Our latest article — dealing with MD simulations of Wzp polysaccharide secretion porins — has now been published in ACS Omega!
In collaboration with the LaPlante lab, molecular dynamics simulations in an outer-membrane bilayer of the Wzp porins we identified in Myxo were run. This was done to examine the stability of AlphaFold model structures in a simulated membrane environment. Turns, the structures are exceptionally stable; nothing moves except for the surface-gating loops, but even those not by much. This suggests that, in the absence of an external force (say, maybe a polymer being secreted THROUGH the channel), the surface-gating loops of the porins do NOT open enough on their own to allow stuff to come out. Virtual screening using a commercial compound library then allowed for the identification of druggable hotspots in surface cavities of each protein, to be applied to downstream attempts to selectively "plug" each barrel.
Check out the story here: