Figure 7.

Plasma Membrane Mimetic Simulations

(A) Final snapshots of SMO embedded in a PC (yellow), PE (gray), PS (ochre), PIP₂ (red), and cholesterol (green) membrane. Protein and lipids are rendered as surfaces. The formation of a PIP₂-SMO complex (orange box) is apparent. Water and ions have been omitted for clarity. Other lipid species have been omitted from the right-hand image of the PIP₂ encounter complex.

(B) Mean number of PIP₂ contacts mapped onto structure, with each residue colored from white (no contact) to red (high contact). The predominant mode of PIP₂ contact with SMO can be seen to occur in the head group region, with the acyl tails forming comparatively less contact. Contacts were calculated over an ensemble of 8 × 10 μs of CGMD, using a 6 Å distance cutoff. See the STAR Methods for further details of contact analysis. Each simulation was initiated from a different random distribution of lipids around the protein.