampling of these variables during the AWH simulation. (B) Final potential of mean force (PMF) profile calculated at t = 2.050 µs. The heat map represents free energies in kJ/mol. The energy well corresponding to site 1 interaction is circled in orange. (C) Three snapshots extracted from the AWH MD simulation at t = 0.02, 0.03, and 0.09 µs are superimposed, which sample the global energy minimum of the PMF.

Figure 7—video 1. Time evolution of the CCR5-LukE model conformation and estimated PMF during AWH MD.

Download video file ^{(3.2MB, mp4)}

The movie contains 206 frames from t = 0 to t = 2.05 µs (with a 10 ns timestep). Note the sampling of ‘site 1’ free energy basin in the first 100 ns of the simulation.