Fig. 4: Interactions between SecR and secretin during MD simulations.

a Hydrogen bonds between SecR and secretin. The total occupancy (% frames) of each atom is plotted onto the equilibrated complex according to a color scale, with SecR atoms never involved in white, secretin atoms never involved in black and atoms highly involved in magenta. The peptide (ball and stick residues indicated with solid lines) is depicted as black, partially transparent ribbon, while the receptor (stick residues indicated with dashed lines) is shown as white, partially transparent ribbon. The central image specifies the relative perspectives from the right and left sides. Right side view) Hydrogen bonds between the N-terminus of secreting and the TM bundle of the SecR; the main interactions involved S2^sec—E373^7.42, D3^sec—R188^2.60, and E9^sec—R135^1.32. Left side view) Hydrogen bonds between the C-terminus of secretin and the ECL1 of the SecR; main intermolecular interactions involved R14^sec, R18^sec, R21^sec on the peptide, and D203^ECL1, D204 ^ECL1, and D209 ^ECL1 on the receptor. b Contacts between SecR and secretin. The total occupancy (% frames) of each atom is plotted onto the surface of the equilibrated SecR according to a color scale, with SecR atoms never involved in blue, and atoms highly involved in red. The peptide is shown as transparent gray ribbon. The central image specifies the relative perspectives from the top and side. Top view) Contacts between secretin and the TM bundle of the SecR (residues from L28^ECD to E133^ECD have been removed for clarity); the bottom figure shows the ribbon representation as reference. Main interactions involved TM1 (R135^1.32, H136^1.33, and L139^1.36), TM2 (L199^2.71), ECL2 (D287^ECL2 and I288^ECL2), TM5 (D299^5.40), and TM7 (E373^7.42). Side view) Contacts between secretin C-terminal and SecR; the bottom figure shows the ribbon representation as reference. Main interactions involved ECL1 (D203^ECL1, D204^ECL1, and D209 ^ECL1), and ECD (R30^ECD, L31 ^ECD, V34 ^ECD, F92^ECD, I73^ECD, and L96^ECD).