Fig. 6: Interpreting adjacent lipid-like densities surrounding TRPV6.

a Snapshot from the interactive PyMOL session comparing lipid poses with site densities surrounding TRPV6 (PDBid: 7S88)⁴¹. The lipid poses at five binding sites (BS1, BS3, BS4, BS5, BS13) are shown as sticks and partitioned site density maps are shown as mesh. b Relative residence times and c selected top-ranked lipid binding poses for BS1 across n = 10 ×15 μs independent CG simulations. Residence times were derived from k_off values obtained via bi-exponential curve fitting of the interaction survival function. Error bars correspond to k_off values obtained from bootstrapping to the same data. Lipid poses correspond to those directly backmapped from CG simulations (without refinement using atomistic simulations). Partitioned site densities are shown as mesh while the density of interest and modelled lipids/acyls are shown in grey. d, e As in b/c for BS13. Lipids are coloured as in Fig. 4 throughout. f Lipid-like densities (numbered i-iv) at BS3. Those modelled within the structure are grey. An additional density visible at a higher sigma value is shown in cyan. g Comparison of all lipid poses with densities at BS3, showing conservation of the headgroup position and tail variability. Overlay of h PIP₂/POPS/DOPS and i POPC/DOPC/POPE/DOPE poses with densities at BS3. Relative residence time plots for j BS3 and k BS4 (defined as in b). l Overlay of one tail of all lipid poses for BS4 (lilac) with a single tail of densities modelled as POPC (grey). The top-ranked cholesterol pose from the neighbouring binding site (BS5) is shown in green. m Comparison of the BS5 cholesterol pose with the density assigned to the second tail of the modelled POPC (grey).