Fig. 8: MD simulations corroborate the role of G1-NT and G1-dCT in interactions with Gβγ and the prenylation tail, Gγprenyl.
a the initial AlphaFold 3 models of complexes of G1NC and G2NC with prenylated Gβγ (see Supplementary Table 11 for further details). b heatmaps illustrating the G1NC and G2NC residues contributing to Gβγ binding. CG analysis was carried out on five 5-µs production runs for G1NC and ten for G2NC. Darker coloring corresponds to greater overall contacts between the channel and Gβγ across all production runs. The magenta rectangles superimposed onto the heatmaps correspond to the Gβγ-binding segments identified by the peptide arrays (Fig. 6). The cyan rectangle outlines the main Gγprenyl-binding segment, the beginning of G1-NT. c heatmaps of interactions of G1NC and G2NC and their truncated versions with Gγprenyl. % binding is the percentage of time when at least one prenylation tail is bound to the channel. Note that the Gγprenyl interaction with the most prominent site, a.a. 1-20 of G1-NT (cyan rectangle), is lost after G1-dCT removal (details in Supplementary Table 13). d the histograms show % of time spent by G1NC a.a. residues in contact with the Gγprenyl in simulations without membrane (top; 5×5-µs runs) and with added POPC (1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane (bottom; 3 × 5-µs runs). e, f the interaction between G1-NT and G1-dCT in G1NC. A frame with a contact was defined as one in which at least one G1-dCT chain is bound to the G1-NT, with a cutoff of 6 Å. G1-NT and G1-dCT were in contact in 98.9 ± 0.5% of the frames in the five runs. The structures of G1NC (e) are shown at the beginning and at the end (1 µs) of a representative run. Areas of contact are highlighted. The heatmap (f) indicates that the main interaction segment in G1-NT is a.a. 25-32. Full details of all analyses are provided in Supplementary Tables 11–14.
