Fig. 6: Molecular Dynamics Analysis of the SpoIVFB:Pro-σK Complex.
From: Substrate engagement by the intramembrane metalloprotease SpoIVFB
A, B Rotated views of the SpoIVFB:Pro-σK complex (SpoIVFB is colored blue, Pro-σK is colored orange). A map showing the average occupancy of water calculated across one replicate 250 ns simulation is shown as a gray surface. Water fills the area in front of the membrane reentrant loop (A) and in the region of the zinc binding site (B). C, D Zoomed in views of the SpoIVFB active site from the final frame of one replicate MD simulation showing positions of waters at the end of the simulation. E Overlay of the SpoIVFB:Pro-σK cryo-EM structure (dark blue and orange) with the final frame from one replicate 250 ns MD simulation (light blue and yellow). The LMNG detergent molecule observed in the cryo-EM structure is shown in magenta ball and sticks, and a DAG lipid observed in one replicate MD simulation is shown in green ball and sticks. The acyl chains of LMNG mimic the acyl chains of the DAG lipid. F66 at the apex of the membrane reentrant loop is shown for clarity. F Surface representation of SpoIVFB with the surface colored according to hydrophobicity. The pro-sequence of Pro-σK is shown as yellow sticks, and the LMNG in the cryo-EM structure is shown in magenta sticks. The acyl chains of the detergent molecule stick into a hydrophobic pocket located behind the membrane reentrant loop.
