OmpT: Molecular Dynamics Simulations of an Outer Membrane Enzyme

ABSTRACT

Five molecular dynamics simulations (total duration >25 ns) have been performed on the Escherichia coli outer membrane protease OmpT embedded in a dimyristoylphosphatidylcholine lipid bilayer. Globally the protein is conformationally stable. Some degree of tilt of the β-barrel is observed relative to the bilayer plane. The greatest degree of conformational flexibility is seen in the extracellular loops. A complex network of fluctuating H-bonds is formed between the active site residues, such that the Asp^sup 210^-His^sup 212^ interaction is maintained throughout, whereas His^sup 212^ and Asp^sup 83^ are often bridged by a water molecule. This supports a catalytic …