Fig 1.
Representative snapshots of CXCR1 embedded in a lipid bilayer and membrane interaction of its N-terminal region.
A visual representation of (A) the starting conformation with an extended N-terminal region, (B) the membrane-embedded N-terminal conformer and (C) the receptor-contacted N-terminal conformer. The receptor is depicted in magenta, the N-terminal region in orange, and the lipid headgroups and tails in yellow and gray, respectively. Water and ions are not displayed for clarity. The residue W10 of the N-terminal region, which interacts with the lipid bilayer is shown as cyan colored beads. (D) The minimum distance between the lipid bilayer and the distal part of the N-terminal region (residues 1–10) is plotted for 20 simulations of apo-CXCR1 as a function of time. The color bar denotes minimum distance in nm. A distance of ~0.4 nm (dark blue patches) indicates the binding of the N-terminal region to the lipid bilayer. (E) The radius of gyration of the N-terminal region is plotted for apo-CXCR1 as a function of time. The color bar denotes radius of gyration in nm. See Methods for more details.
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.
Fig 3.
Conformational dynamics of the N-terminal region of CXCR1.
Intra-protein contact maps of the N-terminal region of CXCR1 in presence (lower matrix) and absence (upper matrix) of the ligand. Residue-wise contact probabilities of the N-terminal region in apo- and IL8-bound CXCR1 are plotted in the top and bottom diagonal of the matrix, respectively. The amino acid sequence of the N-terminal region is displayed on the top and right. The values of contact probabilities (0.5 nm distance cutoff) are denoted in the color bar. See Methods for more details.
Fig 4.
Conformational landscape of the N-terminal region of CXCR1.
Population density map of the conformations sampled by the N-terminal region plotted as a function of backbone RMSD of the N-terminal region and the distance between side chains of two representative residues (Met1 and Asp26) for (A) apo-CXCR1 and (B) IL8-bound CXCR1. The most populated conformations are shown below the plots. The N-terminal region is shown in cyan and rest of the receptor is in pink. See Methods for more details.
Fig 5.
Residue-wise interactions of the N-terminal region of CXCR1 with IL8.
(A) Residue-wise contact probabilities of the N-terminal region interacting with IL8. (B) Predicted chemical shift changes in the N-terminal region between the apo- and ligand-bound state. (C) The N-terminal residues with chemical shift perturbations above a cutoff (dotted lines in panel (B)) mapped onto the receptor structure. The cyan transparent spheres represent residues from the predictions. The orange and yellow spheres represent residues showing significant chemical shift changes as reported from NMR measurements [37,42]. See Methods and text for more details.
Fig 6.
Binding modes of IL8 characterizing its interactions with the N-terminal region of CXCR1.
(A) The most populated binding modes of IL8 characterized by the contacts formed by each of its structural element with the N-terminal region of CXCR1. The structural elements are denoted as I: N-domain, II: β1-strand, III: β2-strand, IV: β3-strand, and V: α-helix. The binding modes are numbered 1 to 5, in decreasing order of population. The green and red boxes represent interacting and non-interacting regions, respectively. (B) IL8 residues involved in binding to CXCR1 mapped on the cartoon representation of IL8. The cyan spheres represent interacting residues identified from our simulations. The orange and violet spheres represent interacting residues determined from previous NMR [37,42] and mutagenesis [43–47] studies, respectively. See Methods and text for more details.