OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme
Topic:  1H Membrane Proteins ;  8E Molecular Dynamics
Presentation Time: Monday, 10:45 a.m.
Marc Baaden¹, Mark S. P. Sansom².
¹IBPC, CNRS UPR9080, Paris, France, ²University of Oxford, Oxford, United Kingdom.
Presentation Number: 911-Plat
MD simulations (total duration >25 ns) on the E. coli outer membrane protease OmpT embedded in a DMPC lipid bilayer show that the protein is conformationally stable with the greatest degree of flexibility in the extracellular loops. Some tilting of the beta-barrel is observed relative to the bilayer plane. The active site residues form a network of H-bonds which supports a catalytic mechanism whereby Asp83 and His212 bind a water molecule which attacks the peptide carbonyl. Docking calculations corroborated a possible attack by this water molecule. The trajectories of water molecules reveal exchange of waters between the intracellular compartment and the barrel interior but no exchange at the extracellular mouth. This suggests that the 'pore-like' region in the centre of OmpT may enable access of water to the active site 'from below'. The simulations appear to reveal the presence of specific lipid interaction sites on the surface of the OmpT barrel.