Figure 4 -. YhdP AlphaFold model contains a continuous hydrophobic groove along the majority of its length.

(A) Molecular surface representation of the YhdP AlphaFold prediction (white) indicating the existence of a solvent exposed channel along all but the extreme N-terminus of YhdP (blue). (B) Lipophilic potential mapped to a surface representation of the AlphaFold YhdP prediction. Surfaces are coloured from hydrophilic (dark cyan) to hydrophobic (gold). Lipophilicity potential was calculated using the ChimeraX mlp command. Inset (right) depicts a cross section of the YhdP groove highlighting the lipophilicity of its lining. (C) Coulombic electrostatic potential mapped to a surface representation of the AlphaFold YhdP prediction. Surfaces are coloured from positive charge (blue) to negative charge (red). Electrostatic potential was calculated using the ChimeraX coulombic command. Inset (left) depicts a cross section of the YhdP groove highlighting the absence of charge within its lining. (D) Representative surface and backbone snapshots from one of the 5 µs simulations of the N-terminal fragment (residues 1–387). In Stage 0, PLs are in the membrane without any association with YhdP. In Stage 1, PLs rotate their lipid tails towards the mouth of the YhdP hydrophobic groove while lipid headgroups remain away. In Stage 2, an acyl tail explores further up the hydrophobic groove, while the lipid headgroup remains solvated. In Stage 3, the lipid headgroup moves inside the hydrophobic groove, followed by Stage 4 where the lipid headgroup then re-emerges from the hydrophobic groove into a cavity within the surface of YhdP. In stage 5 the lipid moves further within the groove and the headgroup emerges from a second cavity within the surface of YhdP. Lipid colour key: acyl beads in cyan, glycerol beads in lime, phosphate beads in gold. Stick representation of YhdP cavity residues shown in red. Backbone of YhdP shown in grey.