Membrane Porin Protein: OmpF  (OmpK36, OmpC and PhoE)


     Porins are integral outer-membrane proteins of Gram-negative bacteria that function as molecular sieves (with exclusion limits of around 600 Da) and are responsible for the uptake of small molecular nutrients and the removal of waste products.  Since porin exists only in (gram negative) bacteria, it is the ideal target of antibacterial agents.


THE BACTERIAL CELL WALL STRUCTURE


Gram-positive organisms
Gram-negative organisms
The lipid bilayer cell membrane of most of the Gram-positive bacteria is covered by a porous peptidoglycan layer which does not exclude most antimicrobial agents.
Gram-negative bacteria are surrounded by two membranes. The outer membrane functions as an efficient permeability barrier because it contains lipopolysaccharides (LPS)and porins.
lipid bilayer peptidoglycan 
lipid + LPS porins 

 

    X-ray stucture have revealed a large 16-stranded antiparallel barrel structure enclosing the transmembrane pore.  Three subunits form a timmer. The 3-fold axis is approximately parallel to the barrel axis.
 



Figure1.  X-ray structure of porin protein OmpF
(Cowin et al. Nature 358 727-733 (1992))


     Our main concerns are the following:

1. Electrostatics of porin pore region (i.e. L3 Loop).
2. Finding binding mode of polyamine to porin by Docking simulation
3. Dynamics of L3 loop of normal and ion(charge) induced status by MD simulation.

 
 


Figure 2. Spermine (a polyamine) binding structure to OmpF was revealed by
DOCKING simulation (AUTODOCK3.0 and LGA algorithm). Six
key residues (K16, R42, R82, D113, E117, R132) are shown in the stick
model.


[More Porin Information from Paul's Homepage at Davidson College]