Conformational plasticity and dynamic interactions of the N-terminal domain of the chemokine receptor CXCR1
Fig 2
Interactions between the extracellular domains of CXCR1 and IL8.
(A) A representative snapshot of IL8 bound to CXCR1. The receptor is shown in magenta, IL8 in green, and lipid headgroups and tails in yellow and gray, respectively. The N-terminal region of the receptor is highlighted in orange. Water molecules and ions are not shown for clarity. (B) The minimum distance (closest approach) between IL8 and CXCR1 plotted for the first 1.5 μs in forty simulations. The white stretches represent the unbound regime and the blue stretches represent the ligand-bound regime. Time of binding (t = 0) is defined as the time of first contact in the binding regime (0.5 nm distance cutoff) which remains undissociated till the end of the simulation. (C) The minimum distance between IL8 and various domains of the receptor as a function of time, considering the time of binding as t = 0. The values are averaged over all sets from the time of binding and plotted for the first 100 ns (left panel) and the last 100 ns (right panel). The color bar denotes minimum distance between IL8 and CXCR1 domains. See Methods for more details.