Figure 2 -. Molecular dynamics simulations suggest that helices at the N- and C-termini of YhdP interact with the inner and outer membranes.

(A) Cartoon representation of the N-terminus of the YhdP AlphaFold model. The TM domain and P-helix are highlighted in blue and yellow respectively. (B-C) Representative snapshots from 3 × 5 μs of an N-terminal YhdP fragment (residues 1–387) in a PL bilayer. (B) Surface representation of the N-terminal fragment, coloured by residue hydropathy. (C) Ribbon representation of YhdP with key membrane inserting residues shown as sticks. (D) Cartoon representation of the C-terminus of YhdP. Chelix_1 (residues 1203–1237) and Chelix_2 (residues 1121–1144) are highlighted in green and pink respectively. (E-F) Representative structures from 6 × 5 μs of membrane self-assembly with a C-terminal fragment of YhdP (residues 1098–1266). (E) Surface representation coloured by residue hydropathy revealing the two C-helices form a largely hydrophobic patch. (F) Ribbon representation of the C-terminal fragment revealing that residues of the C-helices remain associated within one leaflet of the membrane. Side chains are coloured thus: strongly hydrophobic residues are purple, residues which are neutral in terms of hydropathy are grey, and hydrophilic residues are green. The backbone is shown in dark grey. Headgroup beads are shown in gold and acyl beads in cyan.